Metabolic Engineering of Microorganisms to Produce Pyruvate and Derived Compounds

Pyruvate is a hub of various endogenous metabolic pathways, including glycolysis, TCA cycle, amino acid, and fatty acid biosynthesis. It has also been used as a precursor for pyruvate-derived compounds such as acetoin, 2,3-butanediol (2,3-BD), butanol, butyrate, and L-alanine biosynthesis. Pyruvate and derivatives are widely utilized in food, pharmaceuticals, pesticides, feed additives, and bioenergy industries. However, compounds such as pyruvate, acetoin, and butanol are often chemically synthesized from fossil feedstocks, resulting in declining fossil fuels and increasing environmental pollution. Metabolic engineering is a powerful tool for producing eco-friendly chemicals from renewable biomass resources through microbial fermentation. Here, we review and systematically summarize recent advances in the biosynthesis pathways, regulatory mechanisms, and metabolic engineering strategies for pyruvate and derivatives. Furthermore, the establishment of sustainable industrial synthesis platforms based on alternative substrates and new tools to produce these compounds is elaborated. Finally, we discuss the potential difficulties in the current metabolic engineering of pyruvate and derivatives and promising strategies for constructing efficient producers.

[1]  K. Yu,et al.  The Production of Pyruvate in Biological Technology: A Critical Review , 2022, Microorganisms.

[2]  C. Unkefer,et al.  Precise Genomic Riboregulator Control of Metabolic Flux in Microbial Systems , 2022, ACS synthetic biology.

[3]  Ke Jiang,et al.  Regulation of carbon flux and NADH/NAD+ supply to enhance 2,3-butanediol production in Enterobacter aerogenes. , 2022, Journal of biotechnology.

[4]  Yinjie J. Tang,et al.  A comparative evaluation of machine learning algorithms for predicting syngas fermentation outcomes , 2022, Biochemical Engineering Journal.

[5]  V. Müller A synthetic bacterial microcompartment as production platform for pyruvate from formate and acetate , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[6]  R. Takors,et al.  CRISPRi enables fast growth followed by stable aerobic pyruvate formation in Escherichia coli without auxotrophy , 2021, Engineering in life sciences.

[7]  P. Petrova,et al.  Current Advances in Microbial Production of Acetoin and 2,3-Butanediol by Bacillus spp. , 2021, Fermentation.

[8]  N. Scrutton,et al.  Combinatorial use of environmental stresses and genetic engineering to increase ethanol titres in cyanobacteria , 2021, Biotechnology for Biofuels.

[9]  Wei-hsin Chen,et al.  Recent advances in lignocellulosic biomass for biofuels and value-added bioproducts - A critical review. , 2021, Bioresource technology.

[10]  T. Hanai,et al.  Dynamic metabolic engineering of Escherichia coli improves fermentation for the production of pyruvate and its derivatives. , 2021, Journal of bioscience and bioengineering.

[11]  Shuangyan Han,et al.  Cell-Free Biosynthesis System: Methodology and Perspective of in Vitro Efficient Platform for Pyruvate Biosynthesis and Transformation. , 2021, ACS synthetic biology.

[12]  Xueli Zhang,et al.  Metabolic engineering of microorganisms for L-alanine production , 2021, Journal of industrial microbiology & biotechnology.

[13]  P. Lindblad,et al.  Current advances in engineering cyanobacteria and their applications for photosynthetic butanol production. , 2021, Current opinion in biotechnology.

[14]  Xueqin Lv,et al.  Multilayer Genetic Circuits for Dynamic Regulation of Metabolic Pathways. , 2021, ACS synthetic biology.

[15]  T. Hanai,et al.  Design of Synthetic Quorum Sensing Achieving Induction Timing-Independent Signal Stabilization for Dynamic Metabolic Engineering of E. coli. , 2021, ACS synthetic biology.

[16]  Shangtian Yang,et al.  Engineering the 2,3-BD pathway in Bacillus subtilis by shifting the carbon flux in favor of 2,3-BD synthesis , 2021 .

