DOCSLIB.ORG

Biochemical Pathways Supporting Beta-Lactam Biosynthesis in the Springtail Folsomia Candida Wouter Suring, Janine Mariën, Rhody Broekman, Nico M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Biochemical Pathways Supporting Beta-Lactam Biosynthesis in the Springtail Folsomia Candida Wouter Suring, Janine Mariën, Rhody Broekman, Nico M © 2016. Published by The Company of Biologists Ltd | Biology Open (2016) 5, 1784-1789 doi:10.1242/bio.019620 RESEARCH ARTICLE Biochemical pathways supporting beta-lactam biosynthesis in the springtail Folsomia candida Wouter Suring, Janine Mariën, Rhody Broekman, Nico M. van Straalen and Dick Roelofs* ABSTRACT aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS), as well as Recently, an active set of beta-lactam biosynthesis genes was a functional isopenicillin N synthase (IPNS) enzyme that catalyzes reported in the genome of the arthropod springtail Folsomia candida the formation of the beta-lactam ring structure from the product of (Collembola). Evidence was provided that these genes were acquired ACVS activity. Beta-lactam biosynthesis genes are involved in the through horizontal gene transfer. However, successful integration stress response of F. candida and are upregulated upon exposure to a of fungal- or bacterial-derived beta-lactam biosynthesis into the variety of stressors (de Boer et al., 2015). Most probably, F. candida metabolism of an animal requires the beta-lactam precursor L-α- acquired its beta-lactam genes through horizontal gene transfer aminoadipic acid and a phosphopantetheinyl transferase for activation (Roelofs et al., 2013). However, in addition to the core biosynthesis of the first enzyme of the pathway, δ-(L-α-aminoadipoyl)-L-cysteinyl-D- pathway, other pathways are required for beta-lactam biosynthesis. valine synthetase (ACVS). In this study, we characterized these In the first step of penicillin and cephalosporin biosynthesis, the α supporting pathways and their transcriptional regulation in F. candida. tripeptide ACV is synthesized from L-cysteine, L-valine, and L- - We identified one phosphopantetheinyl transferase and three aminoadipic acid by ACVS, an enzyme belonging to the class of pathways for L-α-aminoadipic acid production, distinct from the nonribosomal peptide syntethases (NRPSs). Like other NRPSs, pathways utilized by microorganisms. We found that after heat ACVS requires its peptide carrier protein domains to be ′ shock, the phosphopantetheinyl transferase was co-regulated with phosphopantetheinylated by a 4 -phosphopantetheinyl transferase ACVS, confirming its role in activating ACVS. Two of the three L-α- (PPTase) to convert them to their active configuration (Wu et al., aminoadipic acid production pathways were downregulated, while 2012). Only in its active form can ACVS bind the amino acids PIPOX, an enzyme participating in the pipecolate pathway, was required for ACV biosynthesis. PPTases also occur in organisms slightly co-regulated with ACVS. This indicates that L-α-aminoadipic without nonribosomal peptide synthetases because they are acid may not be a limiting factor in beta-lactam biosynthesis in essential for phosphopantetheinylation of acyl carrier proteins F. candida, in contrast to microorganisms. In conclusion, we show that involved in fatty acid metabolism (Bhaumik et al., 2005). It is all components for L-α-aminoadipic acid synthesis are present and known that metazoan PPTases can have broad substrate specificity transcriptionally active in F. candida. This demonstrates how and can even activate prokaryotic nonribosomal peptide synthetases springtails could have recruited native enzymes to integrate a beta- in some cases (Joshi et al., 2003). lactam biosynthesis pathway into their metabolism after horizontal One of the substrates of ACVS is the nonproteinogenic amino α gene transfer. acid L- -aminoadipic acid (L-AAA). It