bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Multiple signaling pathways converge onto the regulation of HAD-like phosphatases to modulate cellular resistance to the metabolic inhibitor, 2-deoxyglucose
Quentin Defenouillère1,2, Agathe Verraes1,2, Clotilde Laussel1, Anne Friedrich3, Joseph
Schacherer3 & Sébastien Léon1,4
1: Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-
Diderot, Sorbonne Paris Cité, Paris, France
2: These authors contributed equally to this work
3: Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
4: Author for correspondence:
Sébastien Léon, PhD
Institut Jacques Monod
15 Rue Hélène Brion
75205 Paris Cedex 13, France.
email: [email protected]; tel. +33 (0)1 57 27 80 57.
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Abstract
Cancer cells display an altered metabolism with an increased glycolysis and a lower respiration
rate, leading to an increased glucose uptake. These particularities provide therapeutic opportunities
and anti-cancer strategies targeting glycolysis through metabolic inhibitors have been put forth. One
of these inhibitors, the glucose analogue 2-deoxyglucose (2DG), is imported into cells and
phosphorylated into 2DG-6-phosphate, a toxic by-product that accumulates in cells and inhibits
glycolysis. Recent data suggest that 2DG has additional effects in the cell, and resistance to 2DG has
also been observed. It appears crucial to better understand the mechanisms leading to this resistance.
Using budding yeast as a model system, we engaged an unbiased, mass-spectrometry-based approach
to probe the cellular effects of 2DG exposure on the total proteome and reveal the molecular basis of
2DG resistance. This led to the identification of two 2DG-6-Phosphate phosphatases, Dog1 and Dog2,
that are induced upon exposure to 2DG and participate in 2DG detoxification. We reveal that 2DG
induces Dog2 by upregulating several signaling pathways, such as the MAPK (Hog1/p38)-based stress-
responsive pathway, the Unfolded Protein Response (UPR) pathway triggered by 2DG-induced ER
stress, and the MAPK (Slt2)-based Cell Wall Integrity pathway. Consequently, loss of the UPR or CWI
pathways leads to hypersensitivity to 2DG. Moreover, we show that DOG2 is additionally regulated by
glucose availability in a Snf1/AMPK-dependent manner through the transcriptional repressors
Mig1/Mig2 and Cyc8, explaining why several mutants impaired in this pathway were found as 2DG-
resistant. The isolation and characterization of spontaneous 2DG-resistant mutants revealed that
DOG2 overexpression is a common strategy for 2DG resistance. Thus, 2DG-induced interference with
cellular signaling rewires the expression of these endogenous phosphatases to promote 2DG
resistance. Importantly, a human orthologue of Dog1/Dog2, named HDHD1, displays an in vitro 2DG-
6-phosphate phosphatase activity, and its overexpression confers 2DG resistance in HeLa cells, which
has important implications for potential future chemotherapies involving 2DG.
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1 Introduction
2 Most cancer cells display an altered metabolism, with an increased glucose consumption to
3 support their proliferative metabolism that is based on aerobic glycolysis (Warburg effect) (1, 2).
4 Targeting glycolysis has been proposed as a strategy to target cancer cells and various metabolic
5 inhibitors have been considered (3, 4).
6 2-deoxy-D-glucose (2DG) is a derivative of D-glucose that is actively imported by glucose
7 transporters and is phosphorylated by hexokinase into 2-deoxy-D-glucose-6-phosphate (2DG6P), but
8 cannot be further metabolized due to the 2-deoxy substitution, triggering a decrease in cellular ATP
9 content in tumors (5). Mechanistically, 2DG6P accumulation hampers glycolysis by inhibiting
10 hexokinase activity in a non-competitive manner (6, 7), as well as phospho-glucose isomerase activity
11 in a competitive manner (8). Since cancer cells rely on an increased glycolysis rate for proliferation,
12 2DG has been of interest for cancer therapy, particularly in combination with radiotherapy or other
13 metabolic inhibitors (9-11). These features led to a phase I clinical trial using 2DG in combination with
14 other drugs to treat solid tumors (12). Its derivative 18Fluoro-2DG is also used in cancer imaging (PET
15 scans) as it preferentially accumulates in tumor cells due to their increased glucose uptake (13).
16 Additionally, due to its structural similarity to mannose, 2DG (which could also be referred as to 2-
17 deoxymannose, since mannose is the C2 epimer of glucose) also interferes with N-linked glycosylation
18 and causes ER stress (14-16) and this was proposed to be the main mechanism by which 2DG kills
19 normoxic cells (17). Recently, 2DG toxicity was also linked to the depletion of phosphate pools
20 following 2DG phosphorylation (18). Finally, interference of 2DG with lipid metabolism and calcium
21 homeostasis was also described, but the underlying mechanisms are less clear (19). Intriguingly,
22 despite its pleiotropic mode of action, resistance to 2-deoxyglucose was reported in cell cultures (20).
23 Because these metabolic and signalling pathways are evolutionarily conserved, simpler
24 eukaryotic models such as the budding yeast Saccharomyces cerevisiae can be used to understand the
25 mode of action of 2DG. Moreover, yeast is particularly well-suited for these studies because of its
26 Warburg-like metabolism (21). Akin to cancer cells, Saccharomyces cerevisiae privileges glucose
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1 consumption through glycolysis over respiration, regardless of the presence of oxygen. This is allowed
2 by a glucose-mediated repression of genes involved in respiration and alternative carbon metabolism,
3 which operates at the transcriptional level. This glucose-mediated repression mechanism is relieved
4 upon activation of the yeast orthologue of AMPK, Snf1, which phosphorylates the transcriptional
5 repressor Mig1 and leads to its translocation out of the nucleus (22-25). Previous studies in yeast
6 identified mutations that render yeast cells more tolerant to 2DG (26-31). This suggested the existence
7 of cellular mechanisms that can modulate 2DG toxicity, which are important to characterize if 2DG
8 were to be used for therapies.
9 In yeast, 2DG was initially used to identify genes involved in glucose repression. This was based
10 on the observation that 2DG, like glucose, causes Snf1 inactivation and thus prevents the use of
11 alternative carbon sources (32-34). The characterization of mutants that were able to grow in sucrose
12 medium despite the presence of 2DG allowed the identification of actors of the glucose repression
13 pathway (26, 29, 35). These experiments also revealed that mutations in HXK2, encoding hexokinase
14 II, also rendered yeast cells more tolerant to 2DG, perhaps by limiting 2DG phosphorylation and 2DG6P
15 accumulation (29-31, 36, 37). Finally, several 2DG-resistant mutants displayed an increased 2DG6P
16 phosphatase activity, which could detoxify the cells of this metabolite and dampen its negative effects
17 on cellular physiology (38, 39). Indeed, two 2DG6P phosphatases were subsequently cloned, named
18 DOG1 and DOG2, and their overexpression led to 2DG resistance and prevented the 2DG-mediated
19 repression of genes (33, 40, 41).
20 More recently, the toxicity of 2DG was studied in the context of glucose-grown cells, which may
21 be more relevant for the understanding its mode of action in mammalian cells. In these conditions,
22 2DG toxicity is independent of its effect on the glucose repression of genes, but involves distinct
23 mechanisms, such as a direct inhibition of glycolysis and other cellular pathways (30, 42, 43).
24 Accordingly, several mutations initially identified as leading to 2DG tolerance in sucrose medium have
25 no effect in glucose medium (30, 44). A key finding was that the deletion of REG1, encoding a
26 regulatory subunit of Protein Phosphatase 1 (PP1) that negatively regulates Snf1 (45, 46) leads to 2DG
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1 resistance (30). The resistance of the reg1∆ mutant depends on the presence of Snf1, and the single
2 deletion of SNF1 also renders yeast hypersensitive to 2DG (31). These data demonstrate that Snf1
3 activity is crucial for 2DG resistance. A model was proposed in which the 2DG sensitivity displayed by
4 the snf1∆ mutant involves a misregulated expression and localization of the low-affinity glucose
5 transporters, Hxt1 and Hxt3 (47). Additionally, the deletion of LSM6, which encodes a component of a
6 complex involved in mRNA degradation, also leads to 2DG resistance in a Snf1-dependent manner, but
7 the mechanism by which this occurs is unknown (31). Thus, many aspects of the pathways mediating
8 2DG sensitivity/resistance remain to be explored.
9 In the present study, we engaged an unbiased, mass-spectrometry-based approach in yeast to
10 better understand the cellular response to 2DG. This revealed that the main 2DG6P phosphatase,
11 Dog2, is induced upon exposure to 2DG and participates in 2DG detoxification in glucose medium. We
12 reveal that 2DG induces Dog2 (and Dog1, to a certain extent), by upregulating several stress-responsive
13 signaling pathways (UPR and MAPK-based pathways). Moreover, the expression of DOG2 is
14 additionally regulated by Snf1 and the glucose-repression pathway through the action of downstream
15 transcriptional repressors, and contributes to the resistance of glucose-repression mutants to 2DG.
16 The partial characterization of 24 spontaneous 2DG-resistant mutants revealed that most display an
17 increased DOG2 expression, suggesting it is a common strategy used to acquire 2DG resistance.
18 Particularly, genome resequencing identified that mutations in CYC8, encoding a transcriptional
19 corepressor, cause 2DG resistance through the upregulation of Dog2. The identification of a potential
20 human orthologue of the Dog1/2 proteins, named HDHD1, which displays an in vitro 2-DG-6-
21 phosphate phosphatase activity and which can cause resistance of HeLa cells to 2DG when
22 overexpressed, suggests that HAD-like phosphatases are conserved regulators of 2DG resistance.
23
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1 Results.
2 A proteomic assessment of the cellular response to 2DG reveals an increased expression of
3 metabolic enzymes
4 As a first step to characterize the cellular response of yeast cells to 2-deoxyglucose (2DG) treatment
5 in an unbiased and quantitative manner, we performed proteome-wide mass spectrometry-based
6 proteomics on wild-type cells treated for 2.5 hours with 0.2% 2DG, a concentration that prevents
7 growth of WT cells on plates (30) using untreated cells as a negative control. Overall, 78 proteins were
8 significantly up-regulated, whereas 18 proteins were down-regulated after 2DG treatment (False
9 Discovery Rate of 0.01) (Figure 1A, Figure S1A, Table S1). Among the up-regulated candidates, a
10 significant enrichment of proteins involved in various metabolic processes was noted, including that
11 of glucose, glucose-6-phosphate and other carbohydrates (Figure S1B).
12 Interestingly, these proteomics data revealed an increase in the abundance of the 2-deoxyglucose-
13 6-phosphate phosphatases Dog1 or Dog2, which could not be discriminated at the mass spectrometry
14 level because of their high sequence identity (92%). Dog1 and Dog2 were thus individually GFP-tagged
15 at their chromosomal locus, in order to maintain an endogenous regulation, and their expression was
16 monitored by western blotting. This revealed that both Dog1 and Dog2 expression levels are increased
17 in the presence of 2DG, and that Dog2-GFP is more abundant than Dog1-GFP (Figure 1B).
18 To evaluate the contribution of transcription in the regulation of the DOG1 and DOG2 genes by
19 2DG, the corresponding promoters (1kb) were fused to a beta-galactosidase reporter. This revealed
20 an increased activity of the DOG1 and DOG2 promoters in response to 2DG (Figure 1C), suggesting that
21 the expression of Dog1 and Dog2 is, at least in part, due to an increased transcription. Of note, the
22 deletion of the DOG2 gene strongly sensitized yeast cells to 2-deoxyglucose, but that of DOG1 had little
23 effect (Figure 1D), indicating that Dog2 is functionally more important than Dog1, perhaps due to its
24 higher expression level (Figure 1B).
25 The increased expression of Dog1 and Dog2 in response to 2DG was intriguing because it raised the
26 question of how exposure to this synthetic molecule could trigger an adaptive resistance mechanism
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1 in yeast. Prior work showed that the expression of Dog2, whose endogenous function in regular yeast
2 metabolism is unknown, is induced by various stresses, such as oxidative and osmotic stresses, through
3 the stress-responsive MAP kinase orthologue of p38, Hog1 (48). To determine whether this mechanism
4 takes part in Dog1/2 regulation by 2DG, we first tested the effect of 2DG on Hog1 phosphorylation
5 using an antibody directed against the phosphorylated form of mammalian p38 (49). Hog1 was
6 activated upon 2DG addition, but to a much lower extent as by inducing hyperosmotic shock (Figure
7 1E). The deletion of HOG1 indeed caused a partial decrease in Dog2 induction (Figure 1F-H), but had
8 no discernable effect on the expression of Dog1. Altogether, we conclude that the stress-activated
9 protein kinase Hog1 has no effect on Dog1 induction by 2DG treatment, and only participates in the
10 induction of Dog2. This suggests that upregulation of Dog1 and Dog2 by 2DG involves at least one
11 additional level of regulation.
12
13 The expression of Dog1 and Dog2 is induced by the Unfolded Protein Response pathway through
14 2-deoxyglucose-induced ER stress
15 Exposure of cancer cells to 2-deoxyglucose interferes with N-linked glycosylation, likely because of
16 the structural similarity of 2-deoxyglucose with mannose, a constituent of the N-glycan structures (14).
17 This results in endoplasmic reticulum (ER) stress and consequently, in the induction of the Unfolded
18 Protein response (UPR) in mammalian cells (14). Accordingly, the glucose fluorescent analogue 2-
19 NBDG ((2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose), which was previously used
20 in yeast as a glucose tracer (50) and which, much like 2DG, cannot be fully metabolized because of the
21 lack of a hydroxyl group in position 2, partially co-localized with an ER marker (Figure 2A), suggesting
22 interference with N-glycosylation which takes place at this organelle. Treatment of yeast with 2DG also
23 induced a defect in the glycosylation of carboxypeptidase Y (CPY), a vacuolar (lysosomal) protease
24 whose membrane-anchored precursor is N-glycosylated in the course of its intracellular trafficking
25 (51). This defect was not as extensive as that observed upon treatment of cells with tunicamycin, an
26 inhibitor of the first step of glycosylation that also causes ER stress and is a strong UPR inducer (52, 53)
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1 (Figure 2B). Interestingly, the addition of exogenous mannose in the medium suppressed the
2 glycosylation defects caused by 2DG, but not those caused by tunicamycin (Figure 2B). This supports
3 the idea that 2DG mimics mannose and interferes with its incorporation in N-glycans, as proposed in
4 mammalian cells (14, 17). 2DG treatment also led to the induction of an UPR element-containing
5 reporter, UPRE1-LacZ (53) (Figure 2C). This depended on Hac1, a transcription factor whose regulated
6 splicing occurs in response to ER stress and triggers the onset of the UPR response (53), confirming
7 that 2DG is a bona fide UPR inducer (Figure 2C).
8 We then tested whether this induction of the UPR pathway contributes to the 2DG-mediated
9 induction of Dog2. First, we found that tunicamycin strongly induced the pDOG2-LacZ reporter (Figure
10 2D). Moreover, the induction of this reporter by 2DG was reduced by more than 2-fold in a hac1∆
11 mutant, suggesting a contribution of the UPR in this induction (Figure 2E). Comparable results were
12 obtained for pDOG1-LacZ (Figure S3). These results were confirmed at the protein level for Dog2
13 (Figure 2F-G).
14 Interestingly, UPR-compromised mutants such as hac1∆ and ire1∆ are both hypersensitive to 2DG
15 (Figure 2H), suggesting that they cannot cope with ER stress caused by 2DG. However, the addition of
16 exogenous mannose in the medium restored 2DG-tolerance of these mutants to a comparable level
17 as the WT (Figure 2H). Altogether, these results confirm that 2DG induces ER stress by interfering with
18 N-glycosylation, that the subsequent activation of the UPR pathway upregulates Dog1 and Dog2
19 expression and that UPR mutants display a lower level of Dog1 and Dog2 expression. Noticeably, Dog2
20 overexpression restored the growth of hac1∆ or ire1∆ cells at various concentrations of 2DG (Figure
21 2I).
22
23 2DG also activates the MAPK-based cell-wall integrity pathway which additionally contributes to
24 Dog1 and Dog2 expression
25 To address a possible additional contribution of other signaling pathways that would contribute to
26 the 2-DG-induced expression of Dog1 and Dog2, we ran a bioinformatics analysis on the list of proteins
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1 that were found as upregulated upon 2DG treatment (see Figure 1A, and Table S1) using YEASTRACT
2 (54) to evaluate whether the observed variations in protein expression could reveal a potential
3 transcriptional signature. The best hit (corresponding to 35/78 candidates, p-value=0) was the MADS-
4 box transcription factor Rlm1, a known downstream target of the cell wall integrity (CWI) pathway
5 (55). There are well-established links between CWI signaling and ER stress (56-60), and indeed, 2DG
6 treatment induced the phosphorylation of the CWI MAPK, Slt2, within the first hour of exposure
7 (Figure 3A). Accordingly, 2DG led to the transcriptional induction of an Rlm1-regulated promoter fused
8 to LacZ (Figure 3B). Importantly, the deletion of many genes of the cell-wall integrity pathway acting
9 upstream of Rlm1 caused an increased 2DG sensitivity (Figure 3C) such as those encoding the sensors
10 MID2 and WSC1. Thus, much like the UPR pathway, the CWI pathway is required for 2DG tolerance.
11 We thus questioned whether CWI pathway activation by 2DG contributed to Dog1 and Dog2
12 induction. Indeed, the activity of both promoters was decreased in the slt2∆ mutant (Figure 3D and
13 S4). This was confirmed for Dog2 by analyzing the expression levels of Dog2-GFP (Figure 3E-F). Thus,
14 similarly to tunicamycin (58), 2DG acts as an inducer of cell-wall integrity signaling and participates in
15 Dog1 and Dog2 induction, in addition to the UPR pathway. Interestingly, however, the addition of
16 exogenous mannose did not lead to a better tolerance of CWI mutants to 2DG (Figure 3G). Thus, ER
17 stress relief is not sufficient to suppress 2DG toxicity in these mutants, suggesting that 2DG has other
18 effects in the cell beyond triggering ER stress.
19
20 A third pathway negatively regulates the expression of Dog2, but not Dog1, by glucose availability
21 and participates in the described resistance of glucose-repression mutants to 2DG
22 The toxicity of 2DG also lies in the fact that it impairs glycolysis by inhibiting hexokinase and
23 phosphoglucose isomerase activity (6-8). This leads to an energetic stress and accordingly, 2DG
24 treatment activates AMPK in mammals (61).
25 Several lines of evidence indicate that the activity of the yeast AMPK orthologue, Snf1, is important
26 for 2DG tolerance. Whereas the snf1∆ mutant is hypersensitive to 2DG, the reg1∆ mutant, in which
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1 Snf1 is hyperactive, displays an increased resistance towards 2DG which depends on Snf1 activity (31).
