微生物中一碳代谢网络构建的进展与挑战

郭姝媛; 吴良焕; 刘香健; 王博; 于涛

doi:10.12211/2096-8280.2021-079

您当前的位置：

首页 >

文章列表页 >

微生物中一碳代谢网络构建的进展与挑战

特约评述 | 更新时间：2025-03-20

- 微生物中一碳代谢网络构建的进展与挑战
- Developing C₁-based metabolic network in methylotrophy for biotransformation
- 合成生物学 2022年3卷第1期页码：116-137
- 作者机构：
  
  1.中国科学院深圳先进技术研究院，深圳合成生物学创新研究院，合成生物化学研究中心，广东深圳 518055
  2.中国科学院深圳先进技术研究院，深圳合成生物学创新研究院，中国科学院定量工程生物学重点实验室，广东深圳 518055
- 作者简介：
  
  [ "郭姝媛（1991—），女，博士，博士后。主要从事基于酿酒酵母的甲醇生物转化及产物合成研究。E-mail：sy.guo@siat.ac.cn" ]
  [ "于涛（1986—），男，博士，研究员。主要从事酿酒酵母的合成生物学研究。E-mail：tao.yu@siat.ac.cn" ]
- 基金信息：
  
  中国博士后科学基金(2020M682973);国家重点研发计划(2020YFA0907800);国家自然科学基金(32071416);广东省基础与应用基础研究基金(2020A1515110927);深圳合成生物学创新研究院项目(JCHZ20200003;DWKF20190003;ZTXM20203004)
- DOI：10.12211/2096-8280.2021-079
  中图分类号： Q 815
- 收稿：2021-07-23，
  
  修回：2021-10-21，
  
  纸质出版：2022-02-28
- 稿件说明：
移动端阅览
郭姝媛，吴良焕，刘香健，王博，于涛. 微生物中一碳代谢网络构建的进展与挑战［J］. 合成生物学， 2022， 3（1）： 116-137

GUO Shuyuan， WU Lianghuan， LIU Xiangjian， WANG Bo， YU Tao. Developing C₁-based metabolic network in methylotrophy for biotransformation［J］. Synthetic Biology Journal， 2022， 3（1）： 116-137
郭姝媛，吴良焕，刘香健，王博，于涛. 微生物中一碳代谢网络构建的进展与挑战［J］. 合成生物学， 2022， 3（1）： 116-137 DOI： 10.12211/2096-8280.2021-079.

GUO Shuyuan， WU Lianghuan， LIU Xiangjian， WANG Bo， YU Tao. Developing C₁-based metabolic network in methylotrophy for biotransformation［J］. Synthetic Biology Journal， 2022， 3（1）： 116-137 DOI： 10.12211/2096-8280.2021-079.

摘要

利用来源广、价格低、易制备且储量丰富的一碳化合物作为底物，通过构建甲基营养型细胞工厂，生物合成多种高附加值化学品，不仅可以促进一碳资源的洁净利用，同时可以缓解能源短缺、环境污染等问题。因此，深入了解甲基营养型微生物（天然型和合成型）的一碳代谢网络，是高效利用一碳化合物进行生物炼制的关键。本文综述了多种一碳化合物（甲烷、甲醇、甲酸和二氧化碳）生物炼制的研究进展，主要包括两个部分：（1）甲基营养型微生物（天然型和合成型）的关键代谢酶及多种代谢网络；（2）基于多种甲基营养型微生物进行生物合成的研究现状。文章最后讨论了一碳化合物作为底物进行生物转化所面临的主要瓶颈，并据此提供可行的研究策略，以期推动一碳化合物作为原材料进行生物炼制的工业化进程。

Abstract

One carbon (C

) substrates have generated increasing attention as abundantly available feedstock for biotransformation to produce biofuels and valuable chemicals. Especially

these bioproducts are not only promoting the economic development

but also meet the societal needs for clean energy and environmental protection. Microbial cell factories (MCF) that efficiently convert raw materials to useful chemicals are highly

desirable for C1 based biomanufacturing. Furthermore

more and more attention is being paid to study how the native and synthetic methylotrophic MCFs are capable of utilizing C1 compounds including methane

methanol

formic acid and carbon dioxide (CO

) as raw materials for biosynthesis. Native methylotrophs have multiple pathways for C

utilization so that they can grow with methanol or formate as the sole carbon and energy source. Engineering synthetic methylotrophs are based on available metabolic knowledge and advanced genome engineering tools to modify the platform microorganisms. Hence

it is the key to explore the C

-based metabolic networks of methylotrophy in depth for constructing highly effective methylotrophic cell factory to convert C

substrates. In this review

we firstly summarize in detail key natural pathways for C

-substrate assimilation and bioproducts produced by native methylotrophs. Then we introduce synthetic methylotrophs and major chemical products derived through engineering