[17]  M. Eiteman,et al.  Pyruvate Production by Escherichia coli by Use of Pyruvate Dehydrogenase Variants , 2021, Applied and environmental microbiology.

[18]  Shangtian Yang,et al.  Engineering Clostridium cellulovorans for highly selective n‐butanol production from cellulose in consolidated bioprocessing , 2021, Biotechnology and bioengineering.

[19]  Yulong Yin,et al.  Butyrate in Energy Metabolism: There Is Still More to Learn , 2021, Trends in Endocrinology & Metabolism.

[20]  Ibham Veza,et al.  Recent advances in butanol production by acetone-butanol-ethanol (ABE) fermentation , 2021 .

[21]  D. Dubal,et al.  Pretreatment and fermentation of lignocellulosic biomass: reaction mechanisms and process engineering , 2020 .

[22]  C. Taylor,et al.  Regulation of glycolysis by the hypoxia‐inducible factor (HIF): implications for cellular physiology , 2020, The Journal of physiology.

[23]  Xueqin Lv,et al.  Current advance in biological production of short-chain organic acid , 2020, Applied Microbiology and Biotechnology.

[24]  Long Liu,et al.  Pyruvate-responsive genetic circuits for dynamic control of central metabolism , 2020, Nature Chemical Biology.

[25]  Qipeng Yuan,et al.  Application of dynamic regulation strategies in metabolic engineering , 2020 .

[26]  J. Nielsen,et al.  Rewiring carbon flux in Escherichia coli using a bifunctional molecular switch. , 2020, Metabolic engineering.

[27]  Ethan I. Lan,et al.  Metabolic Engineering Design Strategies for Increasing Acetyl-CoA Flux , 2020, Metabolites.

[28]  C. Kerfeld,et al.  Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering , 2019, BMC Biology.

[29]  M. Eppink,et al.  Integrated Product Recovery Will Boost Industrial Cyanobacterial Processes. , 2019, Trends in biotechnology.

[30]  Christopher A. Voigt,et al.  Retrosynthetic design of metabolic pathways to chemicals not found in nature , 2019, Current Opinion in Systems Biology.

[31]  K. Shanmugam,et al.  Metabolic engineering of Escherichia coli for the production of butyric acid at high titer and productivity , 2019, Biotechnology for Biofuels.

[32]  J. Liao,et al.  Metabolome analysis revealed the knockout of glyoxylate shunt as an effective strategy for improvement of 1-butanol production in transgenic Escherichia coli. , 2019, Journal of bioscience and bioengineering.

[33]  Ethan I. Lan,et al.  Photoautotrophic synthesis of butyrate by metabolically engineered cyanobacteria , 2018, Biotechnology and bioengineering.

[34]  Jian Chen,et al.  Enhancement of pyruvic acid production in Candida glabrata by engineering hypoxia-inducible factor 1. , 2019, Bioresource technology.

[35]  Sven Kerzenmacher,et al.  Engineering of Microbial Electrodes. , 2019, Advances in biochemical engineering/biotechnology.

[36]  S. Pflügl,et al.  Engineered E. coli W enables efficient 2,3-butanediol production from glucose and sugar beet molasses using defined minimal medium as economic basis , 2018, Microbial Cell Factories.

[37]  H. Shimizu,et al.  A pyruvate carbon flux tugging strategy for increasing 2,3-butanediol production and reducing ethanol subgeneration in the yeast Saccharomyces cerevisiae , 2018, Biotechnology for Biofuels.

[38]  Tao Chen,et al.  Highly efficient hemicellulose utilization for acetoin production by an engineeredBacillus subtilis , 2018, Journal of Chemical Technology & Biotechnology.

[39]  Carole Goble,et al.  An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals , 2018, Communications Biology.

[40]  J. Krömer,et al.  Microbial Electrosynthesis of Isobutyric, Butyric, Caproic Acids, and Corresponding Alcohols from Carbon Dioxide , 2018, ACS Sustainable Chemistry & Engineering.

