Research Progress of Methanol Utilization and Bioconversion

doi:10.13523/j.cb.2006048

China Biotechnology

2020, Vol. 40

Issue (10): 65-75 DOI: 10.13523/j.cb.2006048

Research Progress of Methanol Utilization and Bioconversion

SUN Qing^1,²,LIU De-hua^1,²,CHEN Zhen^1,^2,^**(

)

1 Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering,Tsinghua University, Beijing 100084, China
2 Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China

Download:

HTML

PDF(22063KB) HTML
Export: BibTeX | EndNote (RIS)

Abstract

Methanol is an abundant raw material with low price and high reduction degree, which is expected to be a promising feedstock for the next generation biomanufacturing. To convert methanol into value-added chemicals, constructing recombinant microorganisms using synthetic biology has received broad attention in recent years. However, due to the complex regulation of methanol metabolism, the current engineered synthetic methylotrophy still cannot use methanol as the sole carbon source for growth and chemical production. Based on the analysis of methanol metabolic mechanism in natural methylotrophy, this review summarized the main challenges for designing and constructing synthetic methylotrophy and proposed potential strategies to overcome these barriers. Especially, it focused on the following aspects, including: screening and engineering methanol dehydrogenase; optimizing and balancing formaldehyde assimilation pathways; bioconversion of methanol to chemicals.

Key words： Methanol Methylotrophy Methanol dehydrogenase Formaldehyde assimilation Bioconversion Synthetic biology

Received: 24 June 2020 Published: 10 November 2020

ZTFLH:

Q819

Corresponding Authors: Zhen CHEN E-mail: zhenchen2013@mail.tsinghua.edu.cn

	Service
	E-mail this article
	Add to my bookshelf
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	Qing SUN
	De-hua LIU
	Zhen CHEN

Cite this article:

SUN Qing,LIU De-hua,CHEN Zhen. Research Progress of Methanol Utilization and Bioconversion. China Biotechnology, 2020, 40(10): 65-75.

URL:

https://manu60.magtech.com.cn/biotech/10.13523/j.cb.2006048 OR https://manu60.magtech.com.cn/biotech/Y2020/V40/I10/65

Table 1 Classification and comparison of MDH

Fig.1 Outline of the formaldehyde assimilation metabolism (a) RuMP pathway (b) XuMP pathway (c) The serine cycle. Enzymes: MDH, methanol dehydrogenase; RPI, ribose-5-phosphate isomerase; HPS, 3-hexulose-6-phosphate synthase; PHI, 6-phospho-3-hexuloisomerase; RPE, ribulose-phosphate 3-epimerase; TKT, transketolase; TA, transaldolase; SPBase, sedoheptulose 1,7-bisphosphatase; PFK, 6-phosphofructokinase; FBA, fructose-bisphosphate aldolase/sedoheptulose-bisphosphate aldolase; FDH, formate dehydrogenase; AOD, methanol oxidase; CTA, catalase; DAS, dihydroxyacetone synthase; DAK, Dihydroxyacetone kinase; FBP, fructose bisphosphatase; SHMT, serine hydroxymethyltransferase; SGA, serine glyoxylate aminotransferase; HPR, hydroxypyruvate reductase; GLK, glycerate kinase; ENO, enolase; PPC, phosphoenolpyruvate carboxylase; MDH, malate dehydrogenase; MTKAB, malate thiokinase; MCL, malyl-CoA lyase. Metabolites: GSH, glutathione; MySH, mycothiol; H₄F, tetrahydrofolate; H₄MPT, tetrahydromethanopterin; Xu5P, xylulose-5-phosphate; GAP, glyceraldehyde phosphate; DHA, dihydroxyacetone; DHAP, dihydroxyacetone phosphate; FBP, fructose-1,6-bisphosphate; F6P, fructose-6phosphate; GLY, glycine; SER, serine; HPA, hydroxypruvate; GA, glycerate; PGA, 2-phosphate-glycerate; PEP, phosphoenolpyruvate; OAA, oxaloacetate; GLO, glyoxylate