Escherichia coli

Corynebacterium glutamicum

and

Saccharomyces cerevisiae

. In the field of synthetic methylotrophs

many studies focus on utilizing methanol or CO

as the sole carbon source and energy source to construct the MCFs for bio-transformation. In the end

we discuss the barriers and challenges for developing robust methylotrophic cell factory to convert C

substrates

and highlight strategies for commercializing the biotransformation of C

based substrates.

关键词

Keywords

references

CLOMBURG J M , CRUMBLEY A M , GONZALEZ R . Industrial biomanufacturing: The future of chemical production [J ] . Science , 2017 , 355 ( 6320 ): aag0804 .

谭天伟 , 陈必强 , 张会丽 , 等 . 加快推进绿色生物制造助力实现“碳中和” [J ] . 化工进展 , 2021 , 40 ( 3 ): 1137 - 1141 .

TAN T W , CHEN B Q , ZHANG H L , et al . Accelerate promotion of green bio-manufacturing to help achieve “carbon neutrality” [J ] . Chemical Industry and Engineering Progress , 2021 , 40 ( 3 ): 1137 - 1141 .

SINGH A K , KISHORE G M , PAKRASI H B . Emerging platforms for co-utilization of one-carbon substrates by photosynthetic organisms [J ] . Current Opinion in Biotechnology , 2018 , 53 : 201 - 208 .

DÜRRE P , EIKMANNS B J . C1-carbon sources for chemical and fuel production by microbial gas fermentation [J ] . Current Opinion in Biotechnology , 2015 , 35 : 63 - 72 .

KOPKE M , HELD C , HUJER S , et al . Clostridium ljungdahlii represents a microbial production platform based on syngas [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2010 , 107 ( 29 ): 13087 - 13092 .

SCHEFFEN M , MARCHAL D G , BENEYTON T , et al . A new-to-nature carboxylation module to improve natural and synthetic CO 2 fixation [J ] . Nature Catalysis , 2021 , 4 ( 2 ): 105 - 115 .

COTTON C A , EDLICH-MUTH C , BAR-EVEN A . Reinforcing carbon fixation: CO 2 reduction replacing and supporting carboxylation [J ] . Current Opinion in Biotechnology , 2018 , 49 : 49 - 56 .

YISHAI O , LINDNER S N , GONZALEZ DE LA CRUZ J , et al . The formate bio-economy [J ] . Current Opinion in Chemical Biology , 2016 , 35 : 1 - 9 .

WANG Y , FAN L W , TUYISHIME P , et al . Synthetic methylotrophy: A practical solution for methanol-based biomanufacturing [J ] . Trends in Biotechnology , 2020 , 38 ( 6 ): 650 - 666 .

WU Y S , JIANG Z , LU X , et al . Domino electroreduction of CO 2 to methanol on a molecular catalyst [J ] . Nature , 2019 , 575 ( 7784 ): 639 - 642 .

CHISTOSERDOVA L , LIDSTROM M E . Aerobic methylotrophic prokaryotes [M ] //ROSENBERG E.The prokaryotes[M ] . German: Springer Reference , 2013 : 267 .

高教琪 , 周雍进 . 甲醇生物转化的机遇与挑战 [J ] . 合成生物学 , 2020 , 1 ( 2 ): 158 - 173 .

GAO J Q , ZHOU Y J . Advances in methanol bio-transformation [J ] . Synthetic Biology Journal , 2020 , 1 ( 2 ): 158 - 173 .

DEN CAMP H J M O , ISLAM T , STOTT M B , et al . Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia [J ] . Environmental Microbiology Reports , 2009 , 1 ( 5 ): 293 - 306 .

ETTWIG K F , BUTLER M K , LE PASLIER D , et al . Nitrite-driven anaerobic methane oxidation by oxygenic bacteria [J ] . Nature , 2010 , 464 ( 7288 ): 543 - 548 .