[41]  Zak Costello,et al.  A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data , 2018, npj Systems Biology and Applications.

[42]  H. Kawaguchi,et al.  Metabolome analysis-based design and engineering of a metabolic pathway in Corynebacterium glutamicum to match rates of simultaneous utilization of d-glucose and l-arabinose , 2018, Microbial Cell Factories.

[43]  Jing Liang,et al.  Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision , 2018, Nature Biotechnology.

[44]  Jufang Wang,et al.  Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production with high butyrate/acetate ratio , 2018, Applied Microbiology and Biotechnology.

[45]  Jufang Wang,et al.  Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production with high butyrate/acetate ratio , 2018, Applied Microbiology and Biotechnology.

[46]  Q. Zeng,et al.  Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation. , 2018, Bioresource technology.

[47]  Min Liu,et al.  Regulation of NADH Oxidase Expression via a Thermo-regulated Genetic Switch for Pyruvate Production in Escherichia coli , 2018, Biotechnology and Bioprocess Engineering.

[48]  Kristala L. J. Prather,et al.  Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli , 2018, Proceedings of the National Academy of Sciences.

[49]  Lichun Dong,et al.  A novel riboregulator switch system of gene expression for enhanced microbial production of succinic acid , 2018, Journal of Industrial Microbiology & Biotechnology.

[50]  Jian Chen,et al.  Enhanced pyruvate production in Candida glabrata by carrier engineering , 2018, Biotechnology and bioengineering.

[51]  Jufang Wang,et al.  Butyric acid production from lignocellulosic biomass hydrolysates by engineered Clostridium tyrobutyricum overexpressing Class I heat shock protein GroESL. , 2018, Bioresource technology.

[52]  J. Nielsen,et al.  DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. , 2018, Chemical reviews.

[53]  M. Eiteman,et al.  Conversion of glucose‐xylose mixtures to pyruvate using a consortium of metabolically engineered Escherichia coli , 2018, Engineering in life sciences.

[54]  H. Gavala,et al.  Continuous fermentation and kinetic experiments for the conversion of crude glycerol derived from second-generation biodiesel into 1,3 propanediol and butyric acid , 2017 .

[55]  Yi Wang,et al.  Enhancement of solvent production by overexpressing key genes of the acetone-butanol-ethanol fermentation pathway in Clostridium saccharoperbutylacetonicum N1-4. , 2017, Bioresource technology.

[56]  Dae-Hee Lee,et al.  CRISPR interference-guided multiplex repression of endogenous competing pathway genes for redirecting metabolic flux in Escherichia coli , 2017, Microbial Cell Factories.

[57]  M. Oh,et al.  Pathway engineering of Enterobacter aerogenes to improve acetoin production by reducing by-products formation. , 2017, Enzyme and microbial technology.

[58]  Jesús Colprim,et al.  Microbial electrosynthesis of butyrate from carbon dioxide: Production and extraction. , 2017, Bioelectrochemistry.

[59]  Maohua Yang,et al.  Improvement of pyruvate production based on regulation of intracellular redox state in engineered Escherichia coli , 2017, Biotechnology and Bioprocess Engineering.

[60]  Shangtian Yang,et al.  Butyric acid production from lignocellulosic biomass hydrolysates by engineered Clostridium tyrobutyricum overexpressing xylose catabolism genes for glucose and xylose co-utilization. , 2017, Bioresource technology.

[61]  K. Matsushita,et al.  Butyrate production under aerobic growth conditions by engineered Escherichia coli. , 2017, Journal of bioscience and bioengineering.

[62]  M. Eiteman,et al.  Recent Progress in the Microbial Production of Pyruvic Acid , 2017 .

[63]  Akansha Srivastava,et al.  Strategies for Fermentation Medium Optimization: An In-Depth Review , 2017, Front. Microbiol..

[64]  Ryan T Gill,et al.  Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering , 2016, Nature Biotechnology.

