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Genetically Encoded Biosensors for Branched-Chain Amino Acid Metabolism to Monitor

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Genetically Encoded Biosensors for Branched-Chain Amino Acid Metabolism to Monitor bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982801; this version posted March 10, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-ND 4.0 International license. 1 Genetically encoded biosensors for branched-chain amino acid metabolism to monitor 2 mitochondrial and cytosolic production of isobutanol and isopentanol in yeast 3 Yanfei Zhang 1, Sarah K. Hammer 1, Cesar Carrasco-Lopez 1, Sergio A. Garcia Echauri 1, and José 4 L. Avalos * 1, 2, 3 5 6 1 Department of Chemical and Biological Engineering; 2 Andlinger Center for Energy and the 7 Environment; 3 Department of Molecular Biology, Princeton University, Princeton, NJ 8 9 10 11 12 *Corresponding author: José L. Avalos 13 Department of Chemical and Biological Engineering, 14 Princeton University, 15 101 Hoyt Laboratory, William Street, Princeton, NJ 08544, USA 16 Phone office: +1 (609) 258-9881 17 Phone lab: +1 (609) 258-0542 18 Fax: +1 (609) 258-1247 19 Email: [email protected] 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982801; this version posted March 10, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-ND 4.0 International license. 22 Abstract 23 Branched-chain amino acid (BCAA) metabolism can be harnessed to produce many valuable 24 chemicals. Among these, isobutanol, which is derived from valine degradation, has received 25 substantial attention due to its promise as an advanced biofuel. While Saccharomyces cerevisiae is 26 the preferred organism for isobutanol production, the lack of isobutanol biosensors in this organism 27 has limited the ability to screen strains at high throughput. Here, we use a transcriptional regulator of 28 BCAA biosynthesis, Leu3p, to develop the first genetically encoded biosensor for isobutanol 29 production in yeast. Small modifications allowed us to redeploy Leu3p in a second biosensor for 30 isopentanol, another BCAA-derived product of interest. Each biosensor is highly specific to 31 isobutanol or isopentanol, respectively, and was used to engineer metabolic enzymes to increase titers. 32 The isobutanol biosensor was additionally employed to isolate high-producing strains, and guide the 33 construction and enhancement of mitochondrial and cytosolic isobutanol biosynthetic pathways, 34 including in combination with optogenetic actuators to enhance metabolic flux. These biosensors 35 promise to accelerate the development of enzymes and strains for branched-chain higher alcohol 36 production, and offer a blueprint to develop biosensors for other products derived from BCAA 37 metabolism. 38 39 Key Words: Branched-chain amino acid metabolism biosensor, LEU3, isobutanol biosensor, 40 isopentanol biosensor, metabolic engineering, high-throughput screen, enzyme engineering, 41 mitochondrial and cytosolic isobutanol pathways 42 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982801; this version posted March 10, 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-ND 4.0 International license. 43 Introduction 44 The metabolism of branched chain amino acids (BCAAs), including valine, leucine, and 45 isoleucine, has been the subject of countless fundamental and applied studies1-8, and is central to the 46 biosynthesis of many valuable products9-16. Among these products, branched-chain higher alcohols 47 (BCHAs) including isobutanol, isopentanol, and 2-methyl-1-butanol are promising alternatives to the 48 first-generation biofuel, ethanol. These alcohols exhibit superior fuel properties to ethanol, such as 49 higher energy density, as well as lower vapor pressure and water solubility, which result in better 50 compatibility with existing gasoline engines and distribution infrastructure14. The Co-Optimization 51 of Fuels & Engines (Co-Optima) initiative sponsored by the United States Department of Energy 52 (DOE) evaluated more than 400 compounds for their potential to enhance engine efficiency, and 53 found isobutanol and blends of the three BCHAs to be in the top ten performers for boosted spark- 54 ignition engines17,18. Furthermore, BCHAs can be upgraded to jet fuels19, offering a source of 55 renewable energy for air transportation. Co-Optima’s identification of these BCHAs as valuable 56 renewable fuel compounds validates previous work to engineer microbes for the production