GAO L M , CAI M H , SHEN W , et al . Engineered fungal polyketide biosynthesis in Pichia pastoris : a potential excellent host for polyketide production [J ] . Microbial Cell Factories , 2013 , 12 : 77 .

WRIESSNEGGER T , AUGUSTIN P , ENGLEDER M , et al . Production of the sesquiterpenoid (+)-nootkatone by metabolic engineering of Pichia pastoris [J ] . Metabolic Engineering , 2014 , 24 : 18 - 29 .

JEONG E , SHIM W Y , KIM J H . Metabolic engineering of Pichia pastoris for production of hyaluronic acid with high molecular weight [J ] . Journal of Biotechnology , 2014 , 185 : 28 - 36 .

ZHANG T , GE C Y , DENG L , et al . C 4 -dicarboxylic acid production by overexpressing the reductive TCA pathway [J ] . FEMS Microbiology Letters , 2015 , 362 ( 9 ): fnv052 .

ARAYA-GARAY J M , FEIJOO-SIOTA L , ROSA-DOS-SANTOS F , et al . Construction of new Pichia pastoris X-33 strains for product ion of lycopene and β-carotene [J ] . Applied Microbiology and Biotechnology , 2012 , 93 ( 6 ): 2483 - 2492 .

LIU Y Q , TU X H , XU Q , et al . Engineered monoculture and co-culture of methylotrophic yeast for de novo production of monacolin J and lovastatin from methanol [J ] . Metabolic Engineering , 2018 , 45 : 189 - 199 .

LIU Y Q , BAI C X , XU Q , et al . Improved methanol-derived lovastatin production through enhancement of the biosynthetic pathway and intracellular lovastatin efflux in methylotrophic yeast [J ] . Bioresources and Bioprocessing , 2018 , 5 : 22 .

GIDIJALA L , KIEL J A K W , DOUMA R D , et al . An engineered yeast efficiently secreting penicillin [J ] . PLoS One , 2009 , 4 ( 12 ): e8317 .

BRAUTASET T , JAKOBSEN Ø M , JOSEFSEN K D , et al . Bacillus methanolicus : a candidate for industrial production of amino acids from methanol at 50 ℃ [J ] . Applied Microbiology and Biotechnology , 2007 , 74 ( 1 ): 22 - 34 .

JAKOBSEN O M , BRAUTASET T , DEGNES K F , et al . Overexpression of wild-type aspartokinase increases L-lysine production in the thermotolerant methylotrophic bacterium Bacillus methanolicus [J ] . Applied and Environmental Microbiology , 2009 , 75 ( 3 ): 652 - 661 .

BRAUTASET T , JAKOBSEN Ø 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 ℃ [J ] . Applied Microbiology and Biotechnology , 2010 , 87 ( 3 ): 951 - 964 .

NÆRDAL I , NETZER R , IRLA M , et al . L-lysine production by Bacillus methanolicus : genome-based mutational analysis and L-lysine secretion engineering [J ] . Journal of Biotechnology , 2017 , 244 : 25 - 33 .

NAERDAL I , PFEIFENSCHNEIDER J , BRAUTASET T , et al . Methanol-based cadaverine production by genetically engineered Bacillus methanolicus strains [J ] . Microbial Biotechnology , 2015 , 8 ( 2 ): 342 - 350 .

IRLA M , HEGGESET T M B , NÆRDAL I , et al . Genome-based genetic tool development for Bacillus methanolicus : θ -and rolling circle-replicating plasmids for inducible gene expression and application to methanol-based cadaverine production [J ] . Frontiers in Microbiology , 2016 , 7 : 1481 .

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

ORITA I , NISHIKAWA K , NAKAMURA S , et al . Biosynthesis of polyhydroxyalkanoate copolymers from methanol by Methylobacterium extorquens AM1 and the engineered strains under cobalt-deficient conditions [J ] . Applied Microbiology and Biotechnology , 2014 , 98 ( 8 ): 3715 - 3725 .

HU B , LIDSTROM M E . Metabolic engineering of Methylobacterium extorquens AM1 for 1-butanol production [J ] . Biotechnology for Biofuels , 2014 , 7 ( 1 ): 156 .

LIM C K , VILLADA J C , CHALIFOUR A , et al . Designing and engineering Methylorubrum extorquens AM1 for itaconic acid production [J ] . Frontiers in Microbiology , 2019 , 10 : 1027 .

HU B , YANG Y M , BECK D A C , et al . Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance [J ] . Biotechnology for Biofuels , 2016 , 9 : 84 .

