Engineering unnatural methylotrophic cell factories for methanol-based biomanufacturing: Challenges and opportunities.

Methanol is a very promising feedstock alternative to sugar-based raw materials for biomanufacturing because it does not compete with food production, is abundant and potentially sustainable in the future. Although methylotrophic fermentations have been practiced for decades, their applications are limited by technical drawbacks and insufficient knowledge of the physiology and metabolic regulation of native methylotrophs. Synthetic biology offers great opportunities for engineering efficient methylotrophic microbial cell factories by enabling non-methylotrophic model organisms to utilize methanol via the introduction of C1 utilization pathways. This review critically comments C1 metabolism with a focus on comparing different methanol-utilization pathways in light of biomanufacturing, and highlights recent advances in the engineering of synthetic methylotrophs. Most importantly, the unique challenges in the engineering process and possible solutions are also discussed in detail.

[1]  Jesús Picó,et al.  Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity , 2010, BMC Systems Biology.

[2]  P. Kaulfers,et al.  Plasmid-mediated formaldehyde resistance in Escherichia coli: characterization of resistance gene , 1996, Antimicrobial agents and chemotherapy.

[3]  Jürgen Klankermayer,et al.  Selective Catalytic Synthesis Using the Combination of Carbon Dioxide and Hydrogen: Catalytic Chess at the Interface of Energy and Chemistry. , 2016, Angewandte Chemie.

[4]  Honghua Jia,et al.  Metabolic construction strategies for direct methanol utilization in Saccharomyces cerevisiae. , 2017, Bioresource technology.

[5]  B. Maden Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1 metabolism. , 2000, The Biochemical journal.

[6]  A. Bar‐Even,et al.  Core Catalysis of the Reductive Glycine Pathway Demonstrated in Yeast , 2019, ACS synthetic biology.

[7]  A. McEwan,et al.  Formaldehyde Stress Responses in Bacterial Pathogens , 2016, Front. Microbiol..

[8]  C. Anthony The pyrroloquinoline quinone (PQQ)-containing quinoprotein dehydrogenases. , 1998, Biochemical Society transactions.

[9]  Martin Schmidt,et al.  Overexpression of ADH1 confers hyper-resistance to formaldehyde in Saccharomyces cerevisiae , 1996, Current Genetics.

[10]  Hongwu Ma,et al.  Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design , 2019, Nature Communications.

[11]  E. Papoutsakis,et al.  Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol , 2017, ACS synthetic biology.

[12]  James M Clomburg,et al.  2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion , 2019, Nature Chemical Biology.

[13]  S. Kolb Aerobic methanol-oxidizing bacteria in soil. , 2009, FEMS microbiology letters.

[14]  Anton Glieder,et al.  Regulation of methanol utilisation pathway genes in yeasts , 2006 .

[15]  Yin Li,et al.  Fixing carbon, unnaturally , 2016, Science.

[16]  James M. Clomburg,et al.  Industrial biomanufacturing: The future of chemical production , 2017, Science.

[17]  Maciek R Antoniewicz,et al.  Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli. , 2017, Metabolic engineering.

[18]  J. Helmann,et al.  Methylglyoxal resistance in Bacillus subtilis: contributions of bacillithiol‐dependent and independent pathways , 2014, Molecular microbiology.

[19]  James C Liao,et al.  A modified serine cycle in Escherichia coli coverts methanol and CO2 to two-carbon compounds , 2018, Nature Communications.

[20]  V. Brecht,et al.  Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: The ethylmalonyl-CoA pathway , 2007, Proceedings of the National Academy of Sciences.

[21]  Jens Nielsen,et al.  Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals. , 2015, Biotechnology advances.

[22]  Yin Li,et al.  Engineering Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: Reflections and perspectives , 2012, Biotechnology journal.

[23]  J. Liao,et al.  Characterization and evolution of an activator-independent methanol dehydrogenase from Cupriavidus necator N-1 , 2016, Applied Microbiology and Biotechnology.

[24]  Min Zhang,et al.  Guidance for engineering of synthetic methylotrophy based on methanol metabolism in methylotrophy , 2017 .

[25]  G. Olah Beyond oil and gas: the methanol economy. , 2006, Angewandte Chemie.