[65]  Claire R. Shen,et al.  Selection of an endogenous 2,3-butanediol pathway in Escherichia coli by fermentative redox balance. , 2017, Metabolic engineering.

[66]  Hironaga Akita,et al.  Pyruvate production using engineered Escherichia coli , 2016, AMB Express.

[67]  E. Papoutsakis,et al.  Engineering membrane and cell-wall programs for tolerance to toxic chemicals: Beyond solo genes. , 2016, Current opinion in microbiology.

[68]  S. Atsumi,et al.  2,3 Butanediol production in an obligate photoautotrophic cyanobacterium in dark conditions via diverse sugar consumption. , 2016, Metabolic engineering.

[69]  Gaohua Yang,et al.  Improving the performance of solventogenic clostridia by reinforcing the biotin synthetic pathway. , 2016, Metabolic engineering.

[70]  Yin Li,et al.  Engineering Escherichia coli Cell Factories for n-Butanol Production. , 2016, Advances in biochemical engineering/biotechnology.

[71]  Carlos Martín,et al.  Pretreatment of lignocellulose: Formation of inhibitory by-products and strategies for minimizing their effects. , 2016, Bioresource technology.

[72]  Jin-Ho Seo,et al.  Simultaneous conversion of glucose and xylose to 3-hydroxypropionic acid in engineered Escherichia coli by modulation of sugar transport and glycerol synthesis. , 2015, Bioresource technology.

[73]  Huimin Zhao,et al.  Rapid prototyping of microbial cell factories via genome-scale engineering. , 2015, Biotechnology advances.

[74]  Shangtian Yang,et al.  Metabolic engineering of Clostridium tyrobutyricum for n‐butanol production through co‐utilization of glucose and xylose , 2015, Biotechnology and bioengineering.

[75]  B. Jiang,et al.  Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine , 2015, Nature Communications.

[76]  Irene M. Brockman,et al.  Dynamic metabolic engineering: New strategies for developing responsive cell factories , 2015, Biotechnology journal.

[77]  Markus J. Herrgård,et al.  Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production. , 2015, Metabolic engineering.

[78]  Shangtian Yang,et al.  Enhanced 2,3-butanediol production from biodiesel-derived glycerol by engineering of cofactor regeneration and manipulating carbon flux in Bacillus amyloliquefaciens , 2015, Microbial Cell Factories.

[79]  D. Wei,et al.  R-acetoin accumulation and dissimilation in Klebsiella pneumoniae , 2015, Journal of Industrial Microbiology & Biotechnology.

[80]  S. Atsumi,et al.  Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria. , 2015, ACS synthetic biology.

[81]  Q. Gao,et al.  Metabolic engineering of Saccharomyces cerevisiae for accumulating pyruvic acid , 2015, Annals of Microbiology.

[82]  J Colprim,et al.  Microbial electrosynthesis of butyrate from carbon dioxide. , 2015, Chemical communications.

[83]  Li Zhou,et al.  Efficient L-Alanine Production by a Thermo-Regulated Switch in Escherichia coli , 2015, Applied Biochemistry and Biotechnology.

[84]  M. Chang,et al.  Microbial tolerance engineering toward biochemical production: from lignocellulose to products. , 2014, Current opinion in biotechnology.

[85]  Seth D. Axen,et al.  A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method , 2014, PLoS Comput. Biol..

[86]  M. Oh,et al.  Improvement of 2,3-Butanediol Yield in Klebsiella pneumoniae by Deletion of the Pyruvate Formate-Lyase Gene , 2014, Applied and Environmental Microbiology.

[87]  Ali Samy Abdelaal,et al.  Genetic improvement of n-butanol tolerance in Escherichia coli by heterologous overexpression of groESL operon from Clostridium acetobutylicum , 2014, 3 Biotech.

[88]  K. Dercová,et al.  Response Mechanisms of Bacterial Degraders to Environmental Contaminants on the Level of Cell Walls and Cytoplasmic Membrane , 2014, International journal of microbiology.