LIANG W F , CUI L Y , CUI J Y , et al . Biosensor-assisted transcriptional regulator engineering for Methylobacterium extorquens AM1 to improve mevalonate synthesis by increasing the acetyl-CoA supply [J ] . Metabolic Engineering , 2017 , 39 : 159 - 168 .

ROHDE M T , TISCHER S , HARMS H , et al . Production of 2-hydroxyisobutyric acid from methanol by Methylobacterium extorquens AM1 expressing ( R )-3-hydroxybutyryl coenzyme A-isomerizing enzymes [J ] . Applied and Environmental Microbiology , 2017 , 83 ( 3 ). DOI: 10.1128/aem.02622-16 http://dx.doi.org/10.1128/aem.02622-16 .

YANG Y M , CHEN W J , YANG J , et al . Production of 3-hydroxypropionic acid in engineered Methylobacterium extorquens AM1 and its reassimilation through a reductive route [J ] . Microbial Cell Factories , 2017 , 16 ( 1 ): 179 .

YUAN X J , CHEN W J , MA Z X , et al . Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens [J ] . Metabolic Engineering , 2021 , 64 : 95 - 110 .

MA Z X , ZHANG M , ZHANG C T , et al . Metabolomic analysis improves bioconversion of methanol to isobutanol in Methylorubrum extorquens AM1 [J ] . Biotechnology Journal , 2021 , 16 ( 6 ): e2000413 .

SONNTAG F , MÜLLER J E N , KIEFER P , et al . High-level production of ethylmalonyl-CoA pathway-derived dicarboxylic acids by Methylobacterium extorquens under cobalt-deficient conditions and by polyhydroxybutyrate negative strains [J ] . Applied Microbiology and Biotechnology , 2015 , 99 ( 8 ): 3407 - 3419 .

SONNTAG F , KRONER C , LUBUTA P , et al . Engineering Methylobacterium extorquens for de novo synthesis of the sesquiterpenoid α -humulene from methanol [J ] . Metabolic Engineering , 2015 , 32 : 82 - 94 .

ZHU W L , CUI J Y , CUI L Y , et al . Bioconversion of methanol to value-added mevalonate by engineered Methylobacterium extorquens AM1 containing an optimized mevalonate pathway [J ] . Applied Microbiology and Biotechnology , 2016 , 100 ( 5 ): 2171 - 2182 .

YANG J , ZHANG C T , YUAN X J , et al . Metabolic engineering of Methylobacterium extorquens AM1 for the production of butadiene precursor [J ] . Microbial Cell Factories , 2018 , 17 ( 1 ): 194 .

BÉLANGER L , FIGUEIRA M M , BOURQUE D , et al . Production of heterologous protein by Methylobacterium extorquens in high cell density fermentation [J ] . FEMS Microbiology Letters , 2004 , 231 ( 2 ): 197 - 204 .

HÖFER P , CHOI Y J , OSBORNE M J , et al . Production of functionalized polyhydroxyalkanoates by genetically modified Methylobacterium extorquens strains [J ] . Microbial Cell Factories , 2010 , 9 : 70 .

SHEN P H , WU B . Over-expression of a hydroxypyruvate reductase in Methylobacterium sp. MB200 enhances glyoxylate accumulation [J ] . Journal of Industrial Microbiology and Biotechnology , 2007 , 34 ( 10 ): 657 .

SHEN P H , CHAO H J , JIANG C J , et al . Enhancing production of L-serine by increasing the glyA g ene expression in Methylobacterium sp. MB200 [J ] . Applied Biochemistry and Biotechnology , 2010 , 160 ( 3 ): 740 - 750 .

CHAO H , WU B , SHEN P . Overexpression of the methanol dehydrogenase gene mxaF in Methylobacterium sp. MB200 enhances L-serine production [J ] . Letters in Applied Microbiology , 2015 , 61 ( 4 ): 390 - 396 .

LI X , WU B , ZHOU K , et al . Deletion of gene gnd encoding 6-phosphogluconate dehydrogenase promotes L-serine biosynthesis in a genetically engineered strain of Methylobacterium sp. MB200 [J ] . Biotechnology Letters , 2019 , 41 ( 1 ): 69 - 77 .