[26]  J. Vorholt,et al.  Methylobacterium extorquens: methylotrophy and biotechnological applications , 2014, Applied Microbiology and Biotechnology.

[27]  V. Wendisch,et al.  Methylotrophy in the thermophilic Bacillus methanolicus, basic insights and application for commodity production from methanol , 2014, Applied Microbiology and Biotechnology.

[28]  Alexandra B. Graf,et al.  Systems-level organization of yeast methylotrophic lifestyle , 2015, BMC Biology.

[29]  Young Min Kim,et al.  Dihydroxyacetone synthase from a methanol-utilizing carboxydobacterium, Acinetobacter sp. strain JC1 DSM 3803 , 1997, Journal of bacteriology.

[30]  Jean-Charles Portais,et al.  Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics , 2009, Proceedings of the National Academy of Sciences.

[31]  Jonas Grossmann,et al.  Proteomic analysis of the thermophilic methylotroph Bacillus methanolicus MGA3 , 2014, Proteomics.

[32]  S. Noack,et al.  Metabolic Engineering of Corynebacterium glutamicum for Methanol Metabolism , 2015, Applied and Environmental Microbiology.

[33]  Christopher P. Long,et al.  How adaptive evolution reshapes metabolism to improve fitness: recent advances and future outlook. , 2018, Current opinion in chemical engineering.

[34]  Øyvind M. Jakobsen,et al.  Plasmid-Dependent Methylotrophy in Thermotolerant Bacillus methanolicus , 2004, Journal of bacteriology.

[35]  Ping Zheng,et al.  Engineering Corynebacterium glutamicum for methanol-dependent growth and glutamate production. , 2018, Metabolic engineering.

[36]  T. Erb,et al.  A synthetic pathway for the fixation of carbon dioxide in vitro , 2016, Science.

[37]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[38]  J. Keasling,et al.  Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go , 2014, Cell.

[39]  Yin Li,et al.  Synthetic biology for CO2 fixation , 2016, Science China Life Sciences.

[40]  R. Milo,et al.  Sugar Synthesis from CO2 in Escherichia coli , 2016, Cell.

[41]  S. W. Park,et al.  Cloning, characterization and expression of a gene encoding dihydroxyacetone synthase in Mycobacterium sp. strain JC1 DSM 3803. , 2007, Microbiology.

[42]  B. Vallee,et al.  Purification, characterization, and partial sequence of the glutathione-dependent formaldehyde dehydrogenase from Escherichia coli: a class III alcohol dehydrogenase. , 1992, Biochemistry.

[43]  M. Lidstrom,et al.  Novel Dephosphotetrahydromethanopterin Biosynthesis Genes Discovered via Mutagenesis in Methylobacterium extorquens AM1 , 2005, Journal of bacteriology.

[44]  Christian L. Barrett,et al.  Systems biology as a foundation for genome-scale synthetic biology. , 2006, Current opinion in biotechnology.

[45]  A. Bar‐Even,et al.  Engineered Assimilation of Exogenous and Endogenous Formate in Escherichia coli. , 2017, ACS synthetic biology.

[46]  Gregory J. Crowther,et al.  Formate as the Main Branch Point for Methylotrophic Metabolism in Methylobacterium extorquens AM1 , 2008, Journal of bacteriology.

[47]  J. Liao,et al.  Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production. , 2018, Metabolic engineering.

[48]  Yanhe Ma,et al.  Transformation of formaldehyde into functional sugars via multi-enzyme stepwise cascade catalysis , 2017 .

[49]  Eleftherios Papoutsakis,et al.  Scaffoldless engineered enzyme assembly for enhanced methanol utilization , 2016, Proceedings of the National Academy of Sciences.

[50]  Amanda L. Smith,et al.  Computational protein design enables a novel one-carbon assimilation pathway , 2015, Proceedings of the National Academy of Sciences.

[51]  Jean-Charles Portais,et al.  Engineering Escherichia coli for methanol conversion. , 2015, Metabolic engineering.

[52]  Yanping Zhang,et al.  A systematically chromosomally engineered Escherichia coli efficiently produces butanol. , 2017, Metabolic engineering.

[53]  Ludmila Chistoserdova,et al.  Modularity of methylotrophy, revisited. , 2011, Environmental microbiology.