Table 2 Classification and comparison of MDH

Table 3 Applications by native and synthetic methylotrophs using Methanol as carbon source


[1]	Du X L, Jiang Z, Su D S, et al. Research progress on the indirect hydrogenation of carbon dioxide to methanol. ChemSusChem, 2016,9(4):322-332. doi: 10.1002/cssc.201501013 pmid: 26692565

[2]	Schendel F J, Bremmon C E, Flickinger M C, et al. L-lysine production at 50 degrees C by mutants of a newly isolated and characterized methylotrophic Bacillus sp. Applied and Environmental Microbiology, 1990,56(4):963-970. doi: 10.1128/AEM.56.4.963-970.1990 pmid: 2111119

[3]	Zhang W, Zhang T, Wu S, et al. Guidance for engineering of synthetic methylotrophy based on methanol metabolism in methylotrophy. RSC Advances, 2017,7(7):4083-4091.

[4]	Whitaker W B, Sandoval N R, Bennett R K, et al. Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization. Current Opinion in Biotechnology, 2015,33:165-175. doi: 10.1016/j.copbio.2015.01.007 pmid: 25796071

[5]	Antoniewicz M R. Synthetic methylotrophy: strategies to assimilate methanol for growth and chemicals production. Current Opinion in Biotechnology, 2019,59:165-174. doi: 10.1016/j.copbio.2019.07.001 pmid: 31437746

[6]	Krog A, Heggeset T M, Müller J E, et al. Methylotrophic Bacillus methanolicus encodes two chromosomal and one plasmid born NAD+ dependent methanol dehydrogenase paralogs with different catalytic and biochemical properties. PLoS One, 2013,8(3):e59188. doi: 10.1371/journal.pone.0059188 pmid: 23527128

[7]	Anthony C, Williams P A. The structure and mechanism of methanol dehydrogenase. Biochimica et Biophysica Acta, 2003,1647(1):18-23.

[8]	Zhang M, Lidstrom M E. Promoters and transcripts for genes involved in methanol oxidation in Methylobacterium extorquens AM1. Microbiology, 2003,149(4):1033-1040. doi: 10.1099/mic.0.26105-0

[9]	Bennett R K, Steinberg L M, Chen W. et al. Engineering the bioconversion of methane and methanol to fuels and chemicals in native and synthetic methylotrophs. Current Opinion in Biotechnology, 2018,50:81-93. doi: 10.1016/j.copbio.2017.11.010 pmid: 29216497

[10]	Limtong S, Srisuk N, Yongmanitchai W, et al. Ogataea chonburiensis sp. nov. and Ogataea nakhonphanomensis sp. nov., thermotolerant, methylotrophic yeast species isolated in Thailand, and transfer of Pichia siamensis and Pichia thermomethanolica to the genus Ogataea. International Journal of Systematic and Evolutionary Microbiology, 2008,58(1):302-307.

[11]	Sheehan M C, Bailey C J, Dowds B C, et al. A new alcohol dehydrogenase, reactive towards methanol, from Bacillus stearothermophilus. Biochemical Journal, 1988,252(3):661-666. doi: 10.1042/bj2520661 pmid: 3421916

[12]	Kalyuzhnaya M G, Hristova K R, Lidstrom M E, et al. Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. Journal of Bacteriology, 2008,190(11):3817-3823. doi: 10.1128/JB.00180-08 pmid: 18390659

[13]	Zhu T, Zhao T, Bankefa O E, et al. Engineering unnatural methylotrophic cell factories for methanol-based biomanufacturing: challenges and opportunities. Biotechnology Advances, 2020,39:107467. doi: 10.1016/j.biotechadv.2019.107467 pmid: 31697995

[14]	Müller J E N, Litsanov B, Bortfeld-Miller M, et al. Proteomic analysis of the thermophilic methylotroph Bacillus methanolicus MGA3. Proteomics, 2014,14(6):725-737. doi: 10.1002/pmic.201300515 pmid: 24452867