HÖLSCHER T , BREUER U , ADRIAN L , et al . Production of the chiral compound ( R )-3-hydroxybutyrate by a genetically engineered methylotrophic bacterium [J ] . Applied and Environmental Microbiology , 2010 , 76 ( 16 ): 5585 - 5591 .

HAGISHITA T , YOSHIDA T , IZUMI Y , et al . Efficient L-serine production from methanol and glycine by resting cells of Methylobacterium sp. strain MN 43 [J ] . Bioscience, Biotechnology, and Biochemistry , 1996 , 60 ( 10 ): 1604 - 1607 .

MOTOYAMA H , ANAZAWA H , KATSUMATA R , et al . Amino acid production from methanol by Methylobacillus glycogenes mutants: isolation of L-glutamic acid hyper-producing mutants from M. glycogenes strains, and derivation of L-threonine and L-lysine-producing mutants from them [J ] . Bioscience, Biotechnology, and Biochemistry , 1993 , 57 ( 1 ): 82 - 87 .

ISHIKAWA K , GUNJI Y , YASUEDA H , et al . Improvement of L-lysine production by Methylophilus methylotrophus from methanol via the entner-doudoroff pathway, originating in Escherichia coli [J ] . Bioscience, Biotechnology, and Biochemistry , 2008 , 72 ( 10 ): 2535 - 2542 .

LYU Z , JAIN R , SMITH P , et al . Engineering the autotroph Methanococcus maripaludis for geraniol production [J ] . ACS Synthetic Biology , 2016 , 5 ( 7 ): 577 - 581 .

KALYUZHNAYA M G , PURI A W , LIDSTROM M E . Metabolic engineering in methanotrophic bacteria [J ] . Metabolic Engineering , 2015 , 29 : 142 - 152 .

NIELSEN A K , GERDES K , MURRELL J C . Copper-dependent reciprocal transcriptional regulation of methane monooxygenase genes in Methylococcus capsulatus and Methylosinus trichosporium [J ] . Molecular Microbiology , 1997 , 25 ( 2 ): 399 - 409 .

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 [J ] . Current Opinion in Biotechnology , 2015 , 33 : 165 - 175 .

HARTNER F S , GLIEDER A . Regulation of methanol utilisation pathway genes in yeasts [J ] . Microbial Cell Factories , 2006 , 5 : 39 .

PARK H , LEE H , RO Y T , et al . Identification and functional characterization of a gene for the methanol: N , N' -dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803) [J ] . Microbiology , 2010 , 156 ( Pt 2 ): 463 - 471 .

BYSTRYKH L V , GOVORUKHINA N I , DIJKHUIZEN L , et al . Tetrazolium-dye-linked alcohol dehydrogenase of the methylotrophic actinomycete Amycolatopsis methanolica is a three-component complex [J ] . European Journal of Biochemistry , 1997 , 247 ( 1 ): 280 - 287 .

NAGY I , VERHEIJEN S , DE SCHRIJVER A , et al . Characterization of the Rhodococcus sp. NI86/21 gene encoding alcohol: N , N' -dimethyl-4-nitrosoaniline oxidoreductase inducible by atrazine and thiocarbamate herbicides [J ] . Archives of Microbiology , 1995 , 163 ( 6 ): 439 - 446 .

ZHU T C , ZHAO T X , BANKEFA O E , et al . Engineering unnatural methylotrophic cell factories for methanol-based biomanufacturing: challenges and opportunities [J ] . Biotechnology Advances , 2020 , 39 : 107467 .

KROG A , HEGGESET T M B , MÜLLER J E N , et al . Methylotrophic Bacillus methanolicus encodes two chromoso mal and one plasmid born NAD+ dependent methanol dehydrogenase paralogs with different catalytic and biochemical properties [J ] . PLoS One , 2013 , 8 ( 3 ): e59188 .

MÜLLER J E N , MEYER F , LITSANOV B , et al . Engineering Escherichia coli for methanol conversion [J ] . Metabolic Engineering , 2015 , 28 : 190 - 201 .

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

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 [J ] . Applied Microbiology and Biotechnology , 2016 , 100 ( 11 ): 4969 - 4983 .

WHITAKER W B , JONES J A , BENNETT R K , et al . Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli [J ] . Metabolic Engineering , 2017 , 39 : 49 - 59 .

ROTH T B , WOOLSTON B M , STEPHANOPOULOS G , et al . Phage-assisted evolution of Bacillus methanolicus methanol dehydrogenase 2 [J ] . ACS Synthetic Biology , 2019 , 8 ( 4 ): 796 - 806 .