2 A previous study showed that Snf1 positively regulates Dog2 expression (48), so we hypothesized that
3 the snf1∆ mutant may be hypersensitive to 2DG because of a lack of Dog2 expression. To first confirm
4 the effect of Snf1 on Dog1 and Dog2 expression, glucose-grown cells were transferred to a medium
5 containing lactate as a sole carbon source, which is known to cause Snf1 activation and consequently,
6 the de-repression of glucose-repressed genes. The expression of Dog2, was increased in this condition,
7 but not that of Dog1 (Figure 4A). This occurred in a Snf1-dependent manner. In line with these data,
8 the pDOG2-LacZ reporter was induced after transfer to lactate medium, but this response was
9 decreased in the snf1∆ mutant, confirming that DOG2 is subject to a glucose-repression mechanism
10 and is thus constantly repressed in a snf1∆ mutant (Figure 4B), which may explain why the snf1∆
11 mutant is sensitive to 2DG. A previous report indicated that Dog1/2 overexpression in a snf1∆ mutant
12 did not rescue resistance to 2DG, but we thought that this might be due to the fact that these
13 experiments involved a high-copy plasmid in which Dog2 expression was still under the control of its
14 endogenous, i.e. Snf1-regulated, promoter (47). Indeed, when overexpressed using a strong and
15 constitutive promoter (pGPD), Dog2 could rescue Snf1 growth on 2DG (Figure 4C).
16 In contrast, Dog2 expression was increased in glucose-repression mutants which display an
17 increased Snf1 activity, such as mutants lacking the hexokinase Hxk2 or the PP1 regulatory
18 phosphatase Reg1 (44, 62), both at the promoter level and the protein level (Figure 4D-E). In addition,
19 lack of the Snf1-regulated transcriptional repressors Mig1/Mig2 also led to an increase in Dog2
20 expression (Figure 4D-E). A regulatory sequence in the promoter, present between -250 and -350 bp
21 relative to the ATG, combined with a proposed Mig1-binding site located at ca. -200 bp (40, 48) was
22 critical for this glucose-mediated repression (Figure S5). Interestingly, mutants showing an increased
23 Dog2 expression such as reg1∆ or hxk2∆ are known to be more tolerant to 2DG than the WT (30, 31),
24 and we report that this is also the case for the double mutant mig1∆ mig2∆ (Figure 4F). We deleted
25 DOG1 and DOG2 in these mutants to evaluate their contribution to 2DG resistance. The absence of
26 Dog1 and Dog2 sensitized all strains to 2DG (Figure 4F); in particular, the mig1∆ mig2∆ dog1∆ dog2∆
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1 regained a sensitivity comparable to that of the WT, demonstrating that the resistance displayed by
2 the mig1∆ mig2∆ mutant is due to an increased DOG expression. In contrast, the reg1∆ dog1∆ dog2∆
3 and the hxk2∆ dog1∆ dog2∆ strains still remained more resistant than the WT, suggesting additional
4 mechanisms of resistance. Finally, we observed that the snf1∆ mig1∆ mig2∆ was resistant to 2DG
5 despite the absence of Snf1, in line with the idea that the snf1∆ is 2DG-sensitive because of the
6 constitutive repression of Mig1/Mig2 target genes, such as Dog1 and Dog2 and possibly other genes
7 (Figure 4F). Overall, we conclude that Dog2 presents an additional regulation by glucose availability
8 through Snf1/AMPK activity, which participates in the well-described resistance of glucose-repression
9 mutants to 2DG.
10
11 Increased expression of DOG2 is frequently observed in spontaneous 2DG-resistant clones
12 Previous screens led to the identification of 2DG-resistant mutants (26, 29, 35). The initial purpose
13 of these screens was to identify mutants that were insensitive to the repressive effect of 2DG, or that
14 were impaired for glucose phosphorylation (since only 2DG6P is toxic to cells), and consequently, were
15 performed on media containing other carbon sources than glucose.
16 The mechanisms involved in 2DG resistance on glucose medium were tackled much later by
17 screening of the deletion library (30), which led to the identification of resistant mutants, some of
18 which were subsequently confirmed (31). In the course of our experiments, we often found that 2DG-
19 resistant clones could spontaneously arise from wild-type or even 2DG-susceptible strains (see
20 examples in the drop tests of Figure 1D or 2H). Indeed, it was previously noted that yeast acquires 2DG
21 resistance at a high frequency, which can be accompanied by an increase in 2DG-6-phosphatase
22 activity (28, 38). To study whether Dog2, which is functionally the most important paralogue for 2DG
23 resistance, is upregulated during the emergence of spontaneous 2DG-resistant mutants, we spread ca.
24 2x106 cells on a glucose-based medium containing 0.2% 2DG, and selected clones that had appeared
25 after 6 days of growth. Altogether, 24 clones were obtained, whose resistance to 2DG was confirmed
26 (see Figure 5B). Using the pDOG2-LacZ reporter, we found that 13 clones displayed a significantly
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1 increased DOG2 promoter activity as compared to WT strains (Figure 5A). This suggested that Dog2
2 overexpression is a frequent feature of 2DG-resistant clones. Among those, we expected to isolate
3 reg1 and hxk2 mutants because both are resistant to 2DG in glucose medium (See Figure 4F; 30, 31).
4 To identify them, we first tested whether some of the isolated resistant clones displayed phenotypes
5 typical of reg1 mutants, such as sensitivity to tunicamycin (63, 64) or selenite (which enters the cell
6 through the glucose-repressed transporter Jen1: 65, 66), which allowed to discriminate potential reg1
7 mutants from hxk2 mutants (Figure 5B). Indeed, three of the isolated clones were potential reg1
8 mutants based on these phenotypes (Figure 5A). This was further supported by the observation that
9 these 3 mutants displayed a markedly increased activation of Snf1, as measured by using an antibody
10 directed against phosphorylated AMPK (Figure 5C). Sequencing of the REG1 coding sequence in these
11 clones revealed point mutations (substitutions) causing the appearance of stop codons which likely
12 explain Reg1 loss of function (Figure 5D). To additionally identify whether the set of spontaneous
13 resistant clones contained hxk2 mutants, we performed a complementation test and therefore crossed
14 these strains with either a WT strain or an hxk2∆ strain and tested the ability of the resulting diploids
15 to grow on 2DG. All diploids generated through the cross with the WT lost their ability to grow on 2DG,
16 except two (clones #23 and #24) (Figure 5E), indicating that 2DG resistance was generally caused by
17 (a) recessive mutation(s). In contrast, 12 diploids obtained by the cross with the hxk2∆ strain
18 maintained their ability to grow on 2DG (Figure 5E), suggesting that 2DG resistance of the initial strains
19 was caused by a deficiency in HXK2 function. Most of these clones also displayed an increased pDOG2-
20 LacZ expression, in agreement with our previous findings (Figure 4D-E). We PCR-amplified and
21 sequenced the HXK2 ORF in the WT and these mutants (Figure 5F). Out of the 12 mutants identified
22 that are in the same complementation group as HXK2, two did not display any mutation in the HXK2
23 ORF (clones #1 and #8) and may represent regulatory mutants in cis, possibly in regions that were not
24 sequenced. In favor of this hypothesis, we found that their 2DG sensitivity can be restored by re-
25 expression of HXK2 using a multicopy, genomic clone (Figure S6A). The other 10 mutants carried at
26 least one mutation in the HXK2 coding sequence (Figure 5F). Four mutations created a stop codon
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1 (clones #12, #15, #16 and #20) resulting in a predicted protein that was truncated almost fully (#20:
2 mutation Leu4>TAA) or by more than half of its length, which is expected to lead to loss of function
3 since conserved regions present in the C-terminal domain are essential for ATP binding and hexokinase
4 activity (67, 68). Five mutants (#2, #3, #11, #13 and #14) carried a single point mutation in residues
5 conserved across all hexokinase sequences tested (see alignment, Figure S6, B-C). Four of these
6 affected residues in close proximity to glucose binding residues (#2: T212>P; #3: K176>T; #11 and #14:
7 Q299>H) (69). The fifth mutation (#13: G418>C) was located next to S419, proposed to interact with the
8 adenosine moiety of ATP (67, 69). Finally, one mutant (#21) bared two mutations, T75>I and S345>P, the
9 latter of which introduces a Pro residue nearby a putative ADP-binding pocket (69, 70). However, these
10 residues are much less conserved (Figure S6C) so it could be that both mutations combined are
11 required to abolish Hxk2 function, although this is only speculative.
12 Among the 2DG-resistant clones which expressed pDOG2-LacZ at a high level, 2 clones (#9 and #10)
13 remained unaccounted for by mutations in either REG1 or HXK2, suggesting that their resistance
14 involved a novel mechanism. Whole genome resequencing of the genomic DNA isolated from these
15 clones and comparison with that of the parent strain revealed several SNPs (Table S2) including a
16 nonsense mutation in CYC8 (C958>T) that was identified in both strains, causing a premature stop codon
17 at position 320 (Figure 6A). The CYC8 gene is also known as SSN6 (Suppressor of snf1) and mutations
18 in this gene lead to constitutive expression of the glucose-repressed gene encoding invertase (SUC2),
19 even in a snf1 mutant (71, 72). Indeed, CYC8 encodes a transcriptional co-repressor which controls the
20 expression of glucose-regulated genes (73). Because the repression of DOG2 expression by glucose is
21 controlled by Snf1 and Mig1/Mig2 (see Figure 4), we hypothesized that CYC8 could also take part in
22 DOG2 regulation, so that a mutation in CYC8 could lead to increased 2DG resistance through DOG2
23 overexpression. We observed that indeed, mutants #9 and #10 expressed invertase even in when
24 grown in glucose medium (repressive conditions), in agreement with a mutation in CYC8 (Figure 6B).
25 We also observed that these mutants displayed an increased adhesion phenotype, i.e. persistence of
26 colony structures upon washing the plate (74) that is often associated to mutants that are prone to
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1 flocculate, such as cyc8 mutants (75, 76) (Figure 6C). When we introduced a low copy (centromeric)
2 plasmid containing CYC8 under the control of its endogenous promoter, we observed that it
3 suppressed the 2DG resistance of mutants #9 and #10 as well as their adhesion to the agar plate (Figure
4 6C). This was not the case when using a truncated version of CYC8 identified in this screen (Figure 6C),
5 although mutants #9 and and #10 did not display a slow growth contrary to the cyc8∆ mutant,
6 suggesting that it is at least partially active for other functions. Finally, we tested whether the strong
7 activity of the DOG2 promoter observed in mutants #9 and #10 (see Figure 5A) was also due to the
8 lack of a functional CYC8. Indeed, the re-introduction of low-copy vector containing CYC8 led to a
9 decreased reporter expression in these mutants (Figure 6D). This was confirmed by examining Dog2-
10 GFP expression at the protein level (Figure 6E-F). Therefore, DOG2 expression is regulated by Cyc8 and
11 spontaneous cyc8 mutants display an increase in Dog2 expression and increased resistance to 2DG.
12 Altogether, this initial characterization revealed that DOG2 overexpression is a common
13 phenomenon within spontaneous 2DG-resistant clones, both in known 2DG-resistant mutants (reg1
14 and hxk2) and in the novel 2DG-resistant cyc8 mutants that we isolated.
15
16 HDHD1, a human member of the HAD-like phosphatase family, is a new 2DG-6-P phosphatase
17 involved in 2DG resistance
18 The fact that Dog2 expression is increased in various spontaneous 2DG-resistant mutants reminded
19 us of early studies in HeLa cells showing an increased 2DG6P phosphatase activity in isolated 2DG
20 resistant clones (20). Dog1 and Dog2 belong to the family of HAD (Haloacid Dehalogenase)-like
21 phosphatases conserved from bacteria to human (Figure 7A). The bacterial homolog of Dog1/Dog2,
22 named YniC, can also dephosphorylate 2DG6P in vitro (77) and we found that the expression of YniC
23 in the double dog1∆ dog2∆ yeast mutant also restored 2DG resistance (Figure 7B). We used this
24 phenotype to identify potential human orthologues (Figure 7A). Running a PSI-BLAST (78) on the
25 human proteome using the Dog2 protein sequence retrieved HDHD1-isoform a (NP_036212.3) as the
26 best hit (39% homology). HDHD1 (for Haloacid Dehalogenase-like Hydrolase Domain containing 1; also
14 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 named PUDP for pseudouridine-5'-phosphatase) is a HAD-like phosphatase with a demonstrated in
2 vitro activity towards phosphorylated metabolites such as pseudouridine-5'-phosphate (79). When
3 expressed in in the double dog1∆ dog2∆ mutant, HDHD1 was partially able to rescue growth on 2DG
4 containing medium (Figure 7B). The expression of HDHD4 (also named NANP, for N-acylneuraminate-
5 9-phosphatase; 80), which belongs to the same subfamily as HDHD1 within the HAD-phosphatase
6 family (37% homology), did not significantly restore yeast growth on 2DG (Figure 7C, D), neither did
7 that of PSPH (phosphoserine phosphatase; 81), another close family member (Figure 7C). Moreover,
8 among the four predicted isoforms of HDHD1 (isoforms 1-4), only HDHD1-1 rescued the growth of the
9 dog1∆ dog2∆ on 2DG-containing medium (Figure 7E) despite the fact that all isoforms were expressed
10 in yeast, as confirmed by western blotting using anti-HDHD1 antibodies (Figure 7F).
11 The mutation of conserved aspartate residues (D12 and D14, see alignment in Figure 7A), predicted
12 to be essential for the catalytic activity of HAD phosphatases (82) abolished the ability of HDHD1 to
13 restore growth of the dog1∆ dog2∆ mutant on 2DG (Figure 8A, B), suggesting it may act as a 2DG-6P
14 phosphatase. This was confirmed by purifying recombinant HDHD1 (Figure 8C) and testing for a
15 potential 2DG-6-P phosphatase activity. Indeed, HDHD1 could dephosphorylate 2DG-6P in vitro, and
16 this activity depended on the integrity of its putative catalytic residues (Figure 8D). We then tested
17 whether HDHD1 overexpression in HeLa cells could lead to an increased resistance to 2-DG. Low
18 concentrations of 2DG (5 mM) in the presence of glucose (25 mM) were sufficient to inhibit the growth
19 of cells transfected with an empty vector, whereas those that overexpressed HDHD1 were virtually
20 insensitive to 2DG treatment (Figure 8E). Importantly, HDHD1 expression was not influenced by ER
21 stress in HeLa cells, since exposure to 2DG or tunicamycin did not modify the expression level of
22 endogenous HDHD1 (despite affecting the glycosylation of CD147, a heavily glycosylated plasma
23 membrane protein) (Figure 8F). These results suggest that a dysregulated expression of HDHD1 could
24 modulate 2DG resistance.
25
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1 Discussion 2 3 The first studies examining the effect of 2DG on glycolysis in yeast but also in normal and cancer
4 tissues were published more than 60 years ago (83-85). Yet, its mode of action is not fully understood.
5 For a given concentration, 2DG inhibits yeast growth more potently in a medium containing 2% glucose
6 than 5% glucose (86), thus 2DG can be considered as a general competitor of glucose. Because of its
7 structural similarity to glucose and its described effect on the inhibition of glycolytic enzymes (6-8),
8 2DG was mostly considered as a glycolysis inhibitor, but more recent data challenged this view (87).
9 Indeed, exposure of cancer cells to 2-deoxyglucose interferes with N-linked glycosylation, likely
10 because of the structural similarity of 2-deoxyglucose with mannose. This results in endoplasmic
11 reticulum (ER) stress and consequently, in the induction of the Unfolded Protein response (UPR) in
12 mammalian cells (14, 16). Therefore, 2DG interferes with several cellular functions.
13 In this study, we used mass spectrometry as an unbiased approach to describe the cellular effects
14 of 2DG on the total cellular proteome. This revealed that many glycolytic enzymes are upregulated,
15 likely as a consequence of an impaired glycolysis.
16 A second and unexpected observation was to identify, within the list of 2DG-upregulated proteins,
17 the Dog1 and/or Dog2 phosphatase, previously involved in 2DG resistance (33, 40, 41). Our subsequent
18 results on the relative abundance of Dog1 and Dog2 suggest that the protein identified by mass
19 spectrometry, which could not be discriminated at this stage because of the high identity between
20 these paralogues, is likely to be Dog2. Dog2 upregulation upon 2DG treatment was intriguing because
21 it wasn’t clear how a synthetic molecule such as 2DG could trigger the onset of a resistance
22 mechanism. It should be noted that the cellular functions of Dog1/Dog2, beyond 2DG
23 dephosphorylation, are unknown. They can dephosphorylate a range of phosphorylated sugars in vitro
24 (40), in agreement with the fact that other members of the HAD family of phosphatases can
25 accommodate various substrates (77). Therefore, it seemed plausible that Dog1/2 induction was a
26 response to one or more of the cellular consequences of 2DG treatment, and not to 2DG itself. Our
27 study reveals that actually, the expression of Dog1 and Dog2 is controlled by multiple signaling
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1 pathways, each of which are turned on as a response to 2DG (see Working model, Figure 9). This study
2 was also taken as an opportunity to probe the signaling pathways that are activated upon 2DG
3 exposure and precise the causes of these activations.
4 First, we showed that Dog1 and Dog2 are induced by ER stress. We confirmed that 2DG triggers ER
5 stress and the onset of the UPR pathway. This was not unexpected given the proposed mode of action
6 of this drug and the available data in the literature on mammalian cells (14, 16), but this had not been
7 formally proven in yeast with current tools. The induction of an UPR reporter and the hypersensitivity
8 of UPR mutant strains such as hac1∆ or ire1∆ are in agreement with this conclusion. Finally, the
9 hypersensitivity phenotype of UPR mutants to 2DG could be alleviated by restoring N-glycosylation
10 through the addition of mannose in the culture medium, suggesting that 2DG toxicity in UPR mutants
11 is directly due to defects in protein N-glycosylation. These results are in line with high-throughput
12 studies proposing that both DOG1 and DOG2 are UPR-regulated genes (88).
13 Second, we showed that 2DG also activates the MAP kinase-based cell wall integrity (CWI) pathway.
14 Several studies reported connections between ER stress signaling and the CWI pathway (56-60), and
15 2DG-elicited N-glycosylation and ER stress may have repercussions on the CWI pathway. For instance,
16 it was previously observed that CWI pathway mutants are sensitive to tunicamycin because they lack
17 an ER surveillance-pathway which normally prevents the inheritance of stressed ER (58). Many CWI
18 mutants were indeed sensitive to low concentrations (0.05%) of 2DG but unlike UPR mutants, their
19 growth was not restored by the addition of exogenous mannose, suggesting that N-glycosylation
20 defect is not the sole reason why CWI mutants are sensitive to 2DG. 2DG was also shown to interfere
21 with the synthesis of structural polysaccharides that make up the yeast cell wall (mannans and
22 glucans), again because 2DG acts as an antagonist of mannose but also of glucose incorporation into
23 these polymers (42, 89-91). Accordingly, 2DG exposure leads to yeast cell lysis at sites of growth, which
24 is where glucan synthesis occurs (43) and where the major glucan synthase, Fks1, is localized (92).