[89]  Zhenghong Xu,et al.  The rebalanced pathway significantly enhances acetoin production by disruption of acetoin reductase gene and moderate-expression of a new water-forming NADH oxidase in Bacillus subtilis. , 2014, Metabolic engineering.

[90]  Zijun Xiao,et al.  Strategies for enhancing fermentative production of acetoin: a review. , 2014, Biotechnology Advances.

[91]  Nan Xu,et al.  Engineering of carboligase activity reaction in Candida glabrata for acetoin production. , 2014, Metabolic engineering.

[92]  Luis H. Reyes,et al.  Improving carotenoids production in yeast via adaptive laboratory evolution. , 2014, Metabolic engineering.

[93]  Katsunori Yoshikawa,et al.  A Vector Library for Silencing Central Carbon Metabolism Genes with Antisense RNAs in Escherichia coli , 2013, Applied and Environmental Microbiology.

[94]  Z. Rao,et al.  Moderate expression of the transcriptional regulator ALsR enhances acetoin production by Bacillus subtilis , 2013, Journal of Industrial Microbiology & Biotechnology.

[95]  Ralf Takors,et al.  Platform Engineering of Corynebacterium glutamicum with Reduced Pyruvate Dehydrogenase Complex Activity for Improved Production of l-Lysine, l-Valine, and 2-Ketoisovalerate , 2013, Applied and Environmental Microbiology.

[96]  Jong Myoung Park,et al.  In silico aided metabolic engineering of Klebsiella oxytoca and fermentation optimization for enhanced 2,3-butanediol production , 2013, Journal of Industrial Microbiology & Biotechnology.

[97]  He Huang,et al.  Cofactor engineering through heterologous expression of an NADH oxidase and its impact on metabolic flux redistribution in Klebsiella pneumoniae , 2013, Biotechnology for Biofuels.

[98]  Luis H. Reyes,et al.  Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli. , 2012, Metabolic engineering.

[99]  Liao-Yuan Zhang,et al.  Enhanced acetoin production by Serratia marcescens H32 with expression of a water-forming NADH oxidase. , 2012, Bioresource technology.

[100]  James C. Liao,et al.  ATP drives direct photosynthetic production of 1-butanol in cyanobacteria , 2012, Proceedings of the National Academy of Sciences.

[101]  James C Liao,et al.  Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. , 2011, Metabolic engineering.

[102]  M. Oh,et al.  Effects of carbon source and metabolic engineering on butyrate production in Escherichia coli , 2011 .

[103]  K. Rabaey,et al.  Microbial electrosynthesis — revisiting the electrical route for microbial production , 2010, Nature Reviews Microbiology.

[104]  Masayuki Inui,et al.  Engineering of sugar metabolism of Corynebacterium glutamicum for production of amino acid l-alanine under oxygen deprivation , 2010, Applied Microbiology and Biotechnology.

[105]  He Huang,et al.  Engineering Klebsiella oxytoca for efficient 2, 3-butanediol production through insertional inactivation of acetaldehyde dehydrogenase gene , 2010, Applied Microbiology and Biotechnology.

[106]  Liming Liu,et al.  Enhancement of pyruvate productivity by inducible expression of a F(0)F(1)-ATPase inhibitor INH1 in Torulopsis glabrata CCTCC M202019. , 2009, Journal of biotechnology.

[107]  Weihong Jiang,et al.  Disruption of the acetoacetate decarboxylase gene in solvent-producing Clostridium acetobutylicum increases the butanol ratio. , 2009, Metabolic engineering.

[108]  M. Eiteman,et al.  High Glycolytic Flux Improves Pyruvate Production by a Metabolically Engineered Escherichia coli Strain , 2008, Applied and Environmental Microbiology.

[109]  Duane T. Johnson,et al.  The glycerin glut: Options for the value‐added conversion of crude glycerol resulting from biodiesel production , 2007 .