TSURU D , ODA N , MATSUO Y , et al . Glutathione-independent formaldehyde dehydrogenase from Pseudomons putida : survey of functional groups with special regard for cysteine residues [J ] . Bioscience, Biotechnology, and Biochemistry , 1997 , 61 ( 8 ): 1354 - 1357 .

GUTHEIL W G , HOLMQUIST B , VALLEE B L . Purification, characterization, and partial sequence of the glutathione-dependent formaldehyde dehydrogenase from Escherichia coli : a class III alcohol dehydrogenase [J ] . Biochemistry , 1992 , 31 ( 2 ): 475 - 481 .

VORHOLT J A . Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria [J ] . Archives of Microbiology , 2002 , 178 ( 4 ): 239 - 249 .

HATRONGJIT R , PACKDIBAMRUNG K . A novel NADP+-dependent formate dehydrogenase from Burkholderia stabilis 15516: Screening, purification and characterization [J ] . Enzyme and Microbial Technology , 2010 , 46 ( 7 ): 557 - 561 .

MÜLLER J E N , HEGGESET T M B , WENDISCH V F , et al . Methylotrophy in the thermophilic Bacillus methanolicus , basic insights and application for commodity production from methanol [J ] . Applied Microbiology and Biotechnology , 2015 , 99 ( 2 ): 535 - 551 .

RUßMAYER H , BUCHETICS M , GRUBER C , et al . Systems-level organization of yeast methylotrophic lifestyle [J ] . BMC Biology , 2015 , 13 : 80 .

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 [J ] . Metabolic Engineering , 2018 , 45 : 75 - 85 .

LEßMEIER 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 [J ] . Applied Microbiology and Biotechnology , 2015 , 99 ( 23 ): 10163 - 10176 .

WANG Y , FAN L W , TUYISHIME P , et al . Adap tive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum [J ] . Communications Biology , 2020 , 3 ( 1 ): 217 .

TUYISHIME P , WANG Y , FAN L W , et al . Engineering Corynebacterium glutamicum for methanol-dependent growth and glutamate production [J ] . Metabolic Engineering , 2018 , 49 : 220 - 231 .

ZHANG W M , ZHANG T , SONG M , et al . Metabolic engineering of Escherichia coli for high yield production of succinic acid driven by methanol [J ] . ACS Synthetic Biology , 2018 , 7 ( 12 ): 2803 - 2811 .

YU H , LIAO J C . A modified serine cycle in Escherichia coli coverts methanol and CO 2 to two-carbon compounds [J ] . Nature Communications , 2018 , 9 : 3992 .

WANG C , REN J , ZHOU L B , et al . An aldolase-catalyzed new metabolic pathway for the assimilation of formaldehyde and methanol to synthesize 2-keto-4-hydroxybutyrate and 1, 3-propanediol in Escherichia coli [J ] . ACS Synthetic Biology , 2019 , 8 ( 11 ): 2483 - 2493 .

CHOU A , CLOMBURG J M , QIAN S , et al . 2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion [J ] . Nature Chemical Biology , 2019 , 15 ( 9 ): 900 - 906 .

BENNETT R K , DILLON M , GERALD HAR J R , et al . Engineering Escherichia coli for methanol-dependent growth on glucose for metabolite production [J ] . Metabolic Engineering , 2020 , 60 : 45 - 55 .

CHEN C T , CHEN F Y H , BOGORAD I W , et al . Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production [J ] . Metabolic Engineering , 2018 , 49 : 257 - 266 .

LEE P C , YOON Y G , SCHMIDT-DANNERT C . Investigation of cellular targeting of carotenoid pathway enzymes in Pichia pastoris [J ] . Journal of Biotechnology , 2009 , 140 ( 3/4 ): 227 - 233 .

GAO J Q , GAO N , ZHAI X X , et al . Recombination machinery engineering for precise genome editing in methylotrophic yeast Ogataea polymorpha [J ] . iScience , 2021 , 24 ( 3 ): 102168 .

ANTHONY C . How half a century of research was required to understand bacterial growth on C 1 and C 2 compounds; the story of the serine cycle and the ethylmalonyl-CoA pathway [J ] . Science Progress , 2011 , 94 ( Pt 2 ): 109 - 137 .