25 Thus, we propose that 2DG-induced weakening of the cell wall could be responsible for the triggering
26 of the cell wall integrity pathway (Figure 9). This could explain why the main sensors responsible for
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1 sensing cell wall damage, Wsc1 and Mid2 (reviewed in 55), are required for growth on 2DG. In addition,
2 we also report that Dog1 and Dog2 are less expressed in CWI mutants, which could further sensitize
3 these strains to 2DG. Although the effect of 2DG on cell wall synthesis applies to fungi but not to animal
4 cells that do not harbor a cell wall, it denotes the interference of 2DG with UDP-glucose metabolism
5 that is likely to be conserved in animals (93). 2DG may affect metabolic pathways involving these
6 precursors in metazoans, such as glycogen synthesis (94, 95). Additionally, 2DG was shown to be
7 metabolized into GDP-glucose, which incorporates into dolichol-phosphate precursors and further
8 interferes with protein glycosylation (90, 96), but also into phosphoinositol-based lipids (97), the
9 cellular consequences of which are unknown.
10 Our data also reveal that the increased 2DG-6-phosphate phosphatase activity of the reg1 mutants,
11 that has been described very early on (28, 38, 39), is partly due to the glucose-mediated repression of
12 Dog2, the latter being consequently overexpressed in the reg1∆ mutant. This may also contribute to
13 the 2DG resistance of hxk2 and mig1 mutants, which also act in the glucose-repression pathways and
14 were identified in previous screens (29, 35). Indeed, we show that the 2DG resistance displayed by
15 the reg1∆ and hxk2∆ strains was partially due to an increased expression of Dog2. In the hxk2∆ mutant,
16 the lack of hexokinase 2 is compensated by the expression of other glucose-phosphorylating enzymes
17 (such as Hxk1 and glucokinase, Glk1) (98) that may be less prone to phosphorylate 2DG (36), and thus
18 could lead to a lower accumulation of 2DG6P in the cell and further increase 2DG resistance. Hxk2 also
19 has additional, non-metabolic roles beyond sugar phosphorylation, whose loss may additionally
20 contribute to this phenotype (reviewed in Ref. 99). Concerning the reg1∆ strain, the additional
21 mechanisms of resistance also remain to be investigated. A cross-talk between the Snf1/Reg1 couple
22 and the UPR pathway has been described (63, 64), however these studies revealed that the reg1∆
23 mutant is actually hypersensitive to UPR inducers such as tunicamycin (Figure 5B) (63, 64), making its
24 resistance towards 2DG (which is also an UPR inducer) even more striking. What appeared from
25 previous work is that the resistance of the reg1∆ mutant is dependent on Snf1 hyperactivity, since the
26 additional deletion of SNF1 restores 2DG sensitivity to the reg1∆ strain (31). Thus, additional yet Snf1-
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1 dependent mechanisms cooperate with the increased expression of DOG2 to allow reg1∆ cells to resist
2 to 2DG.
3 After 2DG import and phosphorylation, the amount of 2DG6P in cells can exceed that of G6P by up
4 to 80-fold (100). Overexpression of Dog2 was previously shown to revert the repressive effect of 2DG
5 (33), suggesting that it can clear the 2DG6P pool up to a point where 2DG6P is no longer detected by
6 the yet unknown cellular glucose-sensing mechanism. Thus, Dog2 overexpression appears as a good
7 strategy for 2DG resistance, and indeed, it was overexpressed in the majority of the spontaneous
8 resistant mutants we isolated. This included mutants in the REG1 and HXK2 genes, but additionally,
9 we identified two mutants carrying a point mutation in the gene encoding the transcriptional repressor
10 Cyc8, leading to a truncated protein at codon 320, within its 8th predicted tetratricopeptide (TPR)
11 repeat. The TPR repeats are involved in the interaction of Cyc8 with its co-repressor Tup1, and to
12 specify its recruitment to specific promoters, possibly through the recruitment of pathway-specific
13 DNA-binding proteins (101). The identified truncation leads to the de-repression of invertase and
14 Dog2, but does not impact on growth as strongly as the full deletion of the gene. Interestingly, recent
15 data showed that point mutations in TPR units 9 and 10 affect Cyc8 function in a similar manner as the
16 mutation we isolated (i.e. impact on glucose repression but not global growth), suggesting that
17 alterations at this region affect a subset of Cyc8 functions (102). This is in line with a study showing the
18 differential requirement of TPR repeats for the various functions of Cyc8, and in particular the
19 involvement of the TPR repeats 8-10 in glucose repression (103). Altogether, these data describe DOG2
20 overexpression as a successful strategy to overcome 2DG toxicity.
21 Similarly, the selection of HeLa-derived 2-DG-resistant cell lines showed an increase in 2DG6P
22 phosphatase activity, but the responsible enzyme was not identified (20). Based on sequence
23 similarity, we identified HDHD1 as an enzyme displaying in vitro 2DG6P phosphatase activity and
24 whose overexpression in both yeast and HeLa cells allows resistance to 2DG. Actually, we found that
25 HDHD1 has a very low affinity toward 2DG (in the 10-2 M range, unpublished data) as compared to
26 other substrates such as 5ʹ-pseudouridine monophosphate or even 3ʹ-AMP (79). Despite this very low
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1 affinity for 2DG, HDHD1 overexpression in HeLa cells conferred resistance to 2DG. Whether HDHD1 is
2 responsible for the 2DG resistance previously reported in human cells (20) remains to be investigated.
3 Altogether, our work shows that 2DG-induced activation of multiple signaling pathways can rewire
4 the expression of endogenous proteins which can target 2DG6P to promote 2DG tolerance, and whose
5 deregulated expression can lead to 2DG resistance. This mechanism likely superimposes on other
6 resistance mechanisms that should be scrutinized in the future.
7
8 Acknowledgments. 9 10 We would like to thank Nicolas Joly for discussion about the HDHD1 in vitro assay, Gaelle Lelandais
11 for help with Yeastract analysis, Pascual Sanz and Jose Antonio Prieto for the gift of the GST-Dog2
12 construct, Emile Van Schaftingen for the gift of the His-tagged HDHD1 construct, Peter Walter for the
13 gift of the pUPRE1:lacZ reporter, David Levin for the gift of the pCYC(2xRlm1):lacZ reporter, Colin
14 Stirling for the gift of the anti-invertase antibody and Martin Schmidt for advice regarding gDNA
15 extraction for sequencing. We also thank Thibaut Léger and the Proteomics facility of the Institut
16 Jacques Monod (supported by the Region Ile-de-France (SESAME), the Paris-Diderot University (ARS),
17 and CNRS) for assistance. We thank Anna Babour, Myriam Ruault and members of the Léon lab for
18 insightful comments and critical reading. This work was supported by fellowships from the Fondation
19 pour la Recherche Médicale (SPF20150934065 to QD) and the Ligue contre le cancer (TAZK20115 to
20 CL), and by grants from the Agence Nationale pour la Recherche (P-Nut, ANR-16-CE13-0002 to SL)
21 and the Fondation ARC pour la recherche sur le cancer (PJA20181208080 to SL).
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1 Material and Methods 2 3 Yeast strain construction and growth conditions 4 All yeast strains used in this study derive from the Saccharomyces cerevisiae BY4741 or BY4742 5 background and are listed in Supplemental Table S3. Apart from the mutant strains obtained from the 6 yeast deletion collection (Euroscarf) and the fluorescent GFP tagged strains originating from the yeast 7 GFP clone collection (104), all yeast strains were constructed by transformation with the standard 8 lithium acetate-polyethylene glycol protocol using homologous recombination and verified by PCR on 9 genomic DNA prepared with a lithium acetate (200mM) / SDS (0.1%) method (105). 10 Yeast cells were grown in YPD medium (Yeast extract-Peptone-Dextrose 2%) or in synthetic complete 11 medium (SC, containing 1.7g/L yeast nitrogen base (MP Biomedicals), 5g/L ammonium sulfate (Sigma- 12 Aldrich), the appropriate drop-out amino acid preparations (MP Biomedicals) and 2% (w/vol) glucose 13 unless otherwise indicated). Alternatively, SC medium could contain 0.5% lactate as a carbon source 14 (from a 5% stock adjusted to pH=5; Sigma Aldrich). Pre-cultures of 4mL were incubated at 30°C for 8 15 hours and diluted in fresh medium on the evening to 20mL cultures grown overnight with inoculation
16 optical densities (OD600) of 0.0003 for YPD and 0.001 for SC medium, giving a culture at mid-log phase 17 the next morning. 18 For glucose depletion experiments, cultures were centrifuged and resuspended in an equal volume of 19 SC/lactate medium and incubated at 30°C during the indicated times. For 2-deoxyglucose, NaCl and 20 tunicamycin treatments, the compounds were added to mid-log phase yeast cultures grown overnight 21 to respective final concentrations of 0.2% (w/v), 400mM and 1µg/mL and incubated for the indicated 22 times. 2-deoxyglucose and tunicamycin were purchased from Sigma-Aldrich. The mannose- 23 supplemented medium (Fig. 2B) consisted of an SC medium that contained all the element indicated 24 above plus 2% (w/vol) mannose. 25 26 Plasmid construction 27 All the plasmids presented in this study are listed in Supplemental Table S4 and were directly 28 constructed in yeast using plasmid homologous recombination (106). DNA inserts were amplified by 29 PCR using 70-mer primers containing 50nt homology overhangs and Thermo Fisher Phusion High- 30 fidelity DNA Polymerase and receiver plasmids were digested with restriction enzymes targeting the 31 insertion region. Competent yeast cells rinsed with lithium acetate were incubated for 30 minutes at 32 30°C with 20µL of the PCR product and 1µL of the plasmid digestion product, followed by a heat shock 33 at 42°C for 20 minutes and a recovery phase in rich medium (YPD) for 90 minutes at 30°C and plated 34 on synthetic medium without uracil. The pDOG1/2-LacZ vectors were generated using the pJEN1-LacZ
21 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 vector obtained from Bernard Guiard (107) and cloning the pDOG1 or pDOG2 promoters (1kb) at BglII 2 and EcoRI sites. 3 The DOG1, DOG2, HDHD1 (all four isoforms), HDHD4, PSPH and yniC overexpression vectors were 4 obtained by digesting a pRS426 vector (2µ, URA3) containing the pGPD promoter with EcoRI and 5 BamHI enzymes. In parallel, inserts were PCR-amplified using the following DNA templates: DOG1 and 6 DOG2 from yeast genomic DNA preparations (primers: oSL1166/1167 and oSL1141/1142), the yniC 7 ORF from Escherichia coli DH5α cells (oSL1172/1173) and the human gene ORFs (Uniprot identifiers: 8 HDHD1=Q08623-1/2/3/4, HDHD4=Q8TBE9 and PSPH=P78330) from DNA sequences generated by 9 gene synthesis after codon optimization for yeast expression (Eurofins Genomics) (HDHD1: 10 oSL1170/1171 for all isoforms except isoform 3: oSL1170/1216; HDHD4: oSL1214/1215; PSPH: 11 oSL1212/1213). These PCR products were designed to include a 50-bp overlap with the digested 12 plasmid so as to clone them by homologous recombination in yeast after co-transformation. The 13 pGPD-HDHD1-DDAA vector was obtained by PCR amplification (oSL1155/1171) of the HDHD1 DNA 14 sequence obtained by gene synthesis using a specific 5' primer carrying two D>A mutations and 15 insertion of this insert into the pRS426 vector digested with EcoRI and BamHI as described above. This 16 construct was verified by sequencing. The DDAA mutant was PCR amplified (oSL1297/oSL1298) and 17 subcloned at NdeI/BamHI sites into pET15b-6His-HDHD1, a kind gift of Dr. E. Van Schaftingen, to 18 substitute for endogenous HDHD1. 19 Plasmids expressing the wild-type CYC8 gene and the mutant allele present in mutant #9 were 20 obtained by PCR amplification on the corresponding genomic DNAs with primers (oSL1369/1370) 21 containing a 50-bp overlap with a pRS415 vector (CEN, LEU2) digested with XbaI and BamHI, and co- 22 transformation for cloning by homologous recombination in yeast as described above. 23 The plasmids generated in yeast were rescued by extraction (lithium acetate/SDS method (105)) and 24 electroporation in bacteria, then amplified and sequenced before being re-transformed in the 25 appropriate strains. 26 27 Mass spectrometry and proteomics analyses 28 Samples used for the proteome-wide analysis of 2-deoxyglucose treatments were prepared from six 29 liquid cultures (WT strain, BY4741) growing overnight at 30°C in 100mL of rich medium with 2% glucose 30 to mid-log phase. On the next morning, 2-deoxyglucose was added to three of the cultures to a final 31 concentration of 0.2% in order to obtain triplicates treated with 2-DG and triplicates without drug 32 treatment (negative control). After 2.5 hours of incubation at 30°C, the six cultures were centrifuged 33 at 4000g for 5 minutes at 4°C, resuspended in 500µL of 10% trichloroacetic acid (TCA, Sigma-Aldrich) 34 and lysed by shaking after addition of glass beads (0.4-0.6mm, Sartorius) for 10 minutes at 4°C. Cell 35 lysates were retrieved by piercing under the 1.5mL tubes and brief centrifugation. Precipitated
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1 proteins were centrifuged at 16000g for 10 minutes at 4°C, supernatants were discarded and pellets 2 were rinsed 4 times in 1mL of 100% cold acetone.
3 Proteins were then digested overnight at 37°C in 20 μL of 25 mM NH4HCO3 containing sequencing- 4 grade trypsin (12.5 μg/mL; Promega). The resulting peptides were sequentially extracted with 70% 5 acetonitrile, 0.1% formic acid. Digested samples were acidified with 0.1% formic acid. All digests were 6 analyzed by an Orbitrap Fusion equipped with an EASY-Spray nanoelectrospray ion source and coupled 7 to an Easy nano-LC Proxeon 1000 system (all from Thermo Fisher Scientific, San Jose, CA). 8 Chromatographic separation of peptides was performed with the following parameters: Acclaim 9 PepMap100 C18 pre-column (2 cm, 75 μm i.d., 3 μm, 100 Å), Pepmap-RSLC Proxeon C18 column (50 10 cm, 75 μm i.d., 2 μm, 100 Å), 300 nl/min flow, using a gradient rising from 95 % solvent A (water, 0.1 11 % formic acid) to 40 % B (80 % acetonitrile, 0.1% formic acid) in 120 minutes, followed by a column 12 regeneration of 20 min, for a total run of 140 min. Peptides were analyzed in the orbitrap in full-ion 13 scan mode at a resolution of 120,000 (at m/z 200) and with a mass range of m/z 350-1550, and an AGC 14 target of 2x105. Fragments were obtained by higher-energy C-trap dissociation (HCD) activation with 15 a collisional energy of 30 %, and a quadrupole isolation window of 1.6 Da. MS/MS data were acquired 16 in the linear ion trap in a data-dependent mode, in top-speed mode with a total cycle of 3 seconds, 17 with a dynamic exclusion of 50 seconds and an exclusion duration of 60 seconds. The maximum ion 18 accumulation times were set to 250 ms for MS acquisition and 30 ms for MS/MS acquisition in 19 parallelization mode. 20 Raw mass spectrometry data from the Thermo Fisher Orbitrap Fusion were analyzed using the 21 MaxQuant software (108) version 1.5.0.7, which includes the Andromeda peptide search engine (109). 22 Theoretical peptides were created using the Saccharomyces cerevisiae S288C proteome database 23 obtained from Uniprot. Identified spectra were matched to peptides with a main search peptide 24 tolerance of 6ppm. After filtering of contaminants and reverse identifications, the total amount of 25 yeast proteins identified among the six samples was equal to 3425. Protein quantifications were 26 performed using MaxLFQ (110) on proteins identified with a minimum amount of two peptides with a 27 False Discovery Rate threshold of 0.05. LFQ values were then analyzed using Perseus (version 1.5.0.15). 28 For the statistical analysis of yeast proteomes treated with 2-dexogylucose compared to negative 29 control samples, each group of triplicates was gathered into a statistical group in order to perform a 30 Student's t-test. Results are presented in the form of Volcano-plots (111) and significant up-regulated
31 and down-regulated candidates were determined by setting an FDR of 0.01 and an S0 of 2. 32 33 GO-term analyses of proteomics data 34 The 79 significantly up-regulated candidates obtained in the proteomics analysis were used as input 35 for the FunSpec web interface (http://funspec.med.utoronto.ca/) with default settings and a p-value
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1 cutoff of 0.01 in order to determine the Gene Ontology biological processes that are enriched in this 2 list of 79 genes compared to the total Saccharomyces cerevisiae genome annotation (number of total 3 categories=2062). The complete list of enriched GO biological processes with a p-value<0.01, as well 4 as the genes included in each category, are displayed in Supplemental Figure S1A. 5 6 Protein extracts and immunoblotting 7 Yeast cultures used for protein extracts were all grown in synthetic complete medium. For each protein 8 sample, 1.4mL of culture was incubated with 100µL of 100% TCA for 10 minutes on ice to precipitate 9 proteins, centrifuged at 16000g at 4°C for 10 minutes and broken for 10 minutes with glass beads, as 10 described for LC-MS/MS sample preparation. Lysates were transferred to another 1.5mL tube and 11 centrifuged 5 minutes at 16000g at 4°C, supernatants were discarded and protein pellets were
12 resuspended in 50µL*(OD600 of the culture) of sample buffer (50 mM Tris-HCl pH6.8, 100 mM DTT, 2% 13 SDS, 0.1% bromophenol blue, 10% glycerol, complemented with 50mM Tris-Base pH8.8). Protein 14 samples were heated at 95°C for 5 minutes and 10µL were loaded on SDS-PAGE gels (4-20%Mini- 15 PROTEAN TGX Stain-Free, BioRad). After electrophoresis, gels were blotted on nitrocellulose 16 membranes for 60 minutes with a liquid transfer system (BioRad), membranes were blocked in 2% 17 milk for 20 minutes and incubated for at least two hours with the corresponding primary antibodies. 18 Primary and secondary antibodies used in this study as well as their dilutions are listed in Supplemental 19 Table S5. Membranes were washed three times for 10 minutes in Tris-Borate-SDS-Tween20 0.5% 20 buffer and incubated for at least an hour with the corresponding secondary antibody (coupled with 21 Horse Radish Peroxidase). Luminescence signals were acquired with the LAS-4000 imaging system 22 (Fujifilm). Rsp5 was used as a loading control; alternatively, total proteins were visualized in gels using 23 a trihalo compound incorporated in SDS–PAGE gels (stain-free TGX gels, 4–20%; Bio-Rad) after 1 min 24 UV-induced photoactivation and imaging using a Gel Doc EZ Imager (Bio-Rad).
25 Beta-galactosidase assays
26 β-Galactosidase assays were performed using 1mL of mid-log phase yeast cultures carrying the pDOG1-
27 LacZ or pDOG2-LacZ plasmids, grown overnight in SC medium without uracil with glucose 2% and 28 switched to the specified conditions. The OD (600 nm) of the culture was measured, and samples were 29 taken and centrifuged at 16000g at 4°C for 10 minutes, cell pellets were snap frozen in liquid nitrogen
30 and resuspended in 800µL of Buffer Z (pH=7, 50mM NaH2PO4, 45mM Na2HPO4, 10mM MgSO4, 10mM 31 KCl and 38mM β-mercaptoethanol). After addition of 160µL of 4mg/mL ONPG (ortho-nitrophenyl-β-D- 32 galactopyranoside, Sigma-Aldrich), samples were incubated at 37°C. Enzymatic reactions were
33 stopped in the linear phase (60min incubation for pDOG2-LacZ and 120min incubation for the pDOG1-LacZ
34 plasmid, as per initial tests) by addition of 400µL of Na2CO3, and cell debris were discarded by
24 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 centrifugation at 16000g. The absorbance of clarified samples was measured with a 2 spectrophotometer set at 420nm. β-Galactosidase activities (arbitrary units, AU) were calculated using
3 the formula 1000*[A420/(A600* t)], where A420 refers to the enzyme activity and A600 is the turbidity 4 of the culture, and t the incubation time. Each enzymatic assay was repeated independently at least 5 three times.