serves as a building block for nonribosomal peptides, and also functions as an intermediate in KEY WORDS: Beta-lactam, L-α-aminoadipate, Heat shock, lysine metabolism. Both beta-lactam-producing bacteria and fungi Collembola, Gene expression utilize specialized pathways for the production of L-AAA. Although all fungi produce L-AAA as an intermediate in a INTRODUCTION fungal-specific lysine biosynthesis pathway (Xu et al., 2006), Beta-lactam antibiotics are currently the most widely used fungi that synthesize beta-lactams utilize a second pathway in which antimicrobial compounds. Biosynthesis of these compounds has lysine is catabolized to L-AAA using a ω-aminotransferase been described in several species of Actinobacteria and (Naranjo et al., 2005). Similarly, while most bacteria cannot Proteobacteria and in several fungi (Ozcengiz and Demain, 2013). synthesize L-AAA (Neshich et al., 2013), beta-lactam-producing It was not reported in animals until recently, when the first metazoan bacteria can break down lysine to produce L-AAA using the beta-lactam biosynthesis genes were characterized in the springtail enzymes lysine-6-aminotransferase and piperideine-6-carboxylate Folsomia candida (Roelofs et al., 2013). Folsomia candida is a soil- dehydrogenase (de La Fuente et al., 1997; Madduri et al., 1989). dwelling basal hexapod, the closest relatives of the insects (Misof For its beta-lactam biosynthesis pathway to be functional, et al., 2014). This animal contains a gene encoding a δ-(L-α- F. candida needs to synthesize L-AAA. Three pathways have been described in animals in which L-AAA is an intermediate. Humans express two lysine degradation pathways in which L-AAA Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan is produced as an intermediate: the saccharopine pathway and the 1085-1087, Amsterdam 1081 HV, The Netherlands. pipecolate pathway (Hallen et al., 2013). L-AAA also functions as *Author for correspondence ([email protected]) an intermediate in a third degradation pathway starting from 5-hydroxy-L-lysine (Veiga-da-Cunha et al., 2012). In the case of D.R., 0000-0003-3954-3590 arthropods, the saccharopine pathway is present in all model insect This is an Open Access article distributed under the terms of the Creative Commons Attribution species, while the pipecolate pathway is present in multiple species License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. of Ecdysozoa, but appears absent in insects. While supporting pathways for beta-lactam biosynthesis have Received 19 May 2016; Accepted 20 October 2016 been well-studied in microorganisms, it remains unknown how Biology Open 1784 RESEARCH ARTICLE Biology Open (2016) 5, 1784-1789 doi:10.1242/bio.019620 these pathways are organized in the springtail F. candida. This study L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl aims at unraveling genes involved in L-AAA metabolism and transferase. phosphopantetheinylation in F. candida and their transcriptional regulation. To that end, we analyzed the transcriptome of F. candida Expression of ACVS and AASDHPPT and reconstructed full-length cDNAs for L-AAA metabolic Gene expression analysis using qPCR assays show that ACVS pathways and PPTases. We know from previous experiments that was significantly upregulated in response to heat shock (F test, the beta-lactam biosynthesis pathway of F. candida is induced F2,23=19.39, P<0.001) (Fig. 2). The expression reached its during stress events. Here we hypothesize that supporting pathways maximum at six hours after heat shock (mean fold-regulation, will be co-regulated with the expression of beta-lactam biosynthesis M=3.36, standard deviation, s.d.=0.54) and was over 15 times genes during stress. higher compared to controls (M=0.21, s.d.=0.051). At 48 h post heat shock, ACVS expression had returned to a low level (M=0.12, RESULTS s.d.