[15]	Schrader J, Schilling M, Holtmann D, et al. Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends in Biotechnology, 2009,27(2):107-115. doi: 10.1016/j.tibtech.2008.10.009 pmid: 19111927

[16]	Kato N, Yurimoto H & Thauer R K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Bioscience, Biotechnology, and Biochemistry, 2006,70(1):10-21. doi: 10.1271/bbb.70.10 pmid: 16428816

[17]	Brautaset T, Jakobsen Ø M, Flickinger M C, et al. Plasmid-dependent methylotrophy in thermotolerant Bacillus methanolicus. Journal of Bacteriology, 2004,186(5):1229-1238. doi: 10.1128/jb.186.5.1229-1238.2004 pmid: 14973041

[18]	Ochsner A M, Sonntag F, Buchhaupt M, et al. Methylobacterium extorquens: methylotrophy and biotechnological applications. Applied Microbiology and Biotechnology, 2015,99(2):517-534. doi: 10.1007/s00253-014-6240-3 pmid: 25432674

[19]	Crowther G J, Kosály G & Lidstrom M E. Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. Journal of Bacteriology, 2008,190(14):5057-5062. doi: 10.1128/JB.00228-08 pmid: 18502865

[20]	Smejkalová H, Erb T J & Fuchs G, et al. Methanol assimilation in Methylobacterium extorquens AM1: demonstration of all enzymes and their regulation. PLoS One, 2010,5(10):e13001. doi: 10.1371/journal.pone.0013001 pmid: 20957036

[21]	Brautaset T, Williams M D, Dillingham R D, et al. Role of the Bacillus methanolicus citrate synthase II gene, citY, in regulating the secretion of glutamate in L-lysine-secreting mutants. Applied and Environmental Microbiology, 2003,69:3986-3995. doi: 10.1128/aem.69.7.3986-3995.2003 pmid: 12839772

[22]	Brautaset T, Jakobsen O M, Degnes K F, et al. Bacillus methanolicus pyruvate carboxylase and homoserine dehydrogenase I and II and their roles for L-lysine production from methanol at 50 degrees C. Appl. Microbiol. Biotechnol., 2010,87:951-964. doi: 10.1007/s00253-010-2559-6 pmid: 20372887

[23]	Withers S T, Gottlieb S S, Lieu B, et al. Identification of isopentenol biosynthetic genes from Bacillus subtilis by a screening method based on isoprenoid precursor toxicity. Applied and Environmental Microbiology, 2007,73(19):6277-6283. doi: 10.1128/AEM.00861-07 pmid: 17693564

[24]	Müller J E N, Meyer F, Litsanov B, et al. Engineering Escherichia coli for methanol conversion. Metabolic Engineering, 2015,28:190-201. doi: 10.1016/j.ymben.2014.12.008 pmid: 25596507

[25]	Whitaker W B, Jones J A, Bennett R K, et al. Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli. Metabolic Engineering, 2017,39:49-59. doi: 10.1016/j.ymben.2016.10.015 pmid: 27815193

[26]	Witthoff S, Muhlroth A, Marienhagen J, et al. C1 metabolism in Corynebacterium glutamicum an endogenous pathway for oxidation of methanol to carbon dioxide. Applied and Environmental Microbiology, 2013,79(22):6974-6983. doi: 10.1128/AEM.02705-13 pmid: 24014532

[27]	Wu T Y, Chen C T, Liu J T J. et al. Characterization and evolution of an activator-independent methanol dehydrogenase from Cupriavidus necator N-1. Applied Microbiology and Biotechnology, 2016,100(11):4969-4983. doi: 10.1007/s00253-016-7320-3 pmid: 26846745

[28]	Roth T B, Woolston B M, Stephanopoulos G, et al. Phage-assisted evolution of Bacillus methanolicus methanol dehydrogenase 2. ACS Synthetic Biology, 2019,8(4):796-806. doi: 10.1021/acssynbio.8b00481 pmid: 30856338

[29]	Couderc R & Baratti J. Oxidation of methanol by the Yeast, Pichia pastoris. Purification and properties of the alcohol oxidase. Agricultural and Biological Chemistry, 1980,44(10):2279-2289.

