Developing Synthetic Methylotrophs by Metabolic Engineering-Guided Adaptive Laboratory Evolution

Overview

Journal Adv Biochem Eng Biotechnol

Specialties Biochemistry
Biotechnology

Date 2022 Feb 27

PMID 35220456

Authors

Yu Wang

Ping Zheng

Jibin Sun

Affiliations

Soon will be listed here.

Abstract

Methanol is a promising alternative feedstock for biomanufacturing. However, natural platform industrial microorganisms such as Escherichia coli and Corynebacterium glutamicum cannot assimilate methanol. Although some methanol assimilation pathways differ from the typical sugar metabolism by only a few enzymes, engineering platform microorganisms to efficiently utilize methanol is very challenging. Recent advances in creating the first methylotrophic E. coli growing solely on methanol have underscored the value of metabolic engineering-guided adaptive laboratory evolution (ME-ALE) in developing non-natural methanol utilizers. This chapter reviews the recent progress in engineering platform microorganisms to utilize methanol by ME-ALE and discusses the future challenges in developing superior synthetic methylotrophs for methanol-based biomanufacturing.

References

Cotton C, Claassens N, Benito-Vaquerizo S, Bar-Even A . Renewable methanol and formate as microbial feedstocks. Curr Opin Biotechnol. 2019; 62:168-180. DOI: 10.1016/j.copbio.2019.10.002. View

Wang Y, Fan L, Tuyishime P, Zheng P, Sun J . Synthetic Methylotrophy: A Practical Solution for Methanol-Based Biomanufacturing. Trends Biotechnol. 2020; 38(6):650-666. DOI: 10.1016/j.tibtech.2019.12.013. View

Muller J, Heggeset T, Wendisch V, Vorholt J, Brautaset T . Methylotrophy in the thermophilic Bacillus methanolicus, basic insights and application for commodity production from methanol. Appl Microbiol Biotechnol. 2014; 99(2):535-51. DOI: 10.1007/s00253-014-6224-3. View

Ochsner A, Sonntag F, Buchhaupt M, Schrader J, Vorholt J . Methylobacterium extorquens: methylotrophy and biotechnological applications. Appl Microbiol Biotechnol. 2014; 99(2):517-34. DOI: 10.1007/s00253-014-6240-3. View

Haynes C, Gonzalez R . Rethinking biological activation of methane and conversion to liquid fuels. Nat Chem Biol. 2014; 10(5):331-9. DOI: 10.1038/nchembio.1509. View

Whitaker W, Sandoval N, Bennett R, Fast A, Papoutsakis E . Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization. Curr Opin Biotechnol. 2015; 33:165-75. DOI: 10.1016/j.copbio.2015.01.007. View

Bogorad I, Chen C, Theisen M, Wu T, Schlenz A, Lam A . Building carbon-carbon bonds using a biocatalytic methanol condensation cycle. Proc Natl Acad Sci U S A. 2014; 111(45):15928-33. PMC: 4234558. DOI: 10.1073/pnas.1413470111. View

Siegel J, Smith A, Poust S, Wargacki A, Bar-Even A, Louw C . Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci U S A. 2015; 112(12):3704-9. PMC: 4378393. DOI: 10.1073/pnas.1500545112. View

Yu H, Liao J . A modified serine cycle in Escherichia coli coverts methanol and CO to two-carbon compounds. Nat Commun. 2018; 9(1):3992. PMC: 6162302. DOI: 10.1038/s41467-018-06496-4. View

10.

Lu X, Liu Y, Yang Y, Wang S, Wang Q, Wang X . Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design. Nat Commun. 2019; 10(1):1378. PMC: 6435721. DOI: 10.1038/s41467-019-09095-z. View

11.

Chou A, Clomburg J, Qian S, Gonzalez R . 2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion. Nat Chem Biol. 2019; 15(9):900-906. DOI: 10.1038/s41589-019-0328-0. View

12.

Yang X, Yuan Q, Luo H, Li F, Mao Y, Zhao X . Systematic design and in vitro validation of novel one-carbon assimilation pathways. Metab Eng. 2019; 56:142-153. DOI: 10.1016/j.ymben.2019.09.001. View

13.

Wang C, Ren J, Zhou L, Li Z, Chen L, Zeng A . An Aldolase-Catalyzed New Metabolic Pathway for the Assimilation of Formaldehyde and Methanol To Synthesize 2-Keto-4-hydroxybutyrate and 1,3-Propanediol in . ACS Synth Biol. 2019; 8(11):2483-2493. DOI: 10.1021/acssynbio.9b00102. View

14.

He H, Hoper R, Dodenhoft M, Marliere P, Bar-Even A . An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli. Metab Eng. 2020; 60:1-13. DOI: 10.1016/j.ymben.2020.03.002. View

15.

Kim S, Lindner S, Aslan S, Yishai O, Wenk S, Schann K . Growth of E. coli on formate and methanol via the reductive glycine pathway. Nat Chem Biol. 2020; 16(5):538-545. DOI: 10.1038/s41589-020-0473-5. View

16.

Lessmeier L, Pfeifenschneider J, Carnicer M, Heux S, Portais J, Wendisch V . Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate. Appl Microbiol Biotechnol. 2015; 99(23):10163-76. DOI: 10.1007/s00253-015-6906-5. View

17.

Muller J, Meyer F, Litsanov B, Kiefer P, Potthoff E, Heux S . Engineering Escherichia coli for methanol conversion. Metab Eng. 2015; 28:190-201. DOI: 10.1016/j.ymben.2014.12.008. View

18.

Witthoff S, Schmitz K, Niedenfuhr S, Noh K, Noack S, Bott M . Metabolic engineering of Corynebacterium glutamicum for methanol metabolism. Appl Environ Microbiol. 2015; 81(6):2215-25. PMC: 4345391. DOI: 10.1128/AEM.03110-14. View

19.

Zhang W, Zhang T, Song M, Dai Z, Zhang S, Xin F . Metabolic Engineering of Escherichia coli for High Yield Production of Succinic Acid Driven by Methanol. ACS Synth Biol. 2018; 7(12):2803-2811. DOI: 10.1021/acssynbio.8b00109. View

20.

Wang X, Wang X, Lu X, Ma C, Chen K, Ouyang P . Methanol fermentation increases the production of NAD(P)H-dependent chemicals in synthetic methylotrophic . Biotechnol Biofuels. 2019; 12:17. PMC: 6340170. DOI: 10.1186/s13068-019-1356-4. View