6 Drop tests 7 Yeast cells grown in liquid rich or synthetic complete medium for at least 6 hours at 30°C were adjusted 8 to an optical density (600nm) of 0.5. Five serial 10-fold dilutions were prepared in 96-well plates and, 9 using a pin replicator, drops were spotted on plates containing rich or SC medium containing 2% (w/v) 10 agar and when indicated, 2DG (0.05%, or 0.2%, w/vol), sodium selenite (200µM) or tunicamycin 11 (1µg/mL). Plates containing mannose (Fig 2H and 3G) were prepared as regular SC plates into which 12 2% mannose (w/vol) was added. Plates were incubated at 30°C for 3 to 4 days before scanning. For the 13 adhesion test (Figure 6C), the plates were scanned and the colonies were then washed with tap water 14 under a constant flow of water for 1 min as previously described (74). Excess water was removed 15 before the plates were scanned again.
16 2-NBDG treatment and Fluorescence microscopy 17 For 2-NBDG treatments, yeast cells were grown overnight in SC medium containing 2% glucose to the 18 exponential phase, then switched to SC medium with 0.5% lactate and incubated at 30°C for 30 19 minutes. This allowed the clearance of glucose from the medium, without which 2NBDG import was 20 too weak to be observed since Glucose and 2NBDG compete for transport (112). 2NBDG (2-(N-(7- 21 Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose; Cayman Chemical) was then added at a 22 concentration of 300µM for the indicated times. 23 Yeast were then rinsed twice in 1mL of cold water before being mounted on a glass slide and imaged 24 at 25°C with a BX-61 fluorescence microscope (Olympus) equipped with a PlanApo 1.40NA 100X 25 objective (Olympus), a QiClick monochrome camera (QImaging) and acquired using the MetaVue 26 software (Molecular Devices). The 2-NBDG signal was visualized using a GFP filter set (41020 from 27 Chroma Technology, Bellows Falls, VT; excitation HQ480/20X, dichroic Q505LP, emission HQ535/50m). 28 Loa1-mCherry was visualized using an HcRedI filter set (41043 from Chroma Technology, Bellows Falls, 29 VT; excitation HQ575/50X, dichroic Q610lp, emission HQ640/50m). Images were opened with ImageJ 30 and processed for cropping and equivalent contrast adjustment.
31 Isolation of spontaneous mutants and characterization. 32 WT cells transformed with a pDOG2-LacZ plasmid (pSL410) were grown overnight in SC-Ura medium 33 and ca. 2x10(6) cells were spread on SC-Ura plates containing 0.2% 2DG and grown for 6 days at 30°C.
25 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 The clones obtained (24 clones) were restreaked on SC-Ura to isolate single clones. Resistance to 2DG 2 was confirmed by drop tests (see Figure 5B). Beta-galactosidase enzyme assays and total protein 3 extracts were performed on cultures grown to the exponential phase. For beta-galactosidase assays, 4 the results of three independent experiments are shown along and were statistically tested using an 5 unpaired t-test with equal variance. 6 Diploids were obtained by crossing each resistant mutant with a WT or hxk2∆ strain of the opposite 7 mating type (BY4742, Matα) and selecting single diploid clones on selective medium (SC-Met-Lys). 8 Sequencing of the REG1 and HXK2 loci were done after PCR amplification on genomic DNA isolated 9 from the corresponding clones. For whole genome sequencing, genomic DNA of the WT, clone 9 and 10 clone 10 was purified using the Qiagen genomic DNA kit (Genomic-tip 20/G) using 30 OD equivalents 11 of material following the manufacturer’s instructions after zymolyase treatment (Seikagaku). A PCR- 12 free library was generated from 10 µg of gDNA and sequenced at the Beijing Genomics Institute (Hong 13 Kong) on Illumina HiSeq 4000. The mutations in each clone were identified through comparative 14 analysis of the variants detected by mapping their reads to the reference genome (BY4741) (113, 114) 15 and those detected by mapping the WT reads to the reference. The differential variants were filtered 16 by quality (vcf QUAL>1000) and manually inspected through IGV for validation (115).
17 Cell culture and transfection.
18 HeLa cells were maintained at 37°C and 5% CO2 in a humidified incubator and grown in Dulbecco’s 19 modified Eagle’s medium (DMEM), supplemented with 10% fetal calf serum (FCS). Cells were regularly 20 split using Trypsin-EDTA to maintain exponential growth. HeLa cells were transfected with plasmid 21 pCMV-Sport6-HDHD1 and pCS2 (empty control) using Lipofectamine 2000 according to the 22 manufacturer's instructions. All culture media reagents were from Thermo Fisher Scientific. 2DG 23 (Sigma) was used at a final concentration of 5 mM and tunicamycin (from Streptomyces sp; Sigma) was 24 used at a final concentration of 5 µg/mL. For 2DG resistance assays, cells were grown in 10 cm2 flask 25 and split in a 24-well plate in the absence or presence of 5 mM 2DG. Cells were counted each day with 26 a hemocytometer after trypsinization and labeling with Trypan Blue. Total extracts were prepared by 27 incubating cells (10 cm2) on ice for 20 min with 400 µL TSE Triton buffer (50 mM Tris- HCl pH 8.0, NaCl 28 150 mM, 0.5 mM EDTA, 1% Triton X-100) containing protease inhibitors (cOmplete protease inhibitor 29 cocktail, EDTA-Free, Roche Diagnostics). Cells were then lysed mechanically with scrapers, and the 30 lysate was centrifuged at 13,000 g, 4°C for 30 min. Proteins were assayed in the supernatant using the 31 Bio-Rad Protein Assay reagent (Bio-Rad) and 40 µg proteins were loaded on SDS-PAGE gels.
32 33 Recombinant His-tagged HDHD1 and HDHD1-DDAA protein purifications
26 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 E. coli BL21 bacteria were transformed with plasmids allowing the expression of His-tagged HDHD1 or 2 HDHD1-DDAA . A 100mL-preculture was grown overnight in LB+Ampicillin (100 µg/mL), diluted 50-fold 3 into 1L culture. The OD reached 0.7-0.9. IPTG (1 mM) was then added to induce the recombinant 4 protein and cells were further grown at 25°C for 3 hours. Cells were harvested, the pellet was frozen
5 in liquid N2 and thawed on ice. The pellet was resuspended in 20 mL of lysis buffer (HEPES 25mM pH 6 6.7, 300mM NaCl, imidazole 15 mM, beta-mercaptoethanol 2mM, glycerol 10% v/v and protease 7 inhibitor cocktail [cOmplete protease inhibitor cocktail, EDTA-Free, Roche Diagnostics]). Cells were 8 then sonicated and Triton X-100 was added to a final concentration of 1%. The lysate was centrifuged 9 at 12,000rpm in a SW-32 rotor (Beckman Coulter) for 15min at 4°C, and then the supernatant was 10 further centrifuged at 35 000 rpm for 1h at 4°C. The supernatant was incubated with 800 µL of Ni-NTA 11 beads slurry (Qiagen) and rotated overnight at 4°C. The beads were collected by centrifugation (1000g, 12 2min, 4°C), resuspended in lysis buffer, and washed with 50 mL of lysis buffer at 4°C, and then washed
13 again with 50 mL thrombin cleavage buffer (Hepes 50 mM, CaCl2 5 mM, NaCl 100mM, glycerol 10%) at 14 4°C. The His-tag was removed by cleavage with 16 U of thrombin (Ref 27-0846-01, Sigma) added 15 directly onto the beads for 2h at 25°C. The eluate was then collected and incubated with 500 µL 16 benzamidin-sepharose 6B (GE Healthcare) at room temperature for 30 min to remove thrombin. The 17 supernatant was collected and protein content was assayed by SDS-PAGE and colloidal blue staining 18 (Brilliant Blue G-colloidal, Sigma), and protein concentration was assayed by the Bradford method (Bio- 19 Rad protein assay, Bio-Rad). 20 21 Enzyme assays 22 2-DG-6-Phosphate phosphatase assays were performed in 250 µL of reaction containing 1.5mM 2-DG- 23 6-Phosphate (#17149, Cayman Chemicals, Ann Arbor, Michigan, USA) in 50 mM HEPES pH 6.7, 10 mM
24 MgCl2 and 10% glycerol and 30 µg recombinant HDHD1 or HDHD1-DDAA. Samples were incubated at 25 37°C for various times (0, 5, 10, 15min) and the reaction was stopped by adding 150µL EDTA (0.5M). 26 Then, the 2-deoxyglucose generated was assayed by adding 500µL of glucose assay reagent (GAGO20,
27 Sigma) and further incubating at 37°C for 30min. The reaction was stopped by adding 500µL H2SO4 28 (12N) and the absorbance of the reaction was measured at 540 nm. A slope (A540 over time) was 29 calculated to access to the enzyme activity and allowed to see that the reaction was in the linear range. 30 The measurements were repeated 3 times. 31 32 Statistical analysis 33 Mean values calculated using a minimum of three independent measurements from three biological 34 replicates and are plotted with error bars representing standard error of the mean (SEM). Statistical
27 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 significance was determined using a t-test for paired variables, as follows: *: P ≤ 0.05; **: P ≤0.01; 2 ***: P ≤ 0.001; ns: P >0.05.
28 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 References
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1 90. Datema R, Schwarz RT. Formation of 2-deoxyglucose-containing lipid-linked oligosaccharides. 2 Interference with glycosylation of glycoproteins. Eur J Biochem. 1978;90(3):505-16. 3 91. Biely P, Kratky Z, Kovarik J, Bauer S. Effect of 2-deoxyglucose on cell wall formation in 4 Saccharomyces cerevisiae and its relation to cell growth inhibition. J Bacteriol. 1971;107(1):121-9. 5 92. Utsugi T, Minemura M, Hirata A, Abe M, Watanabe D, Ohya Y. Movement of yeast 1,3-beta-glucan 6 synthase is essential for uniform cell wall synthesis. Genes Cells. 2002;7(1):1-9. 7 93. Schmidt MF, Schwarz RT, Scholtissek C. Nucleoside-diphosphate derivatives of 2-deoxy-D-glucose 8 in animal cells. Eur J Biochem. 1974;49(1):237-47. 9 94. Xi H, Kurtoglu M, Lampidis TJ. The wonders of 2-deoxy-D-glucose. IUBMB Life. 2014;66(2):110-21. 10 95. Biely P, Farkas V, Bauer S. Incorporation of 2-deoxy-D-glucose into glycogen. Biochim Biophys Acta. 11 1968;158(3):487-8. 12 96. Lehle L, Schwarz RT. Formation of dolichol monophosphate 2-deoxy-D-glucose and its interference 13 with the glycosylation of mannoproteins in yeast. Eur J Biochem. 1976;67(1):239-45. 14 97. Steiner S, Lester RL. Studies on the diversity of inositol-containing yeast phospholipids: 15 incorporation of 2-deoxyglucose into lipid. J Bacteriol. 1972;109(1):81-8. 16 98. Rodriguez A, De La Cera T, Herrero P, Moreno F. The hexokinase 2 protein regulates the expression 17 of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae. Biochem J. 2001;355(Pt 3):625-31. 18 99. Gancedo JM. The early steps of glucose signalling in yeast. FEMS Microbiol Rev. 2008;32(4):673- 19 704. 20 100. Kuo SC, Lampen JO. Inhibition by 2-deoxy-D-glucose of synthesis of glycoprotein enzymes by 21 protoplasts of Saccharomyces: relation to inhibition of sugar uptake and metabolism. J Bacteriol. 22 1972;111(2):419-29. 23 101. Gounalaki N, Tzamarias D, Vlassi M. Identification of residues in the TPR domain of Ssn6 24 responsible for interaction with the Tup1 protein. FEBS Lett. 2000;473(1):37-41. 25 102. Maqani N, Fine RD, Shahid M, Li M, Enriquez-Hesles E, Smith JS. Spontaneous mutations in 26 CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK. 27 Microb Cell. 2018;5(5):233-48. 28 103. Tzamarias D, Struhl K. Distinct TPR motifs of Cyc8 are involved in recruiting the Cyc8-Tup1 29 corepressor complex to differentially regulated promoters. Genes Dev. 1995;9(7):821-31. 30 104. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, et al. Global analysis of 31 protein localization in budding yeast. Nature. 2003;425(6959):686-91. 32 105. Looke M, Kristjuhan K, Kristjuhan A. Extraction of genomic DNA from yeasts for PCR-based 33 applications. Biotechniques. 2011;50(5):325-8. 34 106. Ma H, Kunes S, Schatz PJ, Botstein D. Plasmid construction by homologous recombination in 35 yeast. Gene. 1987;58(2-3):201-16. 36 107. Lodi T, Fontanesi F, Guiard B. Co-ordinate regulation of lactate metabolism genes in yeast: the 37 role of the lactate permease gene JEN1. Mol Genet Genomics. 2002;266(5):838-47. 38 108. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.- 39 range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 40 2008;26(12):1367-72. 41 109. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide 42 search engine integrated into the MaxQuant environment. Journal of proteome research. 43 2011;10(4):1794-805. 44 110. Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. Accurate proteome-wide label-free 45 quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. 46 Mol Cell Proteomics. 2014;13(9):2513-26. 47 111. Hubner NC, Mann M. Extracting gene function from protein-protein interactions using 48 Quantitative BAC InteraCtomics (QUBIC). Methods. 2011;53(4):453-9. 49 112. Roy A, Dement AD, Cho KH, Kim JH. Assessing glucose uptake through the yeast hexose 50 transporter 1 (Hxt1). PLoS One. 2015;10(3):e0121985. 51 113. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. 52 Bioinformatics. 2009;25(14):1754-60.
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1 114. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome 2 Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. 3 Genome Res. 2010;20(9):1297-303. 4 115. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative 5 genomics viewer. Nat Biotechnol. 2011;29(1):24-6. 6 116. Ayciriex S, Le Guedard M, Camougrand N, Velours G, Schoene M, Léon S, et al. YPR139c/LOA1 7 encodes a novel lysophosphatidic acid acyltransferase associated with lipid droplets and involved 8 in TAG homeostasis. Mol Biol Cell. 2012;23(2):233-46. 9 117. Orlova M, Barrett L, Kuchin S. Detection of endogenous Snf1 and its activation state: 10 application to Saccharomyces and Candida species. Yeast. 2008;25(10):745-54. 11 118. Trimble RB, Maley F. Subunit structure of external invertase from Saccharomyces cerevisiae. J 12 Biol Chem. 1977;252(12):4409-12. 13 119. Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, et al. Designer deletion strains 14 derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR- 15 mediated gene disruption and other applications. Yeast. 1998;14(2):115-32. 16 120. Jones GM, Stalker J, Humphray S, West A, Cox T, Rogers J, et al. A systematic library for 17 comprehensive overexpression screens in Saccharomyces cerevisiae. Nat Methods. 2008;5(3):239- 18 41. 19 121. Jung US, Sobering AK, Romeo MJ, Levin DE. Regulation of the yeast Rlm1 transcription factor 20 by the Mpk1 cell wall integrity MAP kinase. Mol Microbiol. 2002;46(3):781-9. 21 122. Turner DL, Weintraub H. Expression of achaete-scute homolog 3 in Xenopus embryos converts 22 ectodermal cells to a neural fate. Genes Dev. 1994;8(12):1434-47. 23 123. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W 24 and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947-8. 25
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1 Figure Legends
2 3 Figure 1. Proteomics analysis of yeast response to 2DG reveals a transcriptional induction of the 4 2DG6P phosphatases Dog1-Dog2. 5 (A) Volcano-plot representing changes in protein abundance in total protein extracts of wild-type (WT) 6 yeast in response to 2-deoxyglucose (0.2%), obtained by mass spectrometry-based proteomics and
7 analyzed with the MaxQuant software. The x axis corresponds to the log2 value of the abundance ratio 8 (LFQ: Label-Free Quantification) between 2DG treatment and the negative control. The y axis
9 represents the -log10 of the p-value of the statistical t-test for each quantified protein (n=3 independent 10 biological replicates). Line: threshold with a False Discovery Rate of 0.01. (B) Western blot on total 11 protein extracts of yeast cells expressing endogenously tagged Dog1-GFP or Dog2-GFP, before and 12 after 2DG addition for the indicated time, using an anti-GFP antibody. A longer exposure is displayed 13 for Dog1-GFP cells to highlight the higher abundance of Dog1 after 2DG addition. Rsp5, whose levels 14 did not change upon 2DG addition in all of our experiments, is used as a loading control. (C) Beta- 15 galactosidase assays of wild-type yeast cells expressing LacZ under the control of the pDOG1 or pDOG2 16 promoters, before and after 2DG treatments for 3 hours (± SEM, n=3). (D) Serial dilutions of cultures 17 from the indicated strains were spotted onto SD plates containing no DG or 0.05% 2DG, and grown for 18 3 days at 30°C. (E) Western blot on total extracts of wild-type yeast cells grown overnight in SD medium 19 and treated with 0.2% 2DG or 400mM NaCl for the indicated times. The anti-phospho-p38/Hog1 20 antibody enables the detection of phosphorylated Hog1 and the anti-p38/Hog1 antibody is used as a 21 control for Hog1 abundance throughout the time course. (F) Beta-galactosidase assays of wild-type 22 and hog1∆ strains expressing LacZ under the control of the pDOG2 promoter, before and after 2DG 23 treatments for 3 hours. Error bars: SEM (n=3). (G) Western blot on total protein extracts of WT and 24 hog1∆ cells endogenously expressing a Dog2-GFP fusion, before and after 2DG addition for 3h, using 25 an anti-GFP antibody. Total proteins were visualized in gels using a trihalo compound (see Methods). 26 (H) Relative expression of Dog2-GFP in the same conditions as (G) after normalization by total proteins 27 and using WT/untreated as a reference (± SEM, n=3). 28 29 Figure 2. 2DG leads to Dog2 expression through glycosylation defects that trigger ER stress and the 30 Unfolded Protein Response. 31 (A) Cells expressing endogenously-tagged Loa1-mCherry, used as a control of ER localization (116), 32 were grown overnight in SC medium (exponential phase) and treated with 300µM 2NBDG (see 33 Methods) for the indicated times and imaged by fluorescence microscopy. Scale bar: 5 µm. (B) WT cells 34 were grown overnight to mid-log phase in SC medium, centrifuged and resuspended in SC-medium
35 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 containing mannose (2%) or not, and treated with 0.2% 2DG or 1µg/mL tunicamycin for 4 hours. Total 2 protein extracts were prepared and a western blot on was done using anti-Carboxypeptidase Y (CPY) 3 antibodies. (C) Beta-galactosidase assays on WT and hac1∆ cells expressing LacZ under the control of 4 an UPR-inducible promoter (pUPRE1) and treated with 0.2% 2DG or 1µg/mL tunicamycin for 3 hours 5 (± SEM, n=3). (D) Beta-galactosidase assays on WT cells expressing LacZ under the control of the DOG2 6 promoter and treated as in (C) (± SEM, n=3). (E) Beta-galactosidase assays on WT and hac1∆ cells 7 expressing LacZ under the control the DOG2 promoter, before and after 3h 2DG treatments (± SEM, 8 n=3). (F) Western blot on total protein extracts of WT and hac1∆ cells endogenously expressing a Dog2- 9 GFP fusion, before and after 3h treatment with 2DG or tunicamycin, using an anti-GFP antibody. (G) 10 Relative expression of Dog2-GFP in the same conditions as (F) after normalization by total proteins and 11 using WT/untreated as a reference (± SEM, n=3). (H) Serial dilutions of cultures from the indicated 12 strains were spotted onto SC plates (supplemented with 2% mannose when indicated) containing no 13 DG or 0.05% 2DG, and were grown for 3 days at 30°C. (I) Serial dilutions of cultures from the indicated 14 strains overexpressing DOG2 (pGPD-DOG2) or not (Ø) were spotted onto SC-Ura plates containing 0, 15 0.05% or 0.2% 2-deoxyglucose. The plates were scanned after 3 days of incubation at 30°C. 16 17 Figure 3. 2DG activates the MAPK-based cell-wall integrity pathway, which is required for 2DG 18 tolerance and additionally contributes to the regulation of Dog2 expression. 19 (A) A WT strain expressing an endogenously-tagged Slt2-GFP construct was grown in SC medium and 20 treated with 2DG (0.2%) or tunicamycin (1 µg/mL). Total protein extracts were prepared at the 21 indicated times and blotted with the following antibodies: anti-p44/42, to reveal activated 22 (phosphorylated) Slt2, and anti-GFP to reveal total levels of Slt2. (B) Beta-galactosidase assays on WT 23 and slt2∆ cells expressing LacZ under the control of an Rlm1-regulated promoter, before and after 3h 24 2DG (0.2%) or tunicamycin (1 µg/mL) treatments (± SEM, n=3). (C) Left, schematic of the cell wall 25 integrity pathway showing the various actors and their requirement for growth on 2DG (see color code 26 in the inset) based on drop tests showed on the right. Right: Serial dilutions of cultures from the 27 indicated deletion strains were spotted onto SD plates containing no DG or 0.05% 2DG, and grown for 28 3 days at 30°C. (D) Beta-galactosidase assays on WT and slt2∆ cells expressing LacZ under the control 29 the DOG2 promoter, before and after 3h 2DG treatments (± SEM, n=3). (E) Western blot on total 30 protein extracts of WT and slt2∆ cells expressing an endogenously tagged Dog2-GFP fusion, before and 31 after 3h treatment with 2DG, using an anti-GFP antibody. (F) Relative expression of Dog2-GFP in the 32 same conditions as (F) after normalization by total proteins and using WT/untreated as a reference (± 33 SEM, n=3). (G) Serial dilutions of cultures from the indicated strains were spotted onto SC plates 34 (supplemented with 2% mannose when indicated) containing no DG or 0.05% 2DG, and were grown 35 for 3 days at 30°C.