ALBER B E . Biotechnological potential of the ethylmalonyl-CoA pathway [J ] . Applied Microbiology and Biotechnology , 2011 , 89 ( 1 ): 17 - 25 .

BAR-EVEN A . Formate assimilation: the metabolic architecture of natural and synthetic pathways [J ] . Biochemistry , 2016 , 55 ( 28 ): 3851 - 3863 .

KHADEM A F , POL A , WIECZOREK A , et al . Autotrophic methanotrophy in verrucomicrobia : Methylacidiphilum fumariolicum SolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation [J ] . Journal of Bacteriology , 2011 , 193 ( 17 ): 4438 - 4446 .

GASSLER T , SAUER M , GASSER B , et al . The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO 2 [J ] . Nature Biotechnology , 2020 , 38 ( 2 ): 210 - 216 .

CHEN F Y H , JUNG H W , TSUEI C Y , et al . Converting Escherichia coli to a synthetic methylotroph growing solely on methanol [J ] . Cell , 2020 , 182 ( 4 ): 933 - 946.e14 .

BANG J , AHN J H , LEE J A , et al . Synthetic formatotrophs for one-carbon biorefinery [J ] . Advanced Science (Weinheim, Baden-Wurttemberg, Germany) , 2021 , 8 ( 12 ): 2100199 .

KIM S , LINDNER S N , ASLAN S , et al . Growth of E. coli on formate and methanol via the reductive glycine pathway [J ] . Nature Chemical Biology , 2020 , 16 ( 5 ): 538 - 545 .

ANTONOVSKY N , GLEIZER S , NOOR E , et al . Sugar synthesis from CO 2 in Escherichia coli [J ] . Cell , 2016 , 166 ( 1 ): 115 - 125 .

GLEIZER S , BEN-NISSAN R , BAR-ON Y M , et al . Conversion of Escherichia coli to generate all biomass carbon from CO 2 [J ] . Cell , 2019 , 179 ( 6 ): 1255 - 1263 .

WOOLSTON B M , KING J R , REITER M , et al . Improving formaldehyde consumption drives methanol assimilation in engineered E. coli [J ] . Nature Communications , 2018 , 9 : 2387 .

ROHLHILL J , GERALD HAR J R , ANTONIEWICZ M R , et al . Improving synthetic methylotrophy via dynamic formaldehyde regulation of pentose phosphate pathway genes and redox perturbation [J ] . Metabolic Engineering , 2020 , 57 : 247 - 255 .

SIEGEL J B , SMITH A L , POUST S , et al . Computational protein design enables a novel one-carbon assimilation pathway [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2015 , 112 ( 12 ): 3704 - 3709 .

LU X Y , LIU Y W , YANG Y Q , et al . Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design [J ] . Nature Communications , 2019 , 10 : 1378 .

YISHAI O , BOUZON M , DÖRING V , et al . In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli [J ] . ACS Synthetic Biology , 2018 , 7 ( 9 ): 2023 - 2028 .

DÖRING V , DARII E , YISHAI O , et al . Implementation of a reductive route of one-carbon assimilation in Escherichia coli through directed evolution [J ] . ACS Synthetic Biology , 2018 , 7 ( 9 ): 2029 - 2036 .

BANG J , LEE S Y . Assimilation of formic acid and CO 2 by engineered Escherichia coli equipped with reconstructed one-carbon assimilation pathways [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2018 , 115 ( 40 ): E9271 - E9279 .

BANG J , HWANG C H , AHN J H , et al . Escherichia coli is engineered to grow on CO 2 and formic acid [J ] . Nature Microbiology , 2020 , 5 ( 12 ): 1459 - 1463 .

SCHWANDER T , VON BORZYSKOWSKI L S , BURGENER S , et al . A synthetic pathway for the fixation of carbon dioxide in vitro [J ] . Science , 2016 , 354 ( 6314 ): 900 - 904 .

WITTHOFF S , MÜHLROTH A , MARIENHAGEN J , et al . C 1 metabolism in Corynebacterium glutamicum : an endogenous pathway for oxidation of methanol to carbon dioxide [J ] . Applied and Environmental Microbiology , 2013 , 79 ( 22 ): 6974 - 6983 .

YASOKAWA D , MURATA S , IWAHASHI Y , et al . Toxicity of methanol and formaldehyde towards Saccharomyces cerevisiae as assessed by DNA microarray analysis [J ] . Applied Biochemistry and Biotechnology , 2010 , 160 ( 6 ): 1685 - 1698 .