=0.07). The PPTase AASDHPPT showed a similar expression L-α-aminoadipic acid metabolism in F. candida profile compared to ACVS reaching a maximum at the same time Blast searches in combination with conserved domain searches using point (F2,23=54.05, P<0.001). Expression of the PPTase went up Pfam and KEGG (see Materials and Methods section) identified three ∼twofold at 6 h after heat shock (M=2.1, s.d.=0.036) compared to metabolic pathways in F. candida in which L-AAA is an intermediate controls (M=1.0, s.d.=0.089). In conclusion, both genes are (Table 1). From the transcriptome data, we constructed the metazoan significantly upregulated upon heat shock, with ACVS being the saccharopine and pipecolate pathways. In addition, the 5-hydroxy-L- most inducible gene. lysine degradation pathway was identified. All three pathways converge at 2-aminoadipic semialdehyde which is converted to Expression of L-α-aminoadipic acid metabolic genes L-AAA by L-aminoadipate-semialdehyde dehydrogenase (Fig. 1). We obtained expression profiles of the three L-AAA metabolic L-AAA is then available as a substrate for ACVS and thus supports pathways in F. candida that are described in Fig. 1. Expression of beta-lactam biosynthesis. L-AAA can also be catabolized by LKRSDH, the first gene of L-lysine degradation through the kynurenine/2-aminoadipate aminotransferase and further converted saccharopine pathway, was not significantly up- or downregulated to acetyl-CoA at which point it enters the citric acid cycle. The after heat shock (F2,23=2.33, P=0.14). The second gene of the bacteria-specific L-AAA biosynthesis pathway consisting of lysine- saccharopine pathway encodes AASDH, which is the enzyme that 6-aminotransferase (encoded by lat) and piperideine-6-carboxylate catalyzes the formation of L-AAA. This enzyme showed significant dehydrogenase (encoded by pcd), and the fungi-specific ω- regulation in the time interval after heat shock (F2,23=144.4, aminotransferase encoded by oat1 are not present in F. candida. P<0.001). More specifically,
Load more

Recommended publications
  • Measurement of Metabolite Variations and Analysis of Related Gene Expression in Chinese Liquorice (Glycyrrhiza Uralensis) Plants
    www.nature.com/scientificreports OPEN Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice Received: 15 March 2017 Accepted: 28 March 2018 (Glycyrrhiza uralensis) plants under Published: xx xx xxxx UV-B irradiation Xiao Zhang1,2, Xiaoli Ding3,4, Yaxi Ji1,2, Shouchuang Wang5, Yingying Chen1,2, Jie Luo5, Yingbai Shen1,2 & Li Peng3,4 Plants respond to UV-B irradiation (280–315 nm wavelength) via elaborate metabolic regulatory mechanisms that help them adapt to this stress. To investigate the metabolic response of the medicinal herb Chinese liquorice (Glycyrrhiza uralensis) to UV-B irradiation, we performed liquid chromatography tandem mass spectrometry (LC-MS/MS)-based metabolomic analysis, combined with analysis of diferentially expressed genes in the leaves of plants exposed to UV-B irradiation at various time points. Fifty-four metabolites, primarily amino acids and favonoids, exhibited changes in levels after the UV-B treatment. The amino acid metabolism was altered by UV-B irradiation: the Asp family pathway was activated and closely correlated to Glu. Some amino acids appeared to be converted into antioxidants such as γ-aminobutyric acid and glutathione. Hierarchical clustering analysis revealed that various favonoids with characteristic groups were induced by UV-B. In particular, the levels of some ortho- dihydroxylated B-ring favonoids, which might function as scavengers of reactive oxygen species, increased in response to UV-B treatment. In general, unigenes encoding key enzymes involved in amino acid metabolism and favonoid biosynthesis were upregulated by UV-B irradiation. These fndings lay the foundation for further analysis of the mechanism underlying the response of G.