36 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 2 Figure 4. DOG2, but not DOG1, is controlled by glucose availability through transcriptional repression 3 by Mig1-Mig2 and the kinase Snf1. 4 (A) WT and snf1∆ strains, both expressing endogenously tagged Dog1-TAP and Dog2-GFP fusions, were 5 grown overnight in SC medium and then either treated with 0.2% 2DG or switched to an SC-lactate 6 medium for 4 hours. Dog1-TAP was detected with the peroxidase-anti-peroxidase (PAP) complex, 7 Dog2-GFP with anti-GFP antibodies. The anti-Rsp5 antibody was used to control loading. (B) Beta- 8 galactosidase activity on WT and snf1∆ cells expressing LacZ under the control the DOG1 or the DOG2 9 promoter, before and after 3h growth in lactate. The fold-induction after transfer to lactate is indicated 10 for each promoter in each strain (± SEM, n=3). (C) WT and snf1∆ strains, transformed with either a 11 genomic clone containing both DOG1 and DOG2 under the control of their own promoter (pend:DOG, 12 top panels), or with a vector containing DOG2 under the control of the strong GPD promoter 13 (pGPD:DOG2, bottom panels) were grown, serial-diluted and spotted onto SC plates (SC-Leu, top 14 plates, and SC-Ura, bottom plates) with or without 0.2% DG, and grown for 3 days at 30°C. (D) Beta- 15 galactosidase assays on WT and the indicated deletion mutants expressing LacZ under the control the 16 DOG2 promoter after overnight growth in SC medium (exponential phase) (± SEM, n=3). (E) The 17 indicated strains, all expressing an endogenously tagged Dog2-GFP fusion, were grown overnight in SC 18 medium (exponential phase). Total protein extracts were prepared and blotted with anti-GFP 19 antibodies and the anti-Rsp5 antibody was used as a loading control. (F) Serial dilutions of cultures of 20 the indicated mutants were spotted on YPD plates containing 0, 0.2% or 0.5% of 2DG. Plates were 21 scanned after 3 days of growth at 30°C. 22 23 Figure 5. Most clones that become spontaneously resistant to 2DG show an increased Dog2 24 expression. 25 (A) 24 clones showing a spontaneous resistance to 0.2% 2DG were isolated. The beta-galactosidase 26 activity of these mutants, due to the expression of the LacZ reporter driven by the DOG2 promoter, 27 was measured after overnight growth in SC medium (exponential phase) (± SEM, n=3). For colors, see 28 panels (B) and (D). (B) Serial dilutions of cultures from the indicated deletion strains and resistant 29 clones were spotted onto SC plates containing no DG or 0.2% 2DG, as well as 200 µM selenite or 0.5 30 µg/mL tunicamycin and grown for 3 days at 30°C. Note that clone #6 grows very slowly even in absence 31 of 2DG. Orange squares: identified reg1 mutants. (C). A WT strain and the 24 resistant clones were 32 grown in SC medium (exponential phase). Total protein extracts were prepared and blotted using 33 antibodies allowing to reveal phosphorylated (activated) Snf1 (anti-phospho-AMPK) or total Snf1 (anti- 34 polyHis tag, because Snf1 contains a stretch of 13 histidine residues that can be used for its detection) 35 (117). The numbers below indicate the ratio of phospho-Snf1 signal over Snf1 signal, relative to the
37 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 WT. (D) Schematic of the identified mutations within the REG1 ORF in the indicated mutants as 2 obtained by sequencing. (E) The 24 resistant clones were crossed with a WT or an hxk2∆ strain of the 3 opposite mating type, and cultures of the haploid resistant clones (see matrix, left) or the resulting 4 diploids were spotted onto SC medium with or without 0.2% DG. Green squares: identified hxk2 5 mutants. 6 7 Figure 6. The 2DG-resistant phenotype of mutants #9 and #10 is caused by a mutation in CYC8. 8 (A) Schematic of the domain organization of the Cyc8 protein, showing the Poly(Q) and Poly(QA) 9 repeats as well as the N-terminal TPR repeats. Red: mutation identified by whole genome 10 resequencing of the spontaneous 2DG-resistant mutants #9 and #10. (B) A WT strain, the mutant 11 strains #9 and #10 and the reg1∆ mutant (positive control) were grown in SC medium (exponential 12 phase). Total protein extracts were prepared and blotted using anti-invertase antibodies (invertase is 13 heavily glycosylated and migrates as a smear (118)). (C) WT and mutants #9 and #10 were transformed 14 with low-copy (centromeric) plasmid either empty or containing WT CYC8 or mutant cyc8 (Q320*), and 15 were spotted on SC-Leu or SC-Leu + 0.2% 2DG medium, and grown for 3 days at 30°C. Middle panel: 16 the control plate was scanned and then washed for 1 min under a constant flow of water, and then 17 scanned again (see Methods). (D) Beta-galactosidase activity on WT and mutants #9 and #10 18 expressing LacZ under the control the DOG2 promoter and transformed with an empty vector or a low- 19 copy vector containing WT CYC8, after growth in SC medium (normalized to the value of the WT, ± 20 SEM, n=3). (E) Western blot on total protein extracts of WT and mutants #9 and #10 cells expressing 21 an endogenously tagged Dog2-GFP fusion and transformed with either an empty plasmid or a low- 22 copy (centromeric) plasmid containing WT CYC8 after growth in SC medium, using an anti-GFP 23 antibody. (F) Relative expression of Dog2-GFP in the same conditions as (G) after normalization by total 24 proteins and using the WT control as a reference (± SEM, n=3). 25 26 Figure 7. The human phosphatase HDHD1 partially rescues the hypersensitivity of a dog1∆ dog2∆ 27 mutant to 2DG. 28 (A) Multiple protein sequence alignment of yeast Dog1, Dog2, Escherichia coli yniC and the human 29 proteins HDHD1, HDHD4 and PSPH aligned with ClustalX 2.0. The highly conserved catalytic aspartates 30 are displayed in yellow. The six first amino-acids of PSPH were truncated to optimize the N-terminal 31 alignment of its catalytic aspartates with the other phosphatases. (B) Serial dilutions of WT and 32 dog1∆dog2∆ strains transformed with the indicated plasmids were spotted on SC-Ura medium with or 33 without 0.05% 2DG and were scanned after 3 days of growth at 30°C. (C) Serial dilutions of 34 dog1∆dog2∆ strains transformed with the indicated plasmids were spotted on SC-Ura medium with or 35 without 0.05% 2DG and were scanned after 3 days of growth at 30°C. (D) Total proteins extracts of
38 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 dog1∆dog2∆ cells transformed with an empty vector or a vector allowing the overexpression of HDHD4 2 were blotted with an anti-HDHD4 antibody. (E) Serial dilutions of dog1∆dog2∆ strains transformed 3 with an empty vector or the indicated vectors allowing the expression of the indicated HDHD1 isoforms 4 were spotted on SC-Ura medium with or without 0.05% 2DG and were scanned after 3 days of growth 5 at 30°C. (F) Total protein extracts were prepared from the same strains as in (E), and a western blot 6 was revealed with an anti-HDHD1 antibody. The anti-Pgk1 antibody (phosphoglycerate kinase) was 7 used as a loading control. 8 9 Figure 8. HDHD1 has a 2DG6P phosphatase activity and its overexpression leads to 2DG resistance 10 in HeLa cells. 11 (A) Serial dilutions of dog1∆dog2∆ strains transformed with an empty vector or vectors allowing the 12 expression of a HDHD1 or its predicted catalytic mutant, HDHD1-DD>AA (mutations of the N-terminal 13 catalytic aspartates to alanines) were spotted on SC-Ura medium with or without 0.05% 2DG and were 14 scanned after 3 days of growth at 30°C. (B) Total protein extracts were prepared from the same strains 15 as in (A), and a western blot was revealed with an anti-HDHD1 antibody. The anti-Pgk1 antibody 16 (phosphoglycerate kinase) was used as a loading control. (C) Recombinant, His-tagged HDHD1 and 17 HDHD1-DD>AA were expressed in bacteria and purified for in vitro enzymatic tests. 0.7 µg were loaded 18 on a gel to show homogeneity of the protein purification. (D) In vitro 2DG6P phosphatase activity of 19 HDHD1 and HDHD1>DDAA as measured by assaying glucose release from 2DG6P. (E) Growth of HeLa 20 cells transfected with an empty vector (□) or with a construct allowing the overexpression of HDHD1 21 (○) over time in the absence (open symbols) or presence (filled symbol) of 5 mM 2DG. The number of 22 cells is normalized to that of the untransformed/untreated cells after 3 days (± SEM, n=3). (F) Total 23 protein extracts of HeLa cells either untreated (Ø) or treated with 2DG (5 mM) or tunicamycin (5 24 µg/mL) where blotted with anti-HDHD1 antibodies. Cells transfected with HDHD1 were used as a 25 positive control. The effect of 2DG and Tm on the glycosylation profile of CD147 was used as a control 26 of the efficiency of the treatments. 27 28 Figure 9. Working Model. 29 Glucose phosphorylation triggers the onset of the glucose-repression pathway, by which PP1 30 inactivates Snf1/AMPK. This leads to the lack of phosphorylation of Mig1/Mig2, which remain in the 31 nucleus to mediate the glucose-repression of genes such as DOG2. The deletion of REG1, HXK2, or 32 MIG1 and MIG2, or a mutation in CYC8 leads to 2DG resistance, at least in part through an increased 33 expression of DOG2 which dephosphorylates 2DG-6-P. Instead, the deletion of SNF1 causes an 34 increased sensitivity to 2DG, which can be rescued by the deletion of MIG1 and MIG2 or by Dog2 35 overexpression. In parallel, 2DG6P causes (i) ER stress and triggers the UPR pathway, which stimulates
39 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
1 DOG2 expression through the transcription factor Hac1, and (ii) the CWI integrity pathway, likely 2 through interference with polysaccharide and cell wall synthesis, which also induces DOG2 through 3 the transcription factor Rlm1. 4
40 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Supplemental material Table S1. Proteomic response to 2DG treatment. See Excel spreadsheet.
Table S2. Single nucleotide variants in clones #9 and #10 as compared to the WT strain, as identified by analysis of whole genome resequencing Mutation in Clone Chrom. Position Reference Mutation Gene coding region CYC8 c.958C>T #9: chrII 464813 G A (YBR112C) (p.Gln320X) BET3 c.357G>C chrXI 570553 C G (YKR068C) (p.Leu119Phe) c.3204C>G chrXII 969100 C G YLR422W (p.Tyr1068X) CYC8 c.958C>T #10 chrII 464813 G A (YBR112C) (p.Gln320X) Intergenic region GET3-BUG1 chrIV 283345 T A (YDL100C-YDL099W) TRA1 c.952T>C chrVIII 303712 T C (YHR099W) (p.Leu318Leu) PAN1 c.1631C>G chrIX 368278 G C (YIR006C) (p.Thr544Ser) BET3 c.357G>C chrXI 570553 C G (YKR068C) (p.Leu119Phe) DGR1 c.126T>G chrXIV 381266 A C (YNL130C-A) (p.Cys42Trp) c.2738C>T chrXV 499715 G A YOR093C (p.Ser913Leu)
Table S3. Yeast strains used in this study. Name/description Genotype Origin/reference Figures/Panels BY4741 (WT) MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (119) All ySL2289 Dog1-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 1B DOG1::GFP-HIS3MX6 ySL2290 Dog2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) 1B, 1G, 1H, 4E DOG2::GFP-HIS3MX6 ySL2195 dog1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 1D dog1∆::KanMX collection ySL2196 dog2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 1D, 2I dog2∆::KanMX collection ySL2197 dog1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 1D, 7B-F, 8A-B dog2∆ dog1∆-dog2∆::LEU2MX ySL2339 Tdh1-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) S1 TDH1::GFP-HIS3MX6 ySL2340 Stf2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) S1 STF2::GFP-HIS3MX6
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ySL2341 Eno1-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) S1 ENO1::GFP-HIS3MX6 ySL2342 Adh5-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) S1 ADH5::GFP-HIS3MX6 ySL2343 Yro2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) S1 YRO2::GFP-HIS3MX6 ySL2344 Hor7-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) S1 HOR7::GFP-HIS3MX6 ySL2315 hog1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 1F, S2 hog1∆::KanMX collection ySL2416 hog1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 1G, 1H Dog2-GFP hog1∆::KanMX DOG2::GFP-HIS3MX6 ySL0052 Loa1- MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (116) 2A mCherry LOA1::mCherry-KanMX ySL2204 hac1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 2C, 2E-I, 3G, hac1∆::KanMX S3B ySL2205 ire1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 2H, 2I ire1∆::KanMX collection ySL0567 snf1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 2H, 4B-D snf1∆::KanMX collection ySL488 Slt2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 (104) 3A SLT2::GFP-HIS3MX6 ySL1961 slt2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3B-G, S4 slt2∆::KanMX collection ySL557 wsc1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C wsc1∆::KanMX collection ySL2380 wsc2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C wsc2∆::KanMX collection ySL2379 wsc3∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C wsc3∆::KanMX collection ySL2386 mtl1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C mtl1∆::KanMX collection ySL2387 mid2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C mid2∆::KanMX collection ySL481 ack1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C ack1∆::KanMX collection ySL2384 rom1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C rom1∆::KanMX collection ySL590 rom2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C rom2∆::KanMX collection ySL2385 tus1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C tus1∆::KanMX collection ySL2405 bck1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C, 3G bck1∆::KanMX collection ySL2382 mkk1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C mkk1∆::KanMX collection ySL2383 mkk2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C mkk2∆::KanMX collection ySL2381 rlm1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 3C rlm1∆::KanMX collection