[110]  Xueli Zhang,et al.  Production of l-alanine by metabolically engineered Escherichia coli , 2007, Applied Microbiology and Biotechnology.

[111]  P. Xu,et al.  Acetoin Metabolism in Bacteria , 2007, Critical reviews in microbiology.

[112]  Shangtian Yang,et al.  Construction and Characterization of ack Deleted Mutant of Clostridium tyrobutyricum for Enhanced Butyric Acid and Hydrogen Production , 2008, Biotechnology progress.

[113]  Liming Liu,et al.  Enhancement of pyruvate productivity in Torulopsis glabrata: Increase of NAD+ availability. , 2006, Journal of biotechnology.

[114]  Sarah A. Lee,et al.  Fed-batch two-phase production of alanine by a metabolically engineered Escherichia coli , 2006, Biotechnology Letters.

[115]  G. Du,et al.  Increasing glycolytic flux in Torulopsis glabrata by redirecting ATP production from oxidative phosphorylation to substrate‐level phosphorylation , 2006, Journal of applied microbiology.

[116]  M. A. Eiteman,et al.  Aerobic production of alanine by Escherichia coli aceF ldhA mutants expressing the Bacillus sphaericus alaD gene , 2004, Applied Microbiology and Biotechnology.

[117]  B. Svensson,et al.  Alanine as an end product during fermentation of monosaccharides byClostridium strain P2 , 1995, Antonie van Leeuwenhoek.

[118]  Christian Solem,et al.  Glyceraldehyde-3-Phosphate Dehydrogenase Has No Control over Glycolytic Flux in Lactococcus lactis MG1363 , 2003, Journal of bacteriology.

[119]  M. A. Eiteman,et al.  The effect of acetate pathway mutations on the production of pyruvate in Escherichia coli , 2003, Applied Microbiology and Biotechnology.

[120]  K. Shanmugam,et al.  Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: Homoacetate production , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[121]  S. Oliver Metabolism: Demand management in cells , 2002, Nature.

[122]  S. Lun,et al.  Biotechnological production of pyruvic acid , 2001, Applied Microbiology and Biotechnology.

[123]  V. S. Bisaria,et al.  Simultaneous bioconversion of glucose and xylose to ethanol by Saccharomyces cerevisiae in the presence of xylose isomerase , 2000, Applied Microbiology and Biotechnology.

[124]  R. Katsumata,et al.  l-Alanine fermentation by an alanine racemase-deficient mutant of the dl-alanine hyperproducing bacterium Arthrobacter oxydans HAP-1 , 1998 .

[125]  A. Mesecar,et al.  Metal-ion-mediated allosteric triggering of yeast pyruvate kinase. 1. A multidimensional kinetic linked-function analysis. , 1997, Biochemistry.

[126]  H. Shimizu,et al.  Pyruvic acid production by an F1-ATPase-defective mutant of Escherichia coli W1485lip2. , 1994, Bioscience, biotechnology, and biochemistry.

[127]  P. R. Jensen,et al.  Carbon and energy metabolism of atp mutants of Escherichia coli , 1992, Journal of bacteriology.

[128]  T. Montville,et al.  Conversion of Pyruvate to Acetoin Helps To Maintain pH Homeostasis in Lactobacillus plantarum , 1992, Applied and environmental microbiology.

[129]  G. Stephanopoulos,et al.  Network rigidity and metabolic engineering in metabolite overproduction , 1991, Science.

[130]  H Sahm,et al.  Expression of an L-alanine dehydrogenase gene in Zymomonas mobilis and excretion of L-alanine , 1991, Applied and environmental microbiology.

[131]  N. Kosaric,et al.  The Microbial Production of 2,3-Butanediol , 1987 .

[132]  K. Soda,et al.  Purification and properties of alanine dehydrogenase from Bacillus sphaericus. , 1979, European journal of biochemistry.

[133]  U. Henning,et al.  Regulation of pyruvate dehydrogenase activity in Escherichia coli K12. , 1966, Biochimica et biophysica acta.