    [Show full text]
  • Part One Amino Acids As Building Blocks
    Part One Amino Acids as Building Blocks Amino Acids, Peptides and Proteins in Organic Chemistry. Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. Hughes Copyright Ó 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32102-5 j3 1 Amino Acid Biosynthesis Emily J. Parker and Andrew J. Pratt 1.1 Introduction The ribosomal synthesis of proteins utilizes a family of 20 a-amino acids that are universally coded by the translation machinery; in addition, two further a-amino acids, selenocysteine and pyrrolysine, are now believed to be incorporated into proteins via ribosomal synthesis in some organisms. More than 300 other amino acid residues have been identified in proteins, but most are of restricted distribution and produced via post-translational modification of the ubiquitous protein amino acids [1]. The ribosomally encoded a-amino acids described here ultimately derive from a-keto acids by a process corresponding to reductive amination. The most important biosynthetic distinction relates to whether appropriate carbon skeletons are pre-existing in basic metabolism or whether they have to be synthesized de novo and this division underpins the structure of this chapter. There are a small number of a-keto acids ubiquitously found in core metabolism, notably pyruvate (and a related 3-phosphoglycerate derivative from glycolysis), together with two components of the tricarboxylic acid cycle (TCA), oxaloacetate and a-ketoglutarate (a-KG). These building blocks ultimately provide the carbon skeletons for unbranched a-amino acids of three, four, and five carbons, respectively. a-Amino acids with shorter (glycine) or longer (lysine and pyrrolysine) straight chains are made by alternative pathways depending on the available raw materials.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Figure S1. Heat Map of R (Pearson's Correlation Coefficient)
    Figure S1. Heat map of r (Pearson’s correlation coefficient) value among different samples including replicates. The color represented the r value. Figure S2. Distributions of accumulation profiles of lipids, nucleotides, and vitamins detected by widely-targeted UPLC-MC during four fruit developmental stages. The colors indicate the proportional content of each identified metabolites as determined by the average peak response area with R scale normalization. PS1, 2, 3, and 4 represents fruit samples collected at 27, 84, 125, 165 Days After Anthesis (DAA), respectively. Three independent replicates were performed for each stages. Figure S3. Differential metabolites of PS2 vs PS1 group in flavonoid biosynthesis pathway. Figure S4. Differential metabolites of PS2 vs PS1 group in phenylpropanoid biosynthesis pathway. Figure S5. Differential metabolites of PS3 vs PS2 group in flavonoid biosynthesis pathway. Figure S6. Differential metabolites of PS3 vs PS2 group in phenylpropanoid biosynthesis pathway. Figure S7. Differential metabolites of PS4 vs PS3 group in biosynthesis of phenylpropanoids pathway. Figure S8. Differential metabolites of PS2 vs PS1 group in flavonoid biosynthesis pathway and phenylpropanoid biosynthesis pathway combined with RNA-seq results. Table S1. A total of 462 detected metabolites in this study and their peak response areas along the developmental stages of apple fruit. mix0 mix0 mix0 Index Compounds Class PS1a PS1b PS1c PS2a PS2b PS2c PS3a PS3b PS3c PS4a PS4b PS4c ID 1 2 3 Alcohols and 5.25E 7.57E 5.27E 4.24E 5.20E
    [Show full text]
  • 1/05661 1 Al
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date _ . ... - 12 May 2011 (12.05.2011) W 2 11/05661 1 Al (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/00 (2006.0 1) C12Q 1/48 (2006.0 1) kind of national protection available): AE, AG, AL, AM, C12Q 1/42 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (21) Number: International Application DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US20 10/054171 HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (22) International Filing Date: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 26 October 2010 (26.10.2010) ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (25) Filing Language: English SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, (26) Publication Language: English TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 61/255,068 26 October 2009 (26.10.2009) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, (71) Applicant (for all designated States except US): ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, MYREXIS, INC.