42 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
ySL2297 Dog1-TAP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4A Dog2-GFP DOG1::TAP-KanMX, DOG2::GFP- HIS3MX6 ySL2298 Dog1-TAP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4A Dog2-GFP snf1∆ DOG1::TAP-KanMX, DOG2::GFP- HIS3MX6, snf1∆::hphNT1 ySL2292 Dog2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4E mig1∆ DOG2::GFP-HIS3MX6, mig1∆::KanMX ySL2293 Dog2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4E mig2∆ DOG2::GFP-HIS3MX6, mig2∆::KanMX ySL2294 Dog2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4E mig1∆ mig2∆ DOG2::GFP-HIS3MX6, mig1∆::LEU2MX, mig2∆::KanMX ySL2295 Dog2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4E hxk2∆ DOG2::GFP-HIS3MX6, hxk2∆::KanMX ySL2291 Dog2-GFP MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4E reg1∆ DOG2::GFP-HIS3MX6, reg1∆::LEU2MX ySL2192 mig1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 4D mig1∆::KanMX collection ySL2193 mig2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 4D mig2∆::KanMX collection ySL2194 mig1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4D, 4F mig2∆ mig1∆::KanMX, mig2∆::HIS3MX6 ySL2200 hxk2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 Euroscarf deletion 4D, 4F, 5B hxk2∆::KanMX collection ySL2447 hxk2∆ MATalpha, ura3Δ0, his3Δ1, leu2Δ0, Euroscarf deletion 5E met15Δ0 hxk2∆::KanMX collection ySL2199 reg1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4D, 4F, 5B, 6B, reg1∆::HIS3MX6 6G, 6H ySL2201 reg1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4F dog1∆ dog2∆ reg1∆::HIS3MX6, dog1∆-dog2∆::LEU2MX ySL2202 hxk2∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4F dog1∆ dog2∆ hxk2∆::KanMX, dog1∆-dog2∆::LEU2MX ySL2203 mig1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4F mig2∆ dog1∆ dog2∆ mig1∆::KanMX, mig2∆::HIS3MX6, dog1∆-dog2∆::LEU2MX ySL2317 mig1∆ MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0 This study 4F mig2∆ snf1∆ mig1∆::KanMX, mig2∆::HIS3MX6, snf1∆::NatMX ySL2474 mut. #9 Spontaneous mutant arising from This study 5A-C, 6D-G BY4741 strain (MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0) selected on 0.2% 2DG ySL2475 mut. #10 Spontaneous mutant arising from This study 5A-C, 6D-G BY4741 strain (MATa, ura3Δ0, his3Δ1, leu2Δ0, met15Δ0) selected on 0.2% 2DG ySL2476 mut. #9- ySL2474 DOG2::GFP- HIS3MX6 This study 6F-G Dog2-GFP ySL2477 mut. #10- ySL2475 DOG2::GFP- HIS3MX6 This study 6F-G Dog2-GFP
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Table S4. Plasmids used in this study. Name Description Origin/reference pGP564: empty vector control for genomic tiling pSL209 (120) collection, 2µ, LEU2 pSL409 pDOG1(1000bp):lacZ, 2μ, URA3 (Yep58-based) This study pSL410 pDOG2(1000bp):lacZ, 2μ, URA3 (Yep58-based) This study pSL405 pUPRE1:lacZ, 2μ, URA3 (pGA1695-based) P. Walter’s lab, pJC5 (53) pSL385 pCYC(2xRlm1):lacZ , 2µ, URA3 (pLG∆-312-based) D. Levin’s lab, p1434 (121) pSL412 pGPD:DOG2, 2µ, URA3 (pRS426-based) This study pGP564-based genomic clone YGPM10o10 pSL425 containing DOG1 and DOG2; 2µ, LEU2 (genomic (120) tiling collection - chr.VIII:188052-198738) pSL438 pDOG2(150bp):lacZ, 2μ, URA3 (Yep58-based) This study pSL439 pDOG2(250bp):lacZ, 2μ, URA3 (Yep58-based) This study pSL440 pDOG2(350bp):lacZ, 2μ, URA3 (Yep58-based) This study pSL441 pDOG2(500bp):lacZ, 2μ, URA3 (Yep58-based) This study pSL411 pGPD:DOG1, 2µ, URA3 (pRS426-based) This study pSL413 pGPD:yniC, 2µ, URA3 (pRS426-based) This study pSL414 pGPD:HDHD1-isoform 1, 2µ, URA3 (pRS426-based) This study ySL2312 pGPD:HDHD1-isoform 2, 2µ, URA3 (pRS426-based) This study ySL2313 pGPD:HDHD1-isoform 3, 2µ, URA3 (pRS426-based) This study ySL2314 pGPD:HDHD1-isoform 4, 2µ, URA3 (pRS426-based) This study ySL2337 pGPD:HDHD4, 2µ, URA3 (pRS426-based) This study ySL2336 pGPD:PSPH, 2µ, URA3 (pRS426-based) This study pGPD:HDHD1-isoform 1-DD>AA, 2µ, URA3 (pRS426- ySL2335 This study based) pSL422 pCMV-SPORT6-HDHD1 Dharmacon pSL458 pCS2 (empty vector - expression in mammalian cells) (CloneId:4478358)(122) pSL431 pET15b-6His-HDHD1 E. van Schaftigen (79) pSL459 pET15b-6His-HDHD1(DD>AA) (79)This study pGP564-based genomic clone YGPM24j02 pSL460 containing HXK2; 2µ, LEU2 (genomic tiling collection (120) - chr.VII: 23019-35747) pGP564-based genomic clone YGPM2h11 containing pSL465 CYC8; 2µ, LEU2 (genomic tiling collection - chr. II: (120) 458726-473023) pSL466 CYC8 (-1000/+300) ; CEN, LEU2 (pRS415-based) This study cyc8(C958>T) (-1000/+300) ; CEN, LEU2 (pRS415- pSL467 This study based)
Table S5. Antibodies used in this study. Name Description Dilution Reference/Origin Mouse monoclonal against GFP, clones 7.1 11814460001 - α GFP 1/5000 and 13.1 Roche α Rsp5/Nedd4 Rabbit polyclonal antibody against Nedd4 1/5000 ab14592 - Abcam Mouse monoclonal against Tyr182- sc166182 - Santa α ℗p38/℗Hog1 1/1000 phosphorylated p38 (E-1) Cruz
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sc165978 - Santa α p38/Hog1 Mouse monoclonal against human p38 (D-3) 1/1000 Cruz Rabbit polyclonal against Carboxypeptidase α CPY 1/2000 ab34636 - Abcam Y (PRC1) P1291 - Sigma PAP Peroxidase-anti-Peroxidase complex 1/5000 Aldrich Rabbit polyclonal against Thr172- #2535 - Cell α ℗AMPK/℗Snf1 1/1000 phosphorylated human AMPKα Signaling Mouse monoclonal antibody used to reveal α-polyHis tag endogenous Snf1 which contains a stretch of 1/2000 # H1029 - Sigma 13 His residues Rabbit polyclonal against human HDHD1. To α HDHD1 visualize HDHD1 in lysates of yeast or 1/2000 SAB2700505 - Sigma bacteria overexpressing HDHD1. Mouse monoclonal against human HDHD1A NBP2-00487 - Bio- α HDHD1 (7A2). To visualize HDHD1 in HeLa cell 1/1000 Techne extracts (Panel 7F). Mouse monoclonal anti-HDHD4 (NANP) sc-374637 - Santa α HDHD4 Antibody (D8). To visualize HDHD4 in lysates 1/5000 Cruz of yeast overexpressing HDHD4. 555961–BD α-CD147 Mouse monoclonal anti-CD147 (Clone HIM6) 1/5000 Bioscience Rabbit polyclonal against yeast 3- NE130/7S Nordic α-PGK 1/10000 phosphoglycerate kinase MUBio α -Suc2 (invertase) Rabbit polyclonal against invertase 1/5000 C. Stirling A6154 - Sigma α Rabbit IgG Goat secondary antibody against Rabbit IgG 1/5000 Aldrich A5278 - Sigma α Mouse IgG Goat secondary antibody against Mouse IgG 1/5000 Aldrich
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1 Supplemental figure legend. 2 3 Figure S1. Characterization of other candidates upregulated by 2DG treatment. 4 (A). Western blot on total protein extracts of yeast cells expressing the endogenously GFP-tagged 5 proteins indicated, before and after 2.5h 2DG addition, using an anti-GFP antibody. The anti-Rsp5 6 antibody is used as a loading control. (B) Gene Ontology (GO) analysis of the proteins identified as 7 upregulated in response to 2DG treatment along with their p-value and the proteins included in each 8 category. 9 10 Figure S2. DOG1 expression is not regulated by Hog1. 11 Beta-galactosidase assays of wild-type and hog1∆ strains expressing LacZ under the control of the 12 pDOG1 promoter, before and after 2DG treatments for 3 hours. Error bars: SEM (n=3). 13 14 Figure S3. DOG1 expression is regulated by the UPR pathway. 15 (A). Beta-galactosidase assays on WT cells expressing LacZ under the control of the DOG1 promoter 16 and treated with 0.2% 2DG or 1µg/mL tunicamycin for 3 hours (± SEM, n=3). (B). Beta-galactosidase 17 assays on WT and hac1∆ cells expressing LacZ under the control the DOG1 promoter, before and after 18 3h 2DG treatments (± SEM, n=3). 19 20 Figure S4. Slt2 participates in the regulation of DOG1 expression. 21 Beta-galactosidase assays on WT and slt2∆ cells expressing LacZ under the control the DOG1 promoter, 22 before and after 3h 2DG treatments (± SEM, n=3). 23 24 Figure S5. Cis-regions involved in the regulation of the DOG2 promoter by glucose 25 (A). Schematic showing the various constructs generated to study DOG2 promoter regulation by 26 glucose availability. (B). Beta-galactosidase assays on WT cells expressing LacZ under the control of the 27 indicated truncated version of the DOG2 promoter after overnight growth in glucose medium (± SEM, 28 n=3). 29 30 Figure S6. Multiple protein sequence alignment of Hxk2 orthologues and positions of the mutations 31 identified. 32 (A). Growth test showing that the 2DG sensitivity of the 2DG-resistant clones #1 and #8 can be restored 33 by expression of a multicopy, genomic clone containing HXK2. Clone #2 (which displays a mutation in 34 HXK2, see Fig 5) is used as a positive control. (B). List of Hxk2 homologues used for the alignment, as 35 identified using HomoloGene entry #100530 (NCBI). (C). The sequences (numbers refer to their GI
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1 numbers) were aligned using ClustalX 2.1 (123) and formatted using BoxShade server (v.3.21). After 2 the alignment, some sequences were truncated in Nt as indicated. The sequence in bold corresponds 3 to that of S. cerevisiae Hxk2.
47 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which A was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Tdh1 6
Ydl124w 5 Pgm2 Hsp26 Eno1 Glk1 Rav1 Adh4 Pnc1 Stf2 4 Sse2 Spc2 Yer134c Rpl34A/B Pho84 Ypr127w Ssa4 Aps3 Hxt2 Gpd1 Ysc84 Sds24 Yro2 Nqm1 Emi2 Met3 Ypr114w Ubc4/5 Sol4Ccw12/22 Rtn2 Hor7 Hsp12 Ygp1 Rrt14 Bud20 Ero1 Fms1Ser3 Yjr085c Tim9 3 Ade8 Tip1 Tdh2 Tma10 Nyv1 Adh5
10 Yhr112c Acp1 Yil002w-a Ycl019c Yhr214c-b Rrp17 Om45Sol1 Ego4 Ybr085c-a Ost3Arf2 Tat1 Ppz1 Ymr090w -log (p-value) Snu114 Fol1 Dcs2 Puf2 Sip5 Tma7 Gad1 Yra2 Gpg1 Nop15 2 Avt1 Rtc3 Hbt1 Sum1 Nce103 Cue4 Zim17 Inm1 Ydl086w Cwp2 Hfd1 Urh1 Msc1 Ydr391c Glo1 Uga2 Ura8 Pbi2 Tda10 1 Ybr053c Tma17 Rpp1B Pho86 Dog1/2
0 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 log (LFQ 2-DG / LFQ Control) 2
B Dog1-GFP Dog2-GFP C 20 Glc 2-DG 2-DG Glc 2-DG 2-DG -2DG O/N 2.5h 5h O/N 2.5h 5h 15 +2DG
α-GFP - 55 kDa 10
long exp. - 55 kDa (A.U.) 5
α-Rsp5 - 100 kDa 0 β-Galactosidase activity pDOG1:LacZ pDOG2:LacZ
Control 0.05% 2-DG 2DG 0.2% D E Glc O/N 15’ 30’ 45’ 1h 2h 3h 4h 6h WT α-Hog1Ⓟ dog1∆
dog2∆ α-Hog1 dog1∆ dog2∆ NaCl 400mM Glc O/N 15’ 30’ 45’ 1h 2h 3h 4h 6h F 25 α-Hog1Ⓟ ** WT 20 α-Hog1 hog1∆
15 Dog2-GFP G 5 H n WT hog1∆ Glc 10 NS 4 (A.U.) Glc 2DG, Glc 2DG, 2DG 3h 3h 3 inductio
5 P α-GFP 2
β-Galactosidase activity 0 Total 1
- 2DG + 2DG prot. Dog2-GF 0 WT hog1 pDOG2:LacZ Figure 1; Defenouillère, Verraes et al. bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peerVps66 review) is the author/funder. All rights reserved. No reuse allowed without permission. A 2-NBDG mCherry Merge Trans B Control +Mannose Glc 2DG Tm 2DG Tm
O/N 4h 4h 4h 4h
Mock } Glycosylated α- P Glycosylation defects Total 2-NBDG prot. 300µM 2h D 10 Glc 2-NBDG 300µM 8 2DG 5h Tm 6
C (A.U.) 150 4 Glc 2 2DG
Tm β-Galactosidase activity 100 0 pDOG2-LacZ
(A.U.) 8 50 E WT * h 1∆ 6
β-Galactosidase activity 0 pUPRE1-LacZ pUPRE1-LacZ WT h 1∆ 4
(A.U.) NS F Dog2-GFP WT h 1∆ 2 Glc 2DG Tm Glc 2DG Tm O/N 3h 3h O/N 3h 3h β-Galactosidase activity 0 α-GFP -2DG +2DG Total pDOG2-LacZ prot. H Control 0.05% 2-DG G WT 30 1∆ Glc h 1∆ n 2DG 20 Tm 1∆ Mannose
inductio Mannose + 0.05% 2-DG P
10 WT
1∆ Dog2-GF
0 h 1∆ WT h 1∆ 1∆ I Control 0.05% 2-DG 0.2% 2-DG
Ø WT
WT
dog2∆ +pGPD- DOG2 h 1∆
1∆ Figure 2; Defenouillère, Verraes et al. bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
A. Slt2-GFP B. 4 Glc + 2-DG 0.2% + Tm 1µg/mL 2DG 3h t0 15’ 30’ 45’ 60’ 120’ 15’ 30’ 45’ 60’ 120’ MW 3 Tm 3h lt α- -100 2 Slt2 α-GFP -100 Total 1 proteins β-Galactosidase activity 0 C. Control 0.05% 2DG WT 2∆ Rlm1-regulated reporter:LacZ WT
Mtl1 Wsc1 Wsc2 Wsc3 Mid2 : Sensors 1∆ D. 25 Plasma 2∆ WT * membrane 20 ∆ slt2∆ Rho1 Rom1 Rom2 Tus1 15 GEFs 1∆ Ack1 2DG sensitivity: d2∆ 10 Rho1 sensitive partially 5 NS insensitive 1∆
Pkc1 not tested β-Galactosidase activity 1∆ 0 -2DG +2DG Bck1 MAPKKK o 1∆ pDOG2:LacZ
o 2∆ Mkk1 Mkk2 MAPKK Dog2-GFP 1∆ E. Slt2 MAPK WT 2∆ 1∆ Glc 2DG, Glc 2DG, 3h 3h Rlm1 Swi4 2∆ Swi6 α-GFP 2∆ Total 1∆ prot.