[30]	Price J V, Chen L, Whitaker W B, et al. Scaffoldless engineered enzyme assembly for enhanced methanol utilization. Proceedings of the National Academy of Sciences, 2016,113(45):12691-12696.

[31]	Woolston B M, King J R, Reiter M, et al. Improving formaldehyde consumption drives methanol assimilation in engineered E. coli. Nature Communications, 2018,9(1):2387. doi: 10.1038/s41467-018-04795-4 pmid: 29921903

[32]	Chen C T, Chen F Y, Bogorad I W, et al. Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production. Metabolic Engineering, 2018,49:257-266. doi: 10.1016/j.ymben.2018.08.010 pmid: 30172686

[33]	Meyer F, Keller P, Hartl J, et al. Methanol-essential growth of Escherichia coli. Nature Communications, 2018,9(1):1508. doi: 10.1038/s41467-018-03937-y pmid: 29666370

[34]	Wang Y, Fan L, Tuyishime P, et al. Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum. Communications Biology, 2020,3(1):217. doi: 10.1038/s42003-020-0954-9 pmid: 32382107

[35]	Siegel J B, Smith A L, Poust S, et al. Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences, 2015,112(12):3704-3709.

[36]	Yang J, Zhu Y, Qu G, et al. Biosynthesis of dendroketose from different carbon sources using in vitro and in vivo metabolic engineering strategies. Biotechnology for Biofuels, 2018,11(1):290.

[37]	Irla M, Nærdal I, Brautaset T, et al. Methanol-based γ-aminobutyric acid (GABA) production by genetically engineered Bacillus methanolicus strains. Industrial Crops and Products, 2017,106:12-20.

[38]	Witthoff S, Schmitz K, Niedenführ S, et al. Metabolic engineering of Corynebacterium glutamicum for methanol metabolism. Applied and Environmental Microbiology, 2015,81(6):2215-2225. doi: 10.1128/AEM.03110-14 pmid: 25595770

[39]	Leβmeier L, Pfeifenschneider J, Carnicer M, et al. Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate. Applied Microbiology and Biotechnology, 2015,99(23):10163-10176. doi: 10.1007/s00253-015-6906-5 pmid: 26276544

[40]	Zhang W, Zhang T, Song M, et al. Metabolic engineering of Escherichia coli for high yield production of succinic acid driven by methanol. ACS Synthetic Biology, 2018,7(12):2803-2811. doi: 10.1021/acssynbio.8b00109 pmid: 30300546

[41]	Bennett R K, Gonzalez J E, Whitaker W B, et al. Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph. Metabolic Engineering, 2018,45:75-85. doi: 10.1016/j.ymben.2017.11.016 pmid: 29203223

[42]	Wang X, Wang X, Lu X, et al. Methanol fermentation increases the production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli. Biotechnology for Biofuels, 2019,12(1):17.

[43]	Chou A, Clomburg J M, Qian S, et al. 2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion. Nature Chemical Biology, 2019,15(9):900-906. doi: 10.1038/s41589-019-0328-0 pmid: 31383974

[44]	Dai Z, Gu H, Zhang S, et al. Metabolic construction strategies for direct methanol utilization in Saccharomyces cerevisiae. Bioresource Technology, 2017,245(Pt B):1407-1412. doi: 10.1016/j.biortech.2017.05.100 pmid: 28554521

[45]	Tuyishime P, Wang Y, Fan L, et al. Engineering Corynebacterium glutamicum for methanol-dependent growth and glutamate production. Metabolic Engineering, 2018,49:220-231. doi: 10.1016/j.ymben.2018.07.011 pmid: 30048680

[46]	Naerdal I, Pfeifenschneider J, Brautaset T, et al. Methanol-based cadaverine production by genetically engineered Bacillus methanolicus strains. Microbial Biotechnolpgy, 2015,8(2):342-350.

