Application of proteomics and metabolomics in microbial metabolic engineering

doi:10.3724/SP.J.1123.2019.04026

Abstract

Abstract: Construction of microbial cell factories is a feasible strategy for the sustainable production of chemicals, biofuels, and pharmaceutical molecules. However, the complex metabolism and rigid regulation of microbes hinders the efficient synthesis of the products of interest. Proteomics and metabolomics analyze enzymes and metabolites in terms of systems biology, thus unraveling complex biological systems and providing significant clues for microbial metabolic engineering. Here, the applications of proteomics and metabolomics in microbial metabolic engineering were reviewed, including the construction of genome-scale metabolic models, optimization of microbial product synthesis, guidance of microbial stress tolerance engineering, and prediction of rate-limiting steps. In addition, proteomics and metabolomics could be employed to explore secondary metabolic pathways in plants, to reveal novel genes or pathways for microbial synthesis of natural products. Finally, the development of bio-big data was discussed.

Key words: genome-scale metabolic model, metabolomics, microbial metabolic engineering, plant secondary metabolism, proteomics, review

CLC Number:

O658

YU Wei, GAO Jiaoqi, ZHOU Yongjin. Application of proteomics and metabolomics in microbial metabolic engineering[J]. Chinese Journal of Chromatography, 2019, 37(8): 798-805.

References

[1] Zhao M, Huang D, Zhang X, et al. Metab Eng, 2018, 47:254

[2] Gu Y, Lv X, Liu Y, et al. Metab Eng, 2019, 51:59

[3] Zhou Y J, Buijs N A, Zhu Z, et al. Nat Commun, 2016, 7:11709

[4] Luo X, Reiter M A, d'Espaux L, et al. Nature, 2019, 567(7746):123

[5] Nielsen J, Keasling J D. Cell, 2016, 164(6):1185

[6] Yin W, Fu X, Li P. Biotechnology Bulletin, 2014(1):33尹稳, 伏旭, 李平. 生物技术通报, 2014(1):33
[7] Zhang W L. Continuing Medical Education, 2014, 28(1):54张文亮. 继续医学教育, 2014, 28(1):54
[8] Durot M, Bourguignon P Y, Schachter V. FEMS Microbiol Rev, 2009, 33(1):164

[9] Alonso-Gutierrez J, Kim E M, Batth T S, et al. Metab Eng, 2015, 28:123

[10] Gold N D, Gowen C M, Lussier F X, et al. Microb Cell Fact, 2015, 14:73

[11] Hasunuma T, Sanda T, Yamada R, et al. Microb Cell Fact, 2011, 10:1

[12] Noguchi S, Putri S P, Lan E I, et al. Metabolomics, 2016, 12:26

[13] Yang D, Du X, Yang Z, et al. Engineering in Life Sciences, 2014, 14(5):456

[14] Orth J D, Conrad T M, Na J, et al. Mol Syst Biol, 2011, 7:535
[15] Liu X M, Liu Z Y, Zhang Y F. Genomics and Applied Biology, 2016, 35(3):635刘秀梅, 刘占英, 张永峰. 基因组学与应用生物学, 2016, 35(3):635
[16] Xu N, Liu L, Zou W, et al. Mol Biosyst, 2013, 9(2):205

[17] Cereghino J L, Cregg J M. FEMS Microbiol Rev, 2000, 24:45

[18] Ye R, Huang M, Lu H, et al. Bioresour Bioprocess, 2017, 4(1):22

[19] Beopoulos A, Cescut J, Haddouche R, et al. Prog Lipid Res, 2009, 48(6):375

[20] Pan P, Hua Q. PLoS One, 2012, 7(12):e51535
[21] Peralta-Yahya P P, Ouellet M, Chan R, et al. Nat Commun, 2011, 2:483

[22] Redding-Johanson A M, Batth T S, Chan R, et al. Metab Eng, 2011, 13(2):194

[23] Hahn-Hagerdal B, Galbe M, Gorwa-Grauslund M F, et al. Trends Biotechnol, 2006, 24(12):549

[24] Gong Z W, Nielsen J, Zhou Y J. Biotechnol J, 2017, 12(10):1700014

[25] Alper H, Moxley J, Nevoigt E, et al. Science, 2006, 314(8):1565
[26] Teoh S T, Putri S, Mukai Y, et al. Biotechnol Biofuels, 2015, 8:144

[27] Ohta E, Nakayama Y, Mukai Y, et al. J Biosci Bioeng, 2016, 121(4):399

[28] Zhu Y, Pei G, Niu X, et al. Mol Biosyst, 2015, 11(3):770

[29] Wang Y F, Tian J, Ji Z H, et al. Int J Biochem Cell Biol, 2016, 78:297

[30] Niu X, Zhu Y, Pei G, et al. Appl Microbiol Biotechnol, 2015, 99(4):1845

[31] Wang J, Chen L, Tian X, et al. J Proteome Res, 2013, 12(11):5302

[32] Mao S M, Luo Y M, Zhang T R, et al. J Proteome Res, 2010, 9:3046

[33] Jia K, Zhang Y, Li Y. PLoS One, 2012, 7(6):e38815
[34] Qiao J, Wang J, Chen L, et al. J Proteome Res, 2012, 11(11):5286

[35] Song Z, Chen L, Wang J, et al. Mol Cell Proteomics, 2014, 13(12):3519

[36] Liu Y, Liu L, Shin H D, et al. Metab Eng, 2013, 19:107

[37] Tamakawa H, Tomita Y, Yokoyama A, et al. Biosci Biotechnol Biochem, 2013, 77(7):1441

[38] Hasunuma T, Matsuda M, Kondo A. Metab Eng Commun, 2016, 3:130

[39] Ro D K, Paradise E M, Ouellet M, et al. Nature, 2006, 440(7086):940

[40] Decker G, Wanner G, Zenk M H, et al. Electrophoresis, 2000, 21:3500

[41] Lei Z T, Elmer A M, Watson B S, et al. Mol Cell Proteomics, 2005, 4(11):1812

[42] Raamsdonk L M, Teusink B, Broadhurst D, et al. Nat Biotechnol, 2001, 19(1):45

[43] Hirai M Y, Klein M, Fujikawa Y, et al. J Biol Chem, 2005, 280(27):25590

[44] Rohmer M. Nat Prod Rep, 1999, 16:565

[45] Farag M A, Huhman D V, Dixon R A, et al. Plant Physiol, 2008, 146(2):387

[46] Keurentjes J J, Fu J, de Vos C H, et al. Nat Genet, 2006, 38(7):842