WT F. 8 Mannose Glc Control 0.05% 2-DG Mannose + 0.05% 2-DG n G. 6 2DG WT 4 inductio h 1∆ P
2 1∆
Dog2-GF 0 2∆ WT 2∆ Figure 3; Defenouillère, Verraes et al. bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
A WT 1∆ B 20 WT snf1∆ Glc 2-DG Lac Glc 2-DG Lac
m 15 O/N 4h 4h O/N 4h 4h diu 55 kDa - -Gal activity
Dog1-TAP β
PAP me 10 70 kDa - Dog2-GFP anti-GFP actate 5 anti-Rsp5 Rsp5 in l 100 kDa -
Fold-induction of 0 C Control 0.2% 2DG pDOG1:LacZ p 2:LacZ D empty vector T
WT
p d:DOG ty i 10 v i empty vector act 1∆
p d:DOG ase id s
o 5 empty vector act l
WT a 2 G β-
empty vector in glucose medium, rel. to W 0 1∆ WT 1∆ g1∆ g2∆ g1∆ h 2∆ g1∆ g2∆ 2 F Control 0.2% 2DG E WT Dog2-GFP g1∆ g1∆ WT g1∆ g2∆ g2∆ h 2∆ g1∆ 70 kDa - g1∆dog1∆dog2∆ anti-GFP h 2∆ anti-Rsp5 100 kDa - h 2∆dog1∆dog2∆
g1∆ g2∆
g1∆ g2∆dog1∆dog2∆
g1∆ g2∆ 1∆ Figure 4; Defenouillère, Verraes et al. bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
A C Clones: 1 2 3 4 5 6 7 8 9 10 WT n 40 *** α- P n 30 * *** * α- is y ** * Ratio: 1.8 2.1 2.3 5.0 1.0 2.4 5.0 1.4 0.4 0.4 1.0 ** Total 20 * * * * prot. * * - ac activit 10 Clones: 11 12 13 14 15 16 17 18 19 20 WT 21 22 23 24 WT n α- P DOG2
p 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 WT n Resistant clones α- is Ratio: 0.9 1.6 1.2 1.4 1.4 1.5 0.9 0.9 5.8 2.0 1.0 1.6 1.0 2.7 1.2 1.0 +0.2% +Selenite +Tunicamycin B Control Total 2DG 200 µM 0.5 µg/mL prot. WT g1∆ D Glc7 binding 1 464 F 468 3045 WT h 2∆ REG1 #4 Isolated resistant clones: T 1020 > G (Y 340 > TAG) #1 #7 G 1213 > T (E 405 > TAA) #2 #19 C 1435 > T (R 479 > TGA) #3 E #4 Control +2DG #5 Resistant Diploids Diploids Diploids Diploids clones #: a loids (... x hxk2 a loids (... x hxk2 #6 #1 #9 #17 #7 #2 #10 #18 #8 #3 #11 #19 #9 #10 #4 #12 #20 #11 #5 #13 #21
#12 #6 #14 #22
#13 #7 #15 #23 #14 #8 #16 #24 #15 #16 F 1 1461 #17 WT HXK2 #18 #2 #14 634 212 897 299 #19 A > C (T > P) A > C (Q > H) #3 #15 751 251 #20 A527 > C (K 176 > T) C > T (Q > TAA) #11 #16 #21 A897 > C (Q 299 > H) T 929 > A (L310 > TAA) #12 #20 #22 C 751 > T (Q 251 > TAA) T 11 > A (L 4 > TAA) #13 #21 #23 1252 418 G > T (G > C) C 224 > T (T 75 > I) T 1033 > C (S 345 > P) #24
Fi u e e enouill e e aes et al Poly Poly Poly A TPR repeats (Q) (QA) (Q) 1 1 2 3 4 5 6 7 8 9 10 46 398 493 556 587 Q320* Control Control B WT #9 #10 g1∆ MW C Before wash After wash + 2DG 0.2% (kD) Suc2 —130 WT (invertase) + empty mut #9 Total proteins mut #10 The copyright holder for this preprint (which preprint this for holder copyright The D WT Ø + CYC8 mut #9 10 CYC8 mut #10
WT -LacZ 5 + cyc8- mut #9
DOG2 Q320* p this version posted December 21, 2018. 2018. 21, December posted version this ; mut #10
β-Gal activity no ali ed β-Gal activity 0 WT #9 #10 F 8 E Dog2-GFP 6 WT #9 #10 #9 #10 MW CYC8: - - - + + (kD) expression https://doi.org/10.1101/504134
P 4
doi: doi: α-GFP
was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. permission. without allowed reuse No reserved. All rights author/funder. is the review) peer by certified not was —55 Total 2 Dog2-GF prot. 0 bioRxiv preprint preprint bioRxiv WT #9+ #10+ #9+ #10+ Ø Ø CYC8 CYC8 Figure 6; Defenouillère, Verraes et al. bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
A Dog1 1 --MAEFSADLCLFDLDGTIVSTTVAAEKAWTKLCYEYGVD--PSELFKHSHGARTQEVLRRFFP------KLDDTDNKG-VLALEKDIAHSYL Dog2 1 --MPQFSVDLCLFDLDGTIVSTTTAAESAWKKLCRQHGVD--PVELFKHSHGARSQEMMKKFFP------KLDNTDNKG-VLALEKDMADNYL HDHD1 1 MAAPPQPVTHLIFDMDGLLLDTERLYSVVFQEICNRYDKKY-SWDVKSLVMGKKALEAAQIIID------VLQLPMSKEELVEESQTKLKEVF yniC 1 -MSTPRQILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWYARQ-----PWNGPSRQEVVERVIARAISLVE HDHD4 1 --MGLSRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYNTCITDLRTSHWEEAIQETKGGAANRKL PSPH 7 LRKLFYSADAVCFDVDSTVIREE-----GIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTER------LALIQPSREQVQRLIAEQPPHLTP
Dog1 83 DTVSLIPGAENLLLSLDVDTETQKKLPERKWAI---VTSGSPYLAFSWFETILKNVGKPKVFITGFDVKNGKPDPEGYSRARDLLRQDLQLTGK Dog2 83 DTVSLIPGAENLLLSLDVDTETQKKLPERKWAI---VTSGSPYLAFSWFETILKNVGKPKVFITGFDVKNGKPDPEGYSRARDLLRQDLQLTGK HDHD1 87 PTAALMPGAEKLIIHLR-----KHGIPFALATS---SRSASFDMKTSRHKEFFS-LFSHIVLGDDPEVQHGKPDPDIFLACAKRFSPPPAME-- yniC 89 ETRPLLPGVREAVALCK------EQGLLVG---LASASPLHMLEKVLTMFDLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVD------HDHD4 93 AEECYFLWKSTRLQHMTLAEDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPG---- PSPH 90 GIRELVSRLQERNVQVFLISGGFRSIVEHVASK---LNIPATNVFANRLKFYFN--GEYAGFDETQPTAESGGKGKVIKLLKEKFHFK------
Dog1 174 QDLKYVVFEDAPVG-IKAGKAMGAITVGITSSYDKSVLFDAGADYVVCDLTQVSVVKNNENGIVIQVNNPLTRA---- Dog2 174 QDLKYVVFEDAPVG-IKAGKAMGAITVGITSSYDKSVLFDAGADYVVCDLTQVSVVKNNENGIVIQVNNPLTRD---- HDHD1 170 ---KCLVFEDAPNG-VEAALAAGMQVVMVPD------GNLSRDLTTKATLVLNSLQDFQPELFGLPSYE---- yniC 165 -PLTCVALEDSVNG-MIASKAARMRSIVVPAP------EAQNDPRFVLADVKLSSLTELTAKDLLG------HDHD4 183 ---DCVMVGDTLETDIQGGLNAGLKATVWINK------NGIVPLKSSPVPHYMVSSVLELPALLQSIDCKVSMST PSPH 173 ---KIIMIGDGATD-MEACPPADAFIGFGGN------VIRQQVKDNAKWYITDFVELLGELEE------
B Control + 0.05% 2-DG C Control + 0.05% 2-DG WT dog1∆dog2∆ empty vector +empty vector empty vector +pGPD-HDHD1 +pGPD-HDHD1 +pGPD-HDHD4 +pGPD-DOG1 +pGPD-PSPH + 2 dog1∆dog2∆ +pGPD-yniC D dog1∆dog2∆ + Ø pGPD- MW HDHD4 - 35 E α- Control + 0.05% 2-DG - 25 Total dog1∆dog2∆ prot. +empty vector dog1∆dog2∆ +pGPD-HDHD1-1 F +pGPD-HDHD1 isoforms Empty MW +pGPD-HDHD1-2 vector #1 #2 #3 #4 - 25 +pGPD-HDHD1-3 α-
+pGPD-HDHD1-4 α-P - 55 Fi u e e enouill e e aes et al bioRxiv preprint doi: https://doi.org/10.1101/504134Control; this version posted December+ 21, 0.05% 2018. The copyright2-DG holder for this preprint (which A dog1∆dog2∆ was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. +empty vector
+pGPD-HDHD1
+pGPD-HDHD1 D>A
B D 0.15 dog1∆dog2∆ +pGPD-HDHD1 n-1 0.10 WT MW D>A hydrolyzed α- P - 25 0.05
α-P - 55 mg-1 prot.mi
µmol 2DG6 0.00 HDHD1 HDHD1-D>A C HDHD1 HDHD1 MW D>A E 1.5 pCS2 - 2DG 100- pCS2 + 5 mM 2DG - HDHD1 - 2DG
h 1.0 55- HDHD1 + 5 mM 2DG
35- 0.5 Cell growt 25- el to unt eated
15- 0.0 0 1 2 3
F HeLa Treatment: - 2DG Tm -
Vector: Ø Ø Ø HDHD1 MW α- - 25
- FG - 55 α- CG - 35
NG - 25 Figure 8; Defenouillère, Verraes et al. 2DG Glc Cell wall stress Cell wall Plasma Mb
Cell wall synthesis defects Hxk2 Glc CWI 2DG6P 2DG Hxk2 pathway Glycosylation defects Dog2 The copyright holder for this preprint (which preprint this for holder copyright The Glc6P PP1 (Glc7Reg1) ER stress Slt2 Ire1 Snf1 (AMPK) UPR pathway this version posted December 21, 2018. 2018. 21, December posted version this ;
Cyc8 Tup1? Mig1 Rlm1 Hac1 DOG2 Mig2
https://doi.org/10.1101/504134 Mutant is …
doi: doi: … 2DG resistant was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. permission. without allowed reuse No reserved. All rights author/funder. is the review) peer by certified not was … 2DG sensitive Figure preprint bioRxiv 9; Defenouillère, Verraes et al. bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
A Tdh1-GFP Stf2-GFP Eno1-GFP Glc 2-DG Glc 2-DG Glc 2-DG O/N 2h30 O/N 2h30 O/N 2h30
Tdh1-GFP Stf2-GFP Eno1-GFP 63.2kDa 37.1kDa 74.3kDa
Rsp5 Rsp5 Rsp5
Adh5-GFP Yro2-GFP Hor7-GFP Glc 2-DG Glc 2-DG Glc 2-DG O/N 2h30 O/N 2h30 O/N 2h30
Adh5-GFP Yro2-GFP Hor7-GFP 65.1kDa 66.2kDa 33.1kDa
Rsp5 Rsp5 Rsp5
B GO-term category p-value In category from candidates
Glucose metabolic process 1.519e-07 Glk1 Dog2 Dog1 Tdh1 Tdh2 Pgm2
Glucose 6-phosphate metabolic process 5.586e-06 Glk1 Emi2 Pgm2
Glycolysis 1.324e-05 Glk1 Emi2 Eno1 Tdh1 Tdh2 Uga2 Adh5 Gpd1 Ydl124w Ser3 Adh4 Oxidation-reduction process 4.798e-05 Tdh1 Tdh2 Ero1 Fms1 Hfd1 Ypr127w Carbohydrate metabolic process 8.538e-05 Glk1 Gpd1 Emi2 Nqm1 Sol4 Pgm2 Sol1 Uga2 Adh5 Gpd1 Urh1 Ser3 Pnc1 Nqm1 Metabolic process 0.0002521 Dog2 Dog1 Tdh1 Tdh2 Ymr090w Hfd1 Fol1 Pentose-phosphate shunt 0.0004683 Nqm1 Sol4 Sol1
Nicotinate nucleotide salvage 0.0007527 Urh1 Pnc1
Cellular response to oxidative stress 0.0009224 Uga2 Ydl124w Hsp12 Gad1 Nce103
Gluconeogenesis 0.001016 Eno1 Tdh1 Tdh2
Response to stress 0.001597 Tip1 Hsp26 Sse2 Gpd1 Ssa4 Hsp12 Hor7
Amino acid catabolic process to alcohol 0.001854 Adh5 Adh4
Protein folding 0.004526 Hsp26 Sse2 Ssa4 Pho86 Ero1
NADH oxidation 0.005401 Adh5 Gpd1
Defenouillère et al., Figure S 1 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
5 ns WT 4 hog1∆
3
2
ns 1 β-Galactosidase activity 0 - 2DG + 2DG pDOG1:LacZ
Defenouillère et al., Figure S2 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
A B 4 2.0
Glc y WT * y 2DG 1∆ 3 1.5 Tm
2 1.0
1 0.5 ns β-Galactosidase activit β-Galactosidase activit
0 0.0 - G G pDOG1- ac pDOG1- ac
Defenouillère et al., Figure S3 bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
4 * WT slt2∆ 3
2
1 NS β-Galactosidase activity 0 - G G pDOG1 ac
e enouill e et al Fi u e bioRxiv preprint doi: https://doi.org/10.1101/504134; this version posted December 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Putative Mig1-binding site A -206 -188 ATTATTTTTAAATGTGGGG
LacZ pDOG2(1000bp)-LacZ -1000 0
LacZ pDOG2(500bp)-LacZ -500 0
LacZ pDOG2(350bp)-LacZ -350 0
LacZ pDOG2(250bp)-LacZ -250 0
LacZ pDOG2(150bp)-LacZ -150 0 B 50
y Glc ON 40
30
20
10 β-Galactosidase activit 0 p1000 p500 p350 p250 p150 Defenouillère et al., Figure S5 17864242 1 ------MLDA------EVR-----ELMQPFVLSDYQVQEVYSRFCLEVARGLKRSTHPQANVKCFPTYVQDLPTGDEMGKYLALDLGGTNFRVLLVSL A C 18079297 40 ------AALSATEKITTTT-AAATKSATATTNATTATATTTNLTTHSPQQIALLSA------AEKSKMVHELCQQLLLTDEQVQELCYRILHELRRGLAKDTHPKANVKCFVTYVQDLPNGNERGKFLALDLGGTNFRVLLIHL 45551986 1 ------MRKSTRLLTHS-LFGPVFKILFHNKTVCGGCNRKMP------SLVNT------EIE-----AAVKGFLIDQEKMTEVVERMTKEIKMGLAKDTHARAVIKCFVSHVQDLPTGKERGKYLALDLGGSNFRVLLVNL 54606886 366 DDCIAVQHVCAIVSFRSANLIAATLGAILTRLKDNKNTPRLRTTVGIDGSLYKMHPQYARRLHKTVRRLVPESDVRFLLSESGSGKGAALVTAWAYRLADQERQIAETLEEFRLTKDQLLEVKKRMRTEIQNGLSKSTQNTATVKMLPTYVRSTPDGSENGDFLALDLGGTNFRVLLVKI 156717322 366 EDCIAVQHVCTIVSFRSANLVAATLGGILIRLRDNKGVPRLRTTVGIDGSLYKMHPQYARRLHKTVRRLVPESDVRFLLSESGSGKGAAMVTAVAYRLSEQRRQIDETLEEFKLSREQLLEVKRRMRIEIENGLRKKTHESAKVKMLPTYVRSTPDGTENGDFLALDLGGTNFRVLLVKI Control +0.2% 2DG 45383904 366 EDCIAVQHVCTIVSFRSANLAASTLGAILNQLRDNKGVGRLRTTVGVDGSLYKMHPQYARRLHKTTRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLSEQHRLIDETLAEFKLTHEQLLQVKKRMRTEMEAGLKKKSHETAKVKMLPTFVRSTPDGTENGDFLALDLGGTNFRVLLVKI 225735584 366 DDCVSVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKMHPQYSRRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLSHFRLSKQALMEVKKKLRSEMEMGLRKETNSRATVKMLPSYVRSIPDGTEHGDFLALDLGGTNFRVLLVKI 6981022 366 VDCVSVQHICTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKMHPQYSRRFHKTLRRLVPDSDVRFLLSESGTGKGAAMVTAVAYRLAEQHRQIEETLAHFRLSKQTLMEVKKRLRTEMEMGLRKETNSKATVKMLPSFVRSIPDGTEHGDFLALDLGGTNFRVLLVKI 410043908 420 DDCVSVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKTHPQYSRRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFHLTKDMLLEVKKRMRAEMELGLRKQTHNNAAVKMLPSFVRRTPDGTENGDFLALDLGGTNFRVLLVKI 297301245 369 DDCVSVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKTHPQYSRRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFHLTKDMLLEVKKRMRAEMELGLRKQTHNNAVVKMLPSFVRSTPDGTENGDFLALDLGGTNFRVLLVKI 188497754 366 DDCVSVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKTHPQYSRRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFHLTKDMLLEVKKRMRAEMELGLRKQTHNNAVVKMLPSFVRRTPDGTENGDFLALDLGGTNFRVLLVKI 345798984 366 DDCISVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKTHPQYARRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFRLTKDMLLEVKKRMRTEMDMGLRKQTHEKAVVKMLPSFVRSTPDGTEHGDFLALDLGGTNFRVLLVKI WT + Ø 60592784 366 DDCVAVQHVCTIVSFRSANLVAATLGAILSRLRDNKGTPRLRTTVGVDGSLYKTHPQYSRRFHKTLRRLVPDCDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFSLTKEMLLEVKKRMRAEMELGLGKQTHDKAVVKMLPSFVRSTPDGTENGDFLALDLGGTNFRVLLVKI 15224857 1 ------MGKVAVATTVVCS----VAVCAAAALIVRRRMKS------AGKWA------RVIEILKAFEEDCATPIAKLRQVADAMTVEMHAGLASE--GGSKLKMLISYVDNLPSGDETGFFYALDLGGTNFRVMRVLL 15233457 1 ------MGKVAVGATVVCT----AAVCAVAVLVVRRRMQS------SGKWG------RVLAILKAFEEDCATPISKLRQVADAMTVEMHAGLASD--GGSKLKMLISYVDNLPSGDEKGLFYALDLGGTNFRVMRVLL 115464965 1 ------MGKAAAVGTAVVV----AAAVGVAVVLARRRRRRDLELVEGAAAERKR------KVAAVIEDVEHALSTPTALLRGISDAMVTEMERGLRGD--SHAMVKMLITYVDNLPTGNEQGLFYALDLGGTNFRVLRVQL 115439869 1 ------MGKGTVVGTAVVVCAAAAAAVGVAVVVSRRRRSK-----REAEEERRR------RAAAVIEEVEQRFSTPTALLRGIADAMVEEMERGLRAD--PHAPLKMLISYVDNLPTGDEHGLFYALDLGGTNFRVIRVQL #2 + Ø 398364415 1 ------MVHLGPKKPQARKGSMADVP------KELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKK---GGNIPMIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKL 6321184 1 ------MVHLGPKKPQARKGSMADVP------KELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKK---GGNIPMIPGWVMDFPTGKESGDFLAIDLGGTNLRVVLVKL 45198797 1 ------MVHLGPKKPPTRKGSMADVP------KTLVEQIASFERIFTVSAEKLQEITKHFVTELDKGLSKK---GGNIPMIPGWVMDYPTGNETGDYLAIDLGGTNLRVVLVKL 50307177 1 ------MVRLGPKKPPARKGSMADVP------ANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKK---GGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKL 389624569 1 ------MVDAP------KDLVKEIKDLEEMFTVDTAKLKQITNHFVGELERGLSVE---GGDIPMNPTWVMSFPDGYETGTFLALDMGGTNLRVCEITL 164427891 1 ------MASGTLDNLP------KDLRNEIEHLERLFTVDGAKLKEVTNHFVHELEKGLSVQ---GGSIPMNPTWVMSFPDGNETGTYLALDMGGTNLRVCQVTL #2 + HXK2 19113860 1 ------MSLHDAYHWPSRTPSRKGSNIKLN------KTLQDHLDELEEQFTIPTELLHRVTDRFVSELYKGLTTN---PGDVPMVPTWIIGTPDGNEHGSYLALDLGGTNLRVCAVEV