of 57 BCHAs, and encourages future work to this end. 58 The yeast Saccharomyces cerevisiae is a favored industrial host due to its resistance to phage 59 contamination, ability to grow at low pH, and genetic tractability20. For BCHA production in 60 particular, S. cerevisiae benefits from higher tolerance to alcohols than many bacteria21. In addition, 61 BCHAs are naturally produced in S. cerevisiae as products of BCAA degradation. Accordingly, 62 metabolic pathways for BCHA production have been engineered by rewiring BCAA biosynthesis and 63 the Ehrlich degradation pathway (Supplementary Figure 1). The upstream BCAA biosynthetic 64 pathway is comprised of three mitochondrially localized enzymes: acetolactate synthase (ALS, 65 encoded by ILV2), ketol-acid reductoisomerase (KARI, encoded by ILV5), and dehydroxyacid 66 dehydratase (DHAD, encoded by ILV3)22. Ilv2p, Ilv3p, and Ilv5p convert pyruvate to the valine 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982801; this version posted March 10, 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-ND 4.0 International license. 67 precursor a-ketoisovalerate (a-KIV), which can be exported to the cytosol and converted to 68 isobutanol via the downstream BCAA Ehrlich degradation pathway23, comprised of a-ketoacid 69 decarboxylases (a-KDCs) and alcohol dehydrogenases (ADHs). Alternatively, a-KIV can be 70 converted to α-ketoisocaproate (a-KIC) by sequential reactions carried out by a-isopropylmalate 71 synthase (encoded by LEU4 and LEU9), isopropylmalate isomerase (encoded by LEU1), and 3- 72 isopropylmalate dehydrogenase (encoded by LEU2). The LEU4 gene produces two forms of α- 73 isopropylmalate synthase – a short form located in the cytosol, and a long form localized in 74 mitochondria along with Leu9p22. The same Ehrlich degradation pathway converts a-KIC to 75 isopentanol in the cytosol23. The fragmentation of BCHA biosynthesis between the mitochondria and 76 cytosol presents an intracellular transport bottleneck, which has been addressed by 77 compartmentalizing the downstream enzymes in mitochondria24-28 or re-locating the upstream 78 enzymes in the cytosol29-34. 79 The rate at which researchers can introduce diversity into engineered strains greatly outpaces 80 the rate at which strains can be tested for chemical production phenotypes. This challenge can be 81 alleviated by the development of genetically encoded biosensors, which with sufficient sensitivity, 82 specificity, and dynamic range, can enable high throughput screens or selections to identify variants 83 with enhanced chemical productivity35-40. While a general alcohol biosensor that responds to 84 isobutanol has been reported in E.coli41,42, no biosensors for BCHAs have been reported in S. 85 cerevisiae, which has prevented the development of high-throughput analysis of the production of 86 this important class of biofuels in the preferred industrial host. 87 Many biosensors are based on transcription factors (TF) that activate expression of a reporter 88 gene (such as a fluorescent protein) in response to elevated concentrations of a specific molecule, 89 which may be the product of interest or a precursor8,37,38,43,44. Measuring levels of an intermediate 90 intracellular metabolite, as opposed to a secreted product42, is advantageous because it allows the 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982801; this version posted March 10, 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-ND 4.0 International license. 91 biosensor to capture the desired chemical production occurring in each individual cell rather than the 92 extracellular product concentration, which reflects the average production of all cells in the 93 fermentation. In S. cerevisiae, Leu3p, a dual-function TF, regulates several genes involved in BCAA 94 biosynthesis45 (Supplementary Figure 1). Leu3p responds selectively to a-isopropylmalate (a-IPM), 95 acting as a transcriptional activator in the presence of α-IPM and a transcriptional repressor in its 96 absence. Because α-IPM is a byproduct of valine biosynthesis and an intermediate in leucine 97 biosynthesis, its levels are correlated to the metabolic fluxes through both of these pathways and thus 98 isobutanol and isopentanol production. This makes Leu3p an attractive TF with which to engineering 99 a biosensor for BCHA biosynthesis in S. cerevisiae. 100 Here, we report the development and application of the first genetically encoded biosensors 101 for
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