DAI Z X , GU H L , ZHANG S J , et al . Metabolic construction strategies for direct methanol utilization in Saccharomyces cerevisiae [J ] . Bioresource Technology , 2017 , 245 : 1407 - 1412 .

ESPINOSA M I , WILLIAMS T C , PRETORIUS I S , et al . Benchmarking two Saccharomyces cerevisiae laboratory strains for growth and transcriptional response to methanol [J ] . Synthetic and Systems Biotechnology , 2019 , 4 ( 4 ): 180 - 188 .

ESPINOSA M I , GONZALEZ-GARCIA R A , VALGEPEA K , et al . Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae [J ] . Nature Communications , 2020 , 11 : 5564 .

GONZALEZ DE LA CRUZ J , MACHENS F , MESSERSCHMIDT K , et al . Core catalysis of the reductive glycine pathway demonstrated in yeast [J ] . ACS Synthetic Biology , 2019 , 8 ( 5 ): 911 - 917 .

袁姚梦 , 邢新会 , 张翀 . 微生物细胞工厂的设计构建:从诱变育种到全基因组定制化创制 [J ] . 合成生物学 , 2020 , 1 ( 6 ): 656 - 673 .

YUAN Y M , XING X H , ZHANG C . Progress and prospective of engineering microbial cell factories: from random mutagenesis to customized design in genome scale [J ] . Synthetic Biology Journal , 2020 , 1 ( 6 ): 656 - 673 .

YANG Y K , LIU G Q , CHEN X , et al . High efficiency CRISPR/Cas9 genome editing system with an eliminable episomal sgRNA plasmid in Pichia pastoris [J ] . Enzyme and Microbial Technology , 2020 , 138 : 109556 .

WENINGER A , HATZL A M , SCHMID C , et al . Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris [J ] . Journal of Biotechnology , 2016 , 235 : 139 - 149 .

LIU Q , SHI X N , SONG L L , et al . CRISPR-Cas9-mediated genomic multiloci integration in Pichia pastoris [J ] . Microbial Cell Factories , 2019 , 18 ( 1 ): 144 .

CAI P , DUAN X P , WU X Y , et al . Recombination machinery engineering facilitates metabolic engineering of the industrial yeast Pichia pastoris [J ] . Nucleic Acids Research , 2021 , 49 ( 13 ): 7791 - 7805 .

MO X H , ZHANG H , WANG T M , et al . Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis [J ] . Applied Microbiology and Biotechnology , 2020 , 104 ( 10 ): 4515 - 4532 .

ZHU L P , SONG S Z , YANG S . Gene repression using synthetic small regulatory RNA in Methylorubrum extorquens [J ] . Journal of Applied Microbiology , 2021 , 131 ( 6 ): 2861 - 2875 .

NOH M , YOO S M , YANG D , et al . Broad-spectrum gene repression using scaffold engineering of synthetic sRNAs [J ] . ACS Synthetic Biology , 2019 , 8 ( 6 ): 1452 - 1461 .

HU G P , LI Z H , MA D L , et al . Light-driven CO 2 sequestration in Escherichia coli to achieve theoretical yield of chemicals [J ] . Nature Catalysis , 2021 , 4 ( 5 ): 395 - 406 .

STINGELE J , SCHWARZ M S , BLOEMEKE N , et al . A DNA-dependent protease involved in DNA-protein crosslink repair [J ] . Cell , 2014 , 158 ( 2 ): 327 - 338 .

张卉 , 袁姚梦 , 张翀 , 等 . 合成甲基营养细胞工厂同化甲醇的研究进展及未来展望 [J ] . 合成生物学 , 2021 , 2 ( 2 ): 222 - 233 .

ZHANG H , YUAN Y M , ZHANG C , et al . Research progresses and future prospects of synthetic methylotrophic cell factory for methanol assimilation [J ] . Synthetic Biology Journal , 2021 , 2 ( 2 ): 222 - 233 .

HAMMER S K , AVALOS J L . Harnessing yeast organelles for metabolic engineering [J ] . Nature Chemical Biology , 2017 , 13 ( 8 ): 823 - 832 .

浏览量

下载量

CSCD

文章被引用时，请邮件提醒。

提交

工具集

关联资源

合成生物学赋能细胞膜纳米颗粒的精准诊疗

酚酸类化合物：从植物提取到生物合成

合成生物学在农业中的进展及挑战