A Semi-synthetic Regulon Enables Rapid Growth of Yeast on Xylose

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Mar 28

PMID 29581426

Citations 12

Authors

Venkatesh Endalur Gopinarayanan

Nikhil U Nair

Affiliations

Soon will be listed here.

Abstract

Nutrient assimilation is the first step that allows biological systems to proliferate and produce value-added products. Yet, implementation of heterologous catabolic pathways has so far relied on constitutive gene expression without consideration for global regulatory systems that may enhance nutrient assimilation and cell growth. In contrast, natural systems prefer nutrient-responsive gene regulation (called regulons) that control multiple cellular functions necessary for cell survival and growth. Here, in Saccharomyces cerevisiae, by partially- and fully uncoupling galactose (GAL)-responsive regulation and metabolism, we demonstrate the significant growth benefits conferred by the GAL regulon. Next, by adapting the various aspects of the GAL regulon for a non-native nutrient, xylose, we build a semi-synthetic regulon that exhibits higher growth rate, better nutrient consumption, and improved growth fitness compared to the traditional and ubiquitous constitutive expression strategy. This work provides an elegant paradigm to integrate non-native nutrient catabolism with native, global cellular responses to support fast growth.

Citing Articles

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References

Ho S, Jona G, Chen C, Johnston M, Snyder M . Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc Natl Acad Sci U S A. 2006; 103(26):9940-5. PMC: 1502558. DOI: 10.1073/pnas.0509185103. View

Teo W, Chang M . Bacterial XylRs and synthetic promoters function as genetically encoded xylose biosensors in Saccharomyces cerevisiae. Biotechnol J. 2014; 10(2):315-22. DOI: 10.1002/biot.201400159. View

Ren B, Robert F, Wyrick J, Aparicio O, Jennings E, Simon I . Genome-wide location and function of DNA binding proteins. Science. 2000; 290(5500):2306-9. DOI: 10.1126/science.290.5500.2306. View

Zhou H, Cheng J, Wang B, Fink G, Stephanopoulos G . Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng. 2012; 14(6):611-22. DOI: 10.1016/j.ymben.2012.07.011. View

Shao Z, Zhao H, Zhao H . DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res. 2008; 37(2):e16. PMC: 2632897. DOI: 10.1093/nar/gkn991. View

Jenkins V, Barton G, Robertson B, Williams K . Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis. BMC Genomics. 2013; 14:301. PMC: 3662644. DOI: 10.1186/1471-2164-14-301. View

Skjoedt M, Snoek T, Kildegaard K, Arsovska D, Eichenberger M, Goedecke T . Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast. Nat Chem Biol. 2016; 12(11):951-958. DOI: 10.1038/nchembio.2177. View

Ravcheev D, Gelfand M, Mironov A, Rakhmaninova A . [Purine regulon of gamma-proteobacteria: a detailed description]. Genetika. 2002; 38(9):1203-14. View

Kren A, Mamnun Y, Bauer B, Schuller C, Wolfger H, Hatzixanthis K . War1p, a novel transcription factor controlling weak acid stress response in yeast. Mol Cell Biol. 2003; 23(5):1775-85. PMC: 151711. DOI: 10.1128/MCB.23.5.1775-1785.2003. View

10.

den Haan R, van Rensburg E, Rose S, Gorgens J, van Zyl W . Progress and challenges in the engineering of non-cellulolytic microorganisms for consolidated bioprocessing. Curr Opin Biotechnol. 2014; 33:32-8. DOI: 10.1016/j.copbio.2014.10.003. View

11.

Venturelli O, El-Samad H, Murray R . Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response. Proc Natl Acad Sci U S A. 2012; 109(48):E3324-33. PMC: 3511703. DOI: 10.1073/pnas.1211902109. View

12.

Jin Y, Alper H, Yang Y, Stephanopoulos G . Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl Environ Microbiol. 2005; 71(12):8249-56. PMC: 1317456. DOI: 10.1128/AEM.71.12.8249-8256.2005. View

13.

Lewis J, Gasch A . Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor. G3 (Bethesda). 2013; 2(12):1607-12. PMC: 3516482. DOI: 10.1534/g3.112.004127. View

14.

Loll-Krippleber R, Brown G . P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance. Nat Commun. 2017; 8(1):558. PMC: 5601920. DOI: 10.1038/s41467-017-00632-2. View

15.

Santos-Beneit F . The Pho regulon: a huge regulatory network in bacteria. Front Microbiol. 2015; 6:402. PMC: 4415409. DOI: 10.3389/fmicb.2015.00402. View

16.

Kotter P, Amore R, Hollenberg C, Ciriacy M . Isolation and characterization of the Pichia stipitis xylitol dehydrogenase gene, XYL2, and construction of a xylose-utilizing Saccharomyces cerevisiae transformant. Curr Genet. 1990; 18(6):493-500. DOI: 10.1007/BF00327019. View

17.

Rutzler M, Reissaus A, Budzowska M, Bandlow W . SUT2 is a novel multicopy suppressor of low activity of the cAMP/protein kinase A pathway in yeast. Eur J Biochem. 2004; 271(7):1284-91. DOI: 10.1111/j.1432-1033.2004.04034.x. View

18.

Gardonyi M, Jeppsson M, Liden G, Gorwa-Grauslund M, Hahn-Hagerdal B . Control of xylose consumption by xylose transport in recombinant Saccharomyces cerevisiae. Biotechnol Bioeng. 2003; 82(7):818-24. DOI: 10.1002/bit.10631. View

19.

Bernard A, Jin M, Gonzalez-Rodriguez P, Fullgrabe J, Delorme-Axford E, Backues S . Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy. Curr Biol. 2015; 25(5):546-55. PMC: 4348152. DOI: 10.1016/j.cub.2014.12.049. View

20.

Schwank S, Ebbert R, Rautenstrauss K, Schweizer E, Schuller H . Yeast transcriptional activator INO2 interacts as an Ino2p/Ino4p basic helix-loop-helix heteromeric complex with the inositol/choline-responsive element necessary for expression of phospholipid biosynthetic genes in Saccharomyces cerevisiae. Nucleic Acids Res. 1995; 23(2):230-7. PMC: 306659. DOI: 10.1093/nar/23.2.230. View