[54]  M. Oh,et al.  Adaptively evolved Escherichia coli for improved ability of formate utilization as a carbon source in sugar-free conditions , 2019, Biotechnology for Biofuels.

[55]  Adam M. Feist,et al.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.

[56]  E. Papoutsakis,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. , 2018, Metabolic engineering.

[57]  Matthew K. Theisen,et al.  Building carbon–carbon bonds using a biocatalytic methanol condensation cycle , 2014, Proceedings of the National Academy of Sciences.

[58]  U. Rinas,et al.  Physiological response of Pichia pastoris GS115 to methanol-induced high level production of the Hepatitis B surface antigen: catabolic adaptation, stress responses, and autophagic processes , 2012, Microbial Cell Factories.

[59]  David R. Liu,et al.  Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2 , 2019, ACS synthetic biology.

[60]  S. Atsumi,et al.  Electrical-biological hybrid system for CO2 reduction. , 2018, Metabolic engineering.

[61]  G. Fuchs,et al.  Methanol Assimilation in Methylobacterium extorquens AM1: Demonstration of All Enzymes and Their Regulation , 2010, PloS one.

[62]  E. Papoutsakis,et al.  Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization. , 2015, Current opinion in biotechnology.

[63]  P. K. Ajikumar,et al.  The future of metabolic engineering and synthetic biology: towards a systematic practice. , 2012, Metabolic engineering.

[64]  Y. Sakai,et al.  Yeast Methylotrophy: Metabolism, Gene Regulation and Peroxisome Homeostasis , 2011, International journal of microbiology.

[65]  A. Bar‐Even Formate Assimilation: The Metabolic Architecture of Natural and Synthetic Pathways. , 2016, Biochemistry.

[66]  A. Bar‐Even,et al.  The formate bio-economy. , 2016, Current opinion in chemical biology.

[67]  I. J. van der Klei,et al.  Pyruvate carboxylase is an essential protein in the assembly of yeast peroxisomal oligomeric alcohol oxidase. , 2003, Molecular biology of the cell.

[68]  Martin Dragosits,et al.  Adaptive laboratory evolution – principles and applications for biotechnology , 2013, Microbial Cell Factories.

[69]  Flavio Manenti,et al.  Fossil or Renewable Sources for Methanol Production , 2017 .

[70]  S. Ishikawa,et al.  Glutathione-independent formaldehyde dehydrogenase from Pseudomons putida: survey of functional groups with special regard for cysteine residues. , 1997, Bioscience, biotechnology, and biochemistry.

[71]  M. V. Filho,et al.  Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. , 2009, Trends in biotechnology.

[72]  S. Verhelst,et al.  The Chemical Route to a Carbon Dioxide Neutral World. , 2017, ChemSusChem.

[73]  Gregory J. Crowther,et al.  Identification of a Fourth Formate Dehydrogenase in Methylobacterium extorquens AM1 and Confirmation of the Essential Role of Formate Oxidation in Methylotrophy , 2007, Journal of bacteriology.

[74]  J. Vorholt,et al.  Methanol-essential growth of Escherichia coli , 2018, Nature Communications.

[75]  A. Bar‐Even,et al.  In Vivo Assimilation of One-Carbon via a Synthetic Reductive Glycine Pathway in Escherichia coli. , 2018, ACS synthetic biology.

[76]  Ludmila Chistoserdova,et al.  The expanding world of methylotrophic metabolism. , 2009, Annual review of microbiology.

[77]  Y. Sakai,et al.  Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. , 2005, Chemical record.

[78]  M. Jiang,et al.  Metabolic Engineering of Escherichia coli for High Yield Production of Succinic Acid Driven by Methanol. , 2018, ACS synthetic biology.

[79]  P. Ouyang,et al.  Methanol fermentation increases the production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli , 2019, Biotechnology for Biofuels.

[80]  Trond E. Ellingsen,et al.  Methylotrophic Bacillus methanolicus Encodes Two Chromosomal and One Plasmid Born NAD+ Dependent Methanol Dehydrogenase Paralogs with Different Catalytic and Biochemical Properties , 2013, PloS one.

[81]  M. Bott,et al.  C1 Metabolism in Corynebacterium glutamicum: an Endogenous Pathway for Oxidation of Methanol to Carbon Dioxide , 2013, Applied and Environmental Microbiology.