[47]	Wang Y, Fan L, Tuyishime P, et al. Synthetic methylotrophy: a practical solution for methanol-based biomanufacturing. Trends in Biotechnology, 2020,38(6):650-666. doi: 10.1016/j.tibtech.2019.12.013 pmid: 31932066

[1]	MA Ning,WANG Han-jie. Advances of Optogenetics in the Regulation of Bacterial Production[J]. China Biotechnology, 2021, 41(9): 101-109.

[2]	HUANG Huan-bang,WU Yang,YANG You-hui,WANG Zhao-guan,QI Hao. Progress in Incorporation of Non-canonical Amino Acid Based on Archaeal Tyrosyl-tRNA Synthetase[J]. China Biotechnology, 2021, 41(9): 110-125.

[3]	GUO Man-man,TIAN Kai-ren,QIAO Jian-jun,LI Yan-ni. Application of Phage Recombinase Systems in Synthetic Biology[J]. China Biotechnology, 2021, 41(8): 90-102.

[4]	DONG Shu-xin,QIN Lei,LI Chun,LI Jun. Transcription Factor Engineering Harnesses Metabolic Networks to Meet Efficient Production in Cell Factories[J]. China Biotechnology, 2021, 41(4): 55-63.

[5]	ZHENG Yi,GUO Shi-ying,SUI Feng-xiang,YANG Qi-yu,WEI Ya-xuan,LI Xiao-yan. Applications of Quorum Sensing Systems in Synthetic Biology[J]. China Biotechnology, 2021, 41(11): 100-109.

[6]	CHA Ya-ping, ZHU Mu-zi, LI Shuang. *Research Progress on In Vivo* Continuous Directed Evolution**[J]. China Biotechnology, 2021, 41(1): 42-51.

[7]	GUO Er-peng, ZHANG Jian-zhi, SI Tong. Recent Advances in the High-throughput Engineering of Lanthipeptides[J]. China Biotechnology, 2021, 41(1): 30-41.

[8]	CHANG Lu, HUANG Jiao-fang, DONG Hao, ZHOU Bin-hui, ZHU Xiao-juan, ZHUANG Ying-ping. A Review on Bioremediation and Detection of Heavy Metal Pollution by Synthetic Biological Engineered Microorganisms and Biofilms[J]. China Biotechnology, 2021, 41(1): 62-71.

[9]	RAO Hai-mi,LIANG Dong-mei,LI Wei-guo,QIAO Jian-jun,CAI YIN Qing-ge-le. Advances in Synthetic Biology of Fungal Aromatic Polyketides[J]. China Biotechnology, 2020, 40(9): 52-61.

[10]	ZHANG Yu-ting,LI Wei-guo,LIANG Dong-mei,QIAO Jian-jun,CAI YIN Qing-ge-le. Research Progress in Synthetic Biology of P450s in Terpenoid Synthesis[J]. China Biotechnology, 2020, 40(8): 84-96.

[11]	WANG Zhen,LI Xia,YUAN Ying-jin. Advances in Production of Caffeic Acid and Its Ester Derivatives in Heterologous Microbes[J]. China Biotechnology, 2020, 40(7): 91-99.

[12]	LIU Jin-cong,LIU Xue,YU Hong-jian,ZHAO Guang-rong. Recent Advances in Microbial Production of Phloretin and Its Glycosides[J]. China Biotechnology, 2020, 40(10): 76-84.

[13]	Jian YAN,Lu-qiang JIA,Jian DING,Zhong-ping SHI. *Enhancing pIFN-α Production by Pichia pastoris* via Periodic Methanol Induction Control**[J]. China Biotechnology, 2019, 39(6): 32-40.

[14]	Hua-ling XIE,Dong-qiao LI,Pei-juan CHI,Yan-ping YANG. An Analysis on the Competition of Patents in Synthetic Biology[J]. China Biotechnology, 2019, 39(4): 114-123.

[15]	Si-li YU,Xue LIU,Zhao-yu ZHANG,Hong-jian YU,Guang-rong ZHAO. Advances of Betalains Biosynthesis and Metabolic Regulation[J]. China Biotechnology, 2018, 38(8): 84-91.

Viewed

Full text

Abstract

Cited

Shared

Discussed