    [Show full text]
  • Comparison of Gene Expression Profile of the Spinal Cord Of
    Tsujioka and Yamashita BMC Genomics (2019) 20:619 https://doi.org/10.1186/s12864-019-5974-9 RESEARCHARTICLE Open Access Comparison of gene expression profile of the spinal cord of sprouting-capable neonatal and sprouting-incapable adult mice Hiroshi Tsujioka1,2 and Toshihide Yamashita1,2,3,4* Abstract Background: The regenerative ability of severed axons in the central nervous system is limited in mammals. However, after central nervous system injury, neural function is partially recovered by the formation of a compensatory neural circuit. In a mouse pyramidotomy model, axonal sprouting of the intact side of the corticospinal tract is observed in the spinal cord, and the axons make new synapses with the denervated side of propriospinal neurons. Moreover, this sprouting ability is enhanced in neonatal mice compared to that in adult mice. Myelin-associated molecules in the spinal cord or intrinsic factors in corticospinal neurons have been investigated in previous studies, but the factors that determine elevated sprouting ability in neonatal mice are not fully understood. Further, in the early phase after pyramidotomy, glial responses are observed in the spinal cord. To elucidate the basal difference in the spinal cord, we compared gene expression profiles of entire C4–7 cervical cord tissues between neonatal (injured at postnatal day 7) and adult (injured at 8 weeks of age) mice by RNA-sequencing. We also tried to identify discordant gene expression changes that might inhibit axonal sprouting in adult mice at the early phase (3 days) after pyramidotomy. Results: A comparison of neonatal and adult sham groups revealed remarkable basal differences in the spinal cord, such as active neural circuit formation, cell proliferation, the development of myelination, and an immature immune system in neonatal mice compared to that observed in adult mice.
    [Show full text]
  • Accepted Manuscript
    Accepted Manuscript Fibrogenic Activity of MECP2 is Regulated by Phosphorylation in Hepatic Stellate Cells Eva Moran-Salvador, Marina Garcia-Macia, Ashwin Sivaharan, Laura Sabater, Marco Y.W. Zaki, Fiona Oakley, Amber Knox, Agata Page, Saimir Luli, Jelena Mann, Derek A. Mann PII: S0016-5085(19)41126-8 DOI: https://doi.org/10.1053/j.gastro.2019.07.029 Reference: YGAST 62784 To appear in: Gastroenterology Accepted Date: 17 July 2019 Please cite this article as: Moran-Salvador E, Garcia-Macia M, Sivaharan A, Sabater L, Zaki MYW, Oakley F, Knox A, Page A, Luli S, Mann J, Mann DA, Fibrogenic Activity of MECP2 is Regulated by Phosphorylation in Hepatic Stellate Cells, Gastroenterology (2019), doi: https://doi.org/10.1053/ j.gastro.2019.07.029. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Fibrogenic Activity of MECP2 is Regulated by Phosphorylation in Hepatic Stellate Cells ACCEPTED MANUSCRIPT Short title : Mecp2 controls myofibroblast transcriptome Eva Moran-Salvador ###, Marina Garcia-Macia ###, Ashwin Sivaharan ###, Laura Sabater, Marco Y.W. Zaki, Fiona Oakley, Amber Knox, Agata Page, Saimir Luli, Jelena Mann* and Derek A Mann*. Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
    [Show full text]
  • COMPILATION of AMINO ACIDS, DRUGS, METABOLITES and OTHER COMPOUNDS in MASSTRAK AMINO ACID ANALYSIS SOLUTION Paula Hong, Kendon S
    COMPILATION OF AMINO ACIDS, DRUGS, METABOLITES AND OTHER COMPOUNDS IN MASSTRAK AMINO ACID ANALYSIS SOLUTION Paula Hong, Kendon S. Graham, Alexandre Paccou, T homas E. Wheat and Diane M. Diehl INTRODUCTION LC conditions Physiological amino acid analysis is commonly performed to LC System: Waters ACQUITY UPLC® System with TUV monitor and study a wide variety of metabolic processes. A wide Column: MassTrak AAA Column 2.1 x 150 mm, 1.7 µm variety of drugs, foods, and metabolic intermediates that may Column Temp: 43 ˚C be present in biological fluids can appear as peaks in amino Flow Rate: 400 µL/min. acid analysis, therefore, it is important to be able to identify Mobile Phase A: MassTrak AAA Eluent A Concentrate, unknown compounds.1,2,3 The reproducibility and robustness of diluted 1:10 the MassTrak Amino Acid Analysis Solution make this method well Mobile Phase B: MassTrak AAA Eluent B suited to such a study as well.4 Weak Needle Wash: 5/95 Acetonitrile/Water Strong Needle Wash: 95/5 Acetonitrile/Water Gradient: MassTrak AAA Standard Gradient (as provided in kit) Detection: UV @ 260 nm Injection Volume: 1 µL EXPERIMENTAL Injection Mode: Partial Loop with Needle Overfill (PLNO) Compound sample preparation A library of compounds was assembled. Each compound was derivatized individually and spiked into the MassTrak™ AAA Solution Standard prior to chromatographic analysis. The elution RESULTS AND DISCUSSION position of each tested compound could be related to known amino acids. A wide variety of antibiotics, pharmaceutical compounds and metabolite by-products are found in biological fluids. The reten- 1.