17864242 82 KG--HHDATVDSQIYAVPKDLMVGPGVDLFDHIAGCLAKFVEKHD-----MKTAYLPLGFTFSFPCVQLGLKEGILVRWTKGFDCAGVEGEDVGRMLHEAIQRRGD---ADIAVVAILNDTTGTLMSCAHRNADCRVGVIVGTGCNACYVEDVENVDLLRADFKKTKR---SVIVNAEWG 18079297 171 QE--NNDFQMESRIYAIPQHIMIGSGTQLFDHIAECLSNFMAEHN-----VYKERLPLGFTFSFPLRQLGLTKGLLETWTKGFNCAGVVNEDVVQLLKDAIARRGD---VQIDVCAILNDTTGTLMSCAWKNHNCKIGLIVGTGANACYMERVEEAELFAAEDPR-KK---HVLINTEWG #1 + Ø 45551986 118 IS--NSDVETMSKGYNFPQTLMSGSGKALFDFLAECLSEFCHSHG-----LENESLALGFTFSFPLQQQGLSKGILVAWTKGFSCEGVVGKNVVSLLQEAIDRRGD---LKINTVAILNDTVGTLMSCAFYHPNCRIGLIVGTGSNACYVEKTVNAECFEGYQTSPKP---SMIINCEWG 54606886 546 RSGKRRTVEMHNKIYAIPIEVMQGTGEELFDHIVYCISDFLDYMG-----MKNARLPLGFTFSFPCRQTSLDAGLLVNWTKGFKATDCEGEDVVGLLREGIKRREE---FDLDVVAIVNDTVGTMMTCAYEEPTCEVGLIAGTGSNACYMEEMRNIETVSGEEGR------MCVNMEWG 156717322 546 RSGKRRTVEMHNKIYAIPIDVMQGTGEELFDHIAHCISDFLDYMG-----IKGARLPLGFTFSFPCMQTSLDAGILVTWTKGFKATDCEGEDVVNLLREGIKRREE---FDLDVVAIVNDTVGTMMTCAYEDPNCEIGLIVGTGSNACYMEETKNIEMVDGDQGR------MCVNMEWG 45383904 546 RSGKRRTVEMHNKIYAIPIEVMQGTGEELFDHIVTCISDFLDYMG-----IRGARLPLGFTFSFPCKQTSLDAGILLNWTKGFKATDCEGEDVVYLLREGIKRREE---FDLDVVAVVNDTVGTMMTCAYEDPNCEIGLIVGTGSNACYMEEMRNIEMVDGEQGR------MCVNMEWG 225735584 546 RSGKKRTVEMHNKIYSIPLEIMQGTGDELFDHIVSCISDFLDYMG-----IKGPRMPLGFTFSFPCKQTSLDCGILITWTKGFKATDCVGHDVATLLRDAVKRREE---FDLDVVAVVNDTVGTMMTCAYEEPSCEIGLIVGTGSNACYMEEMKNVEMVEGNQGQ------MCINMEWG #1 + HXK2 6981022 546 RSGKKRTVEMHNKIYSIPLEIMQGTGDELFDHIVSCISDFLDYMG-----IKGPRMPLGFTFSFPCHQTNLDCGILISWTKGFKATDCEGHDVASLLRDAVKRREE---FDLDVVAVVNDTVGTMMTCAYEEPTCEIGLIVGTGTNACYMEEMKNVEMVEGNQGQ------MCINMEWG 410043908 600 RSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMG-----IKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREE---FDLDVVAVVNDTVGTMMTCAYEEPSCEVGLIVGTGSNACYMEEMKNVETVEGDQGQ------MCINMEWG 297301245 549 RSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMG-----IKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVATLLRDAIKRREE---FDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGL------MCINMEWG The copyright holder for this preprint (which preprint this for holder copyright The 188497754 546 RSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMG-----IKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREE---FDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQ------MCINMEWG 345798984 546 RSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMG-----IKGPKMPLGFTFSFPCKQTSLDAGILITWTKGFKATDCVGNDVATLLREAIKRREE---FDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMLEGNDGR------MCINMEWG #8 + Ø 60592784 546 RSGKKRSVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMG-----IKGPKMPLGFTFSFPCKQTSLDAGILITWTKGFKATDCVGHDVATLLREAIKRREE---FDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVETLEGNQGQ------MCINMEWG 15224857 115 GGKHDRVVKREFKEESIPPHLMTGKSHELFDFIVDVLAKFVATEGEDFHLPPGRQRELGFTFSFPVKQLSLSSGTLINWTKGFSIDDTVDKDVVGELVKAMERVG----LDMLVAALVNDTIGTLAGGRYTNPDVVVAVILGTGTNAAYVERAHAIPKWHGLLPK-SG---EMVINMEWG 15233457 115 GGKQERVVKQEFEEVSIPPHLMTGGSDELFNFIAEALAKFVATECEDFHLPEGRQRELGFTFSFPVKQTSLSSGSLIKWTKGFSIEEAVGQDVVGALNKALERVG----LDMRIAALVNDTVGTLAGGRYYNPDVVAAVILGTGTNAAYVERATAIPKWHGLLPK-SG---EMVINMEWG 115464965 124 GGKEKRVVQQQYEEVSIPPHLMVGTSMELFDFIASALSKFVDTEGDDFHLPEGRQRELGFTFSFPVSQTSISSGTLIKWTKGFSINDAVGEDVVSELGKAMERQG----LDMKIAALVNDTVGTLAGGRYADNSVVAAIILGTGTNAAYVENANAIPKWTGLLPR-SG---NMVINTEWG 115439869 123 GGREKRVVSQQYEEVAIPPHLMVGTSMELFDFIAAELESFVKTEGEDFHLPEGRQRELGFTFSFPVHQTSISSGTLIKWTKGFSINGTVGEDVVAELSRAMERQG----LDMKVTALVNDTVGTLAGGRYVDNDVAAAVILGTGTNAAYVEHANAIPKWTGLLPR-SG---NMVINMEWG 398364415 100 SGNH-TFDTTQSKYKLPHDMRTTKHQEELWSFIADSLKDFMVEQELLN---TKDTLPLGFTFSYPASQNKINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKR----ELPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKLEGKLADDIPSNSPMAINCEYG #8 + HXK2 6321184 100 GGDR-TFDTTQSKYRLPDAMRTTQNPDELWEFIADSLKAFIDEQFPQG---ISEPIPLGFTFSFPASQNKINEGILQRWTKGFDIPNIENHDVVPMLQKQITKR----NIPIEVVALINDTTGTLVASYYTDPETKMGVIFGTGVNGAYYDVCSDIEKLQGKLSDDIPPSAPMAINCEYG 45198797 100 LGNH-QFDTTQSKYRLPNRMRTTQNASELWDFIAESLKDFLEEQFPEG---VHQTLPLGFTFSYPASQDKINMGILQRWTKGFDIPGVEGHDVVPMLQESLRKV----NVPIEVVALINDTTGTLVASLYTDAETKMGVIFGTGVNGAYYDVVKDIEKLEGRLPEDIPPESAMAINCEYG 50307177 100 GGNH-DFDTTQNKYRLPDHLRTG-TSEQLWSFIAKCLKEFVDEWYPDG---VSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKL----NIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYG 389624569 85 TDQKSEFDIIQSKYRMPEELKTG-QSDELWDYIADCLLQFIETHHGDPK--KIEKLPLGFTFSYPATQNYVDEGILQRWTKGFDIAGVEGKNVAPMLMKALSERDRNQGVPVKLVALINDTTGTLIASAYTDTQMRIGCIFGTGCNAAYMEECGSIPKLA---HMNLPPETPMAINCEWG 164427891 90 TETKSEFDIIQSKYRMPEELKTG-DAEELWEYIADCLMQFIETHHGDPT--KLDALPLGFTFSYPATQNYIDEGILQRWTKGFDIAGVEGHNVVPMFEAALQRR----GVPIKLTALINDTTGTLIASAYTDPKMRIGCIFGTGCNAAYMENCGSIPKLA---HMNLPPDMPMAINCEWG 19113860 104 QGNG-KFDITQSKYRLPQELKVG-TREALFDYIADCIKKFVEEVHPGK----SQNLEIGFTFSYPCVQRSINDASLVAWTKGFDIDGVEGESVGPLLSAALKRVG---CNNVRLNAILSDTTGTLVASNYASPGTEIGVIFGTGCNACYIEKFSEIPKLH---KYDFPEDMNMIINCEWC
17864242 249 AFGEGGQLDFVRTEYDREVDEKSLNRSEQLFEKMTAGMYLGNLVRLVLLRALERK--LIFKQSSRRPEFASVLQRNEEVFETRYISEIEDDSFPEFASTRKIVKNLFGLEKASVEDCQTLRYICECVAKRAATLVAIGVSGLVNRTS----NRR------VIVGMDGSVYRYHPKFDAYM B 18079297 337 AFGDNGALDFVRTEFDRDIDVHSINPGKQTFEKMISGMYMGELVRLVLVKMTQAG--ILFNGQD-----SEVLN-TRGLFFTKYVSEIEADEPGNFTNCR-LVLEELGLTNATDGDCANVRYICECVSKRAAHLVSAGIATLINKMD----EPT------VTVGVDGSVYRFHPKFHNLM 45551986 285 AFGDNGVLEFVRTSYDKAVDKVTPNPGKQTFEKCISGMYMGELVRLVITDMIAKG--FMFHGII-----SEKIQ-ERWSFKTAYISDVESDAPGEYRNCN-KVLSELGILGCQEPDKEALRYICEAVSSRSAKLCACGLVTIINKMN----INE------VAIGIDGSVYRFHPKYHDML 54606886 711 AFGDNGCLDDIRTKYDDAVDDLSLNAGKQKYEKMCSGMYLGEIVRNILIDLTKRG--FLFRGQI-----SETLK-TRGIFETKFLSQIESDRLALLQVRS--ILQHLGLD-STCDDSIIVKEVCGAVSRRAAQLCGAGMAAVVDKIR----ENRGLDHLDITVGVDGTLYKLHPHFSRIM 156717322 711 AFGDNGCLDDIRTVYDKAVDDLSLNSGKQRYEKMISGMYLGEIVRNILIDFTKRG--FLFRGQI-----SEALK-TTSIFETKFLSQIESDRLALLQVRS--ILQQLGLN-STCDDSIIVKEVCGAVSRRAAQVCGAGMAAVVDKIR----ENRGLDHLDVTVGVDGTLYKLHPHFSKIM 45383904 711 AFGDNGCLDDIRTIYDKAVDDYSLNAGKQRYEKMISGMYLGEIVRNILIDFTKRG--FLFRGQI-----SETLK-TRHIFETKFLSQIESDRLALLQVRT--ILQQLGLN-STCDDSIIVKTVCGGVSKRAAQLCGAGMAAVVDKIR----ENRGLEHLEITVGVDGTLYKLHPHFSRIM 225735584 711 AFGDNGCLDDIRTDFDKVVDEYSLNSGKQRFEKMISGMYLGEIVRNILIDFTKKG--FLFRGQI-----SEPLK-TRGIFETKFLSQIESDRLALLQVRA--ILQQLGLN-STCDDSILVKTVCGVVSKRAAQLCGAGMAAVVEKIR----ENRGLDHLNVTVGVDGTLYKLHPHFSRIM 6981022 711 AFGDNGCLDDIRTDFDKVVDEYSLNSGKQRFEKMISGMYLGEIVRNILIDFTKKG--FLFRGQI-----SEPLK-TRGIFETKFLSQIESDRLALLQVRA--ILQQLGLN-STCDDSILVKTVCGVVSKRAAQLCGAGMAAVVEKIR----ENRGLDHLNVTVGVDGTLYKLHPHFSRIM GI Accession Description Species 410043908 765 AFGDNGCLDDIRTHYDRLVDEYSLNAGKQRYEKMISGMYLGEIVRNILIDFTKKG--FLFRGQI-----SETLK-TRGIFETKFLSQIESDRLALLQVRA--ILQQLGLN-STCDDSILVKTVCGVVSRRAAQLCGAGMAAVVDKIR----ENRGLDRLNVTVGVDGTLYKLHPHFSRIM 297301245 714 AFGDNGRLDDIRTQYDRLVDEYSLNAGKQRYEKMISGMYLGEIVRNILIDFTKKG--FLFRGQI-----SEPLK-TRGIFETKFLSQIESDRLALLQVRA--ILQQLGLN-STCDDSILVKTVCGVVSRRAAQLCGAGMAAVVDKIR----ENRGLDRLNVTVGVDGTLYKLHPHFSRIM 188497754 NP_000179.2 hexokinase-1 isoform HKI Homo sapiens 188497754 711 AFGDNGCLDDIRTHYDRLVDEYSLNAGKQRYEKMISGMYLGEIVRNILIDFTKKG--FLFRGQI-----SETLK-TRGIFETKFLSQIESDRLALLQVRA--ILQQLGLN-STCDDSILVKTVCGVVSRRAAQLCGAGMAAVVDKIR----ENRGLDRLNVTVGVDGTLYKLHPHFSRIM 410043908 XP_001169264.2 hexokinase-1 isoform 9 Pan troglodytes 345798984 711 AFGDNGCLDDIRTIYDRLVDEYSLNAGKQRFEKMISGMYLGEIVRNILIDFTKKG--FLFRGQI-----SETLK-TRGIFQTKYLSQIESDRLALLQVRA--ILQQLGLN-STCDDSILVKTVCGVVSKRAAQLCGAGMAAVVDKIR----ENRGLDHLNVTVGVDGTLYKLHPHFSRIM 60592784 711 AFGDNGCLDDIRTIYDKLVDEFSLNSGKQRYEKMISGMYLGEIVRNILIDFAKRG--FLFRGQI-----SEPLK-TRGLFQTKYLSQIESDRLALLQVRA--ILQQLGLN-STCDDSILVKTVCGVVSKRAAQLCGAGMAAVVDKIR----ENRGLDRLNVTVGVDGTLYKLHPHFSRIM 297301245 XP_001110396.2 hexokinase-1-like isoform 6 Macaca mulatta 15224857 287 NFRSS---HLPLTEYDHSLDVDSLNPGEQILEKIISGMYLGEILRRVLLKMAEEA--AFFGDIVP------PKLKIPFIIRTPNMSAMHSDTSPDLKVVGSKLKDILEVQTSSLKMRKVVISLCNIIASRGARLSAAGIYGILKKIGRDATKDG--EAQKSVIAMDGGLFEHYTQFSESM this version posted December 21, 2018. 2018. 21, December posted version this 15233457 287 NFRSS---HLPLTEFDHTLDFESLNPGEQILEKIISGMYLGEILRRVLLKMAEDA--AFFGDTVP------SKLRIPFIIRTPHMSAMHNDTSPDLKIVGSKIKDILEVPTTSLKMRKVVISLCNIIATRGARLSAAGIYGILKKLGRDTTKDE--EVQKSVIAMDGGLFEHYTQFSECM ; 345798984 XP_536376.3 hexokinase-1 isoform X3 Canis lupus familiaris 115464965 296 SFKSD---KLPLSEFDKAMDFESLNPGEQIYEKLISGMYLGEIVRRILLKLAHDA--ALFGDVVP------SKLEQPFVLRTPDMSAMHHDSSHDLKTVGAKLKDIVGVPDTSLEVRYITSHICDIVAERAARLAAAGIYGVLKKLGRDKMPKDGSKMPRTVIALDGGLYEHYKKFSSCL 60592784 NP_001012686.1 hexokinase-1 Bos taurus 115439869 295 NFKSE---RLPRSDYDNALDFESLNPGEQIYEKMISGMYLGEIVRRILLKLAHDA--SLFGDVVP------TKLEQRFILRTPDMSAMHHDTSHDLKHLGAKLKDILGVADTSLEARYITLHVCDLVAERGARLAAAGIYGILKKLGRDRVPSDGSQKQRTVIALDGGLYEHYKKFRTCL 398364415 272 SFDNEH-LVLPRTKYDVAVDEQSPRPGQQAFEKMTSGYYLGELLRLVLLELNEKG--LMLKDQD------LSKLKQPYIMDTSYPARIEDDPFENLEDTDDIFQKDFGVK-TTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRG------YKTGHIAADGSVYNKYPGFKEAA 225735584 NP_001139572.1 hexokinase-1 isoform HK1 Mus musculus 6321184 272 SFDNEH-VVLPRTKYDITIDEESPRPGQQTFEKMSSGYYLGEILRLALMDMYKQG--FIFKNQD------LSKFDKPFVMDTSYPARIEEDPFENLEDTDDLFQNEFGIN-TTVQERKLIRRLSELIGARAARLSVCGIAAICQKRG------YKTGHIAADGSVYNRYPGFKEKA 6981022 NP_036866.1 hexokinase-1 Rattus norvegicus 45198797 272 SFDNEH-LVLPRTKYDILIDEQSPRPGQQAFEKMTSGYYLGEVLRLALLDLHGQG--LIFQGQD------ISKLETPYVMDTSFPARIEDDPFENLEETDDLFKDNLDID-TTRPERKLIRKLSEMIGNRAARLSVCGIAAICQKRG------YETAHIAADGSVFNKYPGFQTRA 50307177 271 SFDNEH-LVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSG--FIFKDQD------ISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIE-TTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRG------YKTAHIAADGSVFNRYPGYKEKA 45383904 NP_989432.1 HK1 gene product Gallus gallus 389624569 259 AFDNQH-KVLPRTPYDVKIDEDSPRPGQQAFEKMIAGLYLGEIFRLILVDLHDNHEVRIFKNQD------ISKLRRAYTLDSSFLSAIEDDPWENLSETLDLFQDKLNLV-PNRNELELIRRTAELIGTRAARLSACGVAAICKKKN------YRSCHVGADGSVFNKYPNFKQRG 164427891 260 AFDNEH-KVLPRTPYDVIIDKDSPRPGQQSFEKMVAGLYLGEIFRLVLVDLHDNQEIKIFPGQD------IAKLRKAYSLDSSFLSLIEEDPFENLSETFELFQTKLGLT-PTGPELELIRRTAELIGTRAARLSACGVAAISKKKG------YKQCHVGADGSVFNKYPNFKARG 54606886 NP_998417.1 hexokinase-1 Danio rerio 19113860 272 DFDNQH-VVLPRTKYDVAIDEESPRPGLQTYEKMIAGCYLGDILRRILLDLYEQG--ALFNGQD------VTKIRDPLAMDTSVLSAIEVDPFENLDETQTLFEETYGLK-TTEEERQFIRRACELIGTRSARLSACGVCALVRKMN------KPSMIVGTDGSVYNLYPRFKDRL 45551986 NP_733151.2 Hex-t2 Drosophila melanogaster 17864242 417 RQTLQKLVK------ADKEWDIMLSEDGSGRGAALVAAVASKTK------17864242 NP_524674.1 hexokinase C Drosophila melanogaster 18079297 498 VEKISQLIK------PGITFDLMLSEDGSGRGAALVAAVACREDILNGKK------18079297 NP_524848.1 hexokinase A, isoform Drosophila melanogaster 45551986 446 QYHMKKLLK------PGVKFELVVSEDGSGRGAALVAATAVQAKSKL------54606886 876 HQTVKELA------PKCNVTFLLSEDGSGKGAALITAVGCRLRQQEQKS------398364415 NP_116711.3 hexokinase 1 Saccharomyces cerevisiae S288C 156717322 876 HQTVKDLA------PKCNVSFLLSEDGSGKGAALITAVACRLRSSEQN------Combined mutations identified in clone #21 6321184 NP_011261.1 hexokinase 2 Saccharomyces cerevisiae S288C 45383904 876 HQTVKDLA------PKCDVTFLLSEDGSGKGAALITAVGCRVRDAEQN------225735584 876 HQTVKELS------PKCTVSFLLSEDGSGKGAALITAVGVRLRGDPTNA------Single mutations identified in other clones 50307177 XP_453567.1 KLLA0_D11352g Kluyveromyces lactis 6981022 876 HQTVKELS------PKCTVSFLLSEDGSGKGAALITAVGVRLRGDPSIA------45198797 NP_985826.1 AFR279Cp Eremothecium gossypii ATCC 10895 410043908 930 HQTVKELS------PKCNVSFLLSEDGSGKGAALITAVGVRLRTEASS------297301245 879 HQTVKELS------PKCNVSFLLSEDGSGKGAALITAVGVRLRTEASS------Glucose-binding residues 19113860 NP_592948.1 hexokinase 1 Schizosaccharomyces pombe 188497754 876 HQTVKELS------PKCNVSFLLSEDGSGKGAALITAVGVRLRTEASS------345798984 876 YQTVKELS------PKCNVSFLLSEDGSGKGAALITAVGVRLREETSS------ATP-binding residues https://doi.org/10.1101/504134 389624569 XP_003709938.1 hexokinase Magnaporthe oryzae 70-15 60592784 876 HQTVKELS------PKCNVSFLLSEDGSGKGAALITAVGVRLRQEMSS------164427891 XP_965673.2 hexokinase Neurospora crassa OR74A 15224857 454 KSSLKELLGD------EVSESVEVILSNDGSGVGAALLAASHSQYLELEDDSETS------15233457 454 ESSLKELLGD------EASGSVEVTHSNDGSGIGAALLAASHSLYLEDS------doi: doi: 15224857 NP_179576.1 hexokinase 2 Arabidopsis thaliana 115464965 465 ESTLTDLLGD------DVSSSVVTKLANDGSGIGAALLAASHSQYAEID------115439869 464 EATLADLLGE------EAASSVVVKLANDGSGIGAALLAASHSQYASVE------15233457 NP_194642.1 hexokinase 1 Arabidopsis thaliana 398364415 432 AKGLRDIYGWTGDA--SKD-PITIVPAEDGSGAGAAVIAALSEKRIAEGKSLGIIGA------was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. permission. without allowed reuse No reserved. All rights author/funder. is the review) peer by certified not was 115464965 NP_001056082.1 Os05g0522500 Oryza sativa Japonica Group 6321184 432 ANALKDIYGWTQTS--LDDYPIKIVPAEDGSGAGAAVIAALAQKRIAEGKSVGIIGA------45198797 432 AEGLRDIYGWEHSS--SQDYPIKIVAAEDGSGAGAAVIAALTTKRLAAGKSVGLPEAQN------115439869 NP_001044214.1 Os01g0742500 Oryza sativa Japonica Group 50307177 431 AQALKDIYNWDVEK--MEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE------156717322 NP_001096201.1 hexokinase-1 Xenopus tropicalis 389624569 421 AQALREILDWPAKEDPKEEDPIEILAAEDGSGVGAALIAALTLKRAKEGNFHGISNPENFK------164427891 422 AQALREILDWPEKADPKEDDPIEILAAEDGSGVGAALIAALTMQRIKQGNMHGILHPENFRTTEPLPA 19113860 432 AQAFKDILGEEIGS------KVVTIPAEDGSGVGAALVSALEAKGKALTSDILAEHLKN------bioRxiv preprint preprint bioRxiv Defenouillère et al., Figure S6