    [Show full text]
  • CHO/LY-B Cell Growth Under Limiting Sphingolipid Supply: Correlation Between Lipid Composition and Biophysical Properties of Sphingolipid- Restricted Cell Membranes+
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.05.188474; this version posted July 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 CHO/LY-B cell growth under limiting sphingolipid supply: correlation between lipid composition and biophysical properties of sphingolipid- restricted cell membranes+. Bingen G. Monasterio1,2, Noemi Jiménez-Rojo3, Aritz B. García-Arribas1,2, Howard 3 1,2 1,2 Riezman , Félix M. Goñi , Alicia Alonso* 1Instituto Biofisika (CSIC, UPV/EHU) and 2Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain; 3NCCR Chemical Biology, Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland. Short title: Sphingolipid-restricted cell membranes. +In memoriam M.J.O. Wakelam (1955-2020), colleague and friend. bioRxiv preprint doi: https://doi.org/10.1101/2020.07.05.188474; this version posted July 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 2 ABSTRACT Sphingolipids (SL) are ubiquitous in mammalian cell membranes, yet there is little data on the behavior of cells under SL-restriction conditions. LY-B cells derive from a CHO line in which serine palmitoyl transferase (SPT), thus de novo SL synthesis, is suppressed, while maintaining the capacity of taking up and metabolizing exogenous sphingoid bases from the culture medium.
    [Show full text]
  • Impacts of Dietary Exposure to Pesticides on Faecal Microbiome
    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.448511; this version posted June 17, 2021. 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 Impacts of dietary exposure to pesticides on faecal microbiome 2 metabolism in adult twins 3 4 Robin Mesnage1, Ruth C E Bowyer2, Souleiman El Balkhi3, Franck Saint-Marcoux3, Arnaud 5 Gardere3, Quinten Raymond Ducarmon4, Anoecim Robecca Geelen4, Romy Daniëlle Zwittink4, 6 Dimitris Tsoukalas5, Evangelia Sarandi5, Efstathia I. Paramera6, Timothy Spector2, Claire J Steves2, 7 Michael N Antoniou1* 8 9 1 Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, 10 Department of Medical and Molecular Genetics, Guy's Hospital, London, SE1 9RT, UK. 11 12 2 Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK 13 14 3 Service de pharmacologie, toxicologie et pharmacovigilance, UF Toxicologie analytique environnementale 15 et santé au travail, CHU de Limoges, Limoges, France 16 17 4 Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The 18 Netherlands 19 20 5 Metabolomic Medicine Clinic, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, 21 Greece 22 23 6 NEOLAB S.A., Medical laboratory, 125 Michalakopoulu Str., 11527 Athens, Greece 24 25 26 *Correspondence: [email protected] 27 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.448511; this version posted June 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • 23 Cerebral Organic Acid Disorders and Other Disorders of Lysine Catabolism
    23 Cerebral Organic Acid Disorders and Other Disorders of Lysine Catabolism Georg F. Hoffmann 23.1 Introduction – 295 23.2 Hyperlysinemia/Saccharopinuria – 295 23.2.1 Clinical Presentation – 295 23.2.2 Metabolic Derangement – 295 23.2.3 Genetics – 296 23.2.4 Diagnostic Tests – 296 23.2.5 Treatment and Prognosis – 296 23.3 Hydroxylysinuria – 296 23.4 2-Amino-/2-Oxo-Adipic Aciduria – 296 23.4.1 Clinical Presentation – 296 23.4.2 Metabolic Derangement – 296 23.4.3 Genetics – 296 23.4.4 Diagnostic Tests – 296 23.4.5 Treatment and Prognosis – 297 23.5 Glutaric Aciduria Type I (Glutaryl-CoA Dehydrogenase Deficiency) – 297 23.5.1 Clinical Presentation – 297 23.5.2 Metabolic Derangement – 297 23.5.3 Genetics – 300 23.5.4 Diagnostic Tests – 300 23.5.5 Treatment and Prognosis – 301 23.6 L-2-Hydroxyglutaric Aciduria – 302 23.6.1 Clinical Presentation – 302 23.6.2 Metabolic Derangement – 303 23.6.3 Genetics – 303 23.6.4 Diagnostic Tests – 303 23.6.5 Treatment and Prognosis – 303 23.7 D-2-Hydroxyglutaric Aciduria – 303 23.7.1 Clinical Presentation – 303 23.7.2 Metabolic Derangement – 303 23.7.3 Genetics – 303 23.7.4 Diagnostic Tests – 304 23.7.5 Treatment and Prognosis – 304 23.8 N-Acetylaspartic Aciduria (Canavan Disease) – 304 23.8.1 Clinical Presentation – 304 23.8.2 Metabolic Derangement – 304 23.8.3 Genetics – 304 23.8.4 Diagnostic Tests – 304 23.8.5 Treatment and Prognosis – 305 References – 305 294 Chapter 23 · Cerebral Organic Acid Disorders and Other Disorders of Lysine Catabolism Catabolism of Lysine, Hydroxylysine, and Tryptophan Lysine, hydroxylysine and tryptophan are degraded with- otide (FAD) and hence to the respiratory chain (.
    [Show full text]
  • SUPPLEMENTAL TABLE Supplementary Table 1: Candidate
    SUPPLEMENTAL TABLE Supplementary Table 1: Candidate Genes differentially expressed in prediabetic BBdp rats Transcript Non- Prediabetic Fold Change ANOVA p- FDR p- Gene Description Cluster ID Diabetic Bi-weight (linear) value value Symbol Bi-weight Avg Signal Prediabetic Avg Signal (log2) vs Non- (log2) Diabetic 17757188 9.27 6.2 -8.4 0.023371 0.722064 Fkbp5 FK506 binding protein 5 17789572 8.49 6.47 -4.06 0.039823 0.729215 Pdk4 pyruvate dehydrogenase kinase, isozyme 4 17852156 8.48 6.54 -3.84 0.078007 0.732342 Zbtb16 zinc finger and BTB domain containing 16 17641972 5.38 3.56 -3.54 0.014342 0.722064 Cyp2c22 cytochrome P450, family 2, subfamily c, polypeptide 22 17687609 6.72 5.38 -2.52 0.065371 0.732342 Atf3 activating transcription factor 3 17684906 7.82 6.56 -2.4 0.084143 0.736308 Rgs2 regulator of G-protein signaling 2 17731134 7.71 6.57 -2.2 0.018149 0.722064 Gnpat glyceronephosphate O-acyltransferase 17734470 6.57 5.44 -2.19 0.008916 0.722064 Fam89a family with sequence similarity 89, member A 17720472 8.27 7.22 -2.08 0.036483 0.72683 Klf6 Kruppel-like factor 6 17639774 7.68 6.65 -2.04 0.01928 0.722064 Cdc42ep2 CDC42 effector protein (Rho GTPase binding) 2; polymerase (DNA directed), alpha 2, accessory subunit 17744919 9.61 8.62 -1.99 0.037564 0.729215 Pik3r1 phosphoinositide-3- kinase, regulatory subunit 1 (alpha) 17700455 8.39 7.42 -1.96 0.05379 0.732342 Klf5 Kruppel-like factor 5 17697954 7.03 6.06 -1.95 0.026784 0.722064 Fbxo34 F-box protein 34 17678380 5.42 4.48 -1.93 0.02868 0.722064 Hrk harakiri, BCL2 interacting protein 17684316
    [Show full text]