Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering.

The advent of various systems metabolic engineering tools and strategies has enabled more sophisticated engineering of microorganisms for the production of industrially useful fuels and chemicals. Advances in systems metabolic engineering have been made in overproducing natural chemicals and producing novel non-natural chemicals. In this paper, we review the tools and strategies of systems metabolic engineering employed for the development of microorganisms for the production of various industrially useful chemicals belonging to fuels, building block chemicals, and specialty chemicals, in particular focusing on those reported in the last three years. It was aimed at providing the current landscape of systems metabolic engineering and suggesting directions to address future challenges towards successfully establishing processes for the bio-based production of fuels and chemicals from renewable resources.

[1]  M. Xian,et al.  Biosynthetic pathways for 3-hydroxypropionic acid production , 2009, Applied Microbiology and Biotechnology.

[2]  王萌,et al.  Latest Advances of Microbial Production of 2,3-Butanediol , 2012 .

[3]  Denis Thieffry,et al.  Dynamical roles of biological regulatory circuits , 2007, Briefings Bioinform..

[4]  Tsewei Wang,et al.  SMET: systematic multiple enzyme targeting - a method to rationally design optimal strains for target chemical overproduction. , 2013, Biotechnology journal.

[5]  C. Nakamura,et al.  Metabolic engineering for the microbial production of 1,3-propanediol. , 2003, Current opinion in biotechnology.

[6]  S. Lee,et al.  Fed‐batch culture of Escherichia coli for L‐valine production based on in silico flux response analysis , 2011, Biotechnology and bioengineering.

[7]  M. Okabe,et al.  Breeding of Aspergillus terreus mutant TN-484 for itaconic acid production with high yield , 1995 .

[8]  J. Keasling,et al.  Microbial production of fatty-acid-derived fuels and chemicals from plant biomass , 2010, Nature.

[9]  Ka-Yiu San,et al.  Fed-batch culture of a metabolically engineered Escherichia coli strain designed for high-level succinate production and yield under aerobic conditions. , 2005, Biotechnology and bioengineering.

[10]  Philippe Soucaille,et al.  A new process for the continuous production of succinic acid from glucose at high yield, titer, and productivity , 2008, Biotechnology and bioengineering.

[11]  Christoph Wittmann,et al.  Metabolic engineering of cellular transport for overproduction of the platform chemical 1,5-diaminopentane in Corynebacterium glutamicum. , 2011, Metabolic engineering.

[12]  H. Takagi,et al.  Metabolic Engineering of Saccharomyces cerevisiae for Astaxanthin Production and Oxidative Stress Tolerance , 2009, Applied and Environmental Microbiology.

[13]  Jong Myoung Park,et al.  Genome-scale analysis of Mannheimia succiniciproducens metabolism. , 2007, Biotechnology and bioengineering.

[14]  Akihiko Kondo,et al.  Enhanced production of 2,3-butanediol by engineered Bacillus subtilis , 2011, Applied Microbiology and Biotechnology.

[15]  James M Clomburg,et al.  Efficient synthesis of L-lactic acid from glycerol by metabolically engineered Escherichia coli , 2013, Microbial Cell Factories.

[16]  Deokjin Jahng,et al.  Enhanced butanol production in Clostridium acetobutylicum ATCC 824 by double overexpression of 6-phosphofructokinase and pyruvate kinase genes , 2013, Applied Microbiology and Biotechnology.

[17]  A. Burgard,et al.  Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. , 2011, Nature chemical biology.

[18]  Y. Jang,et al.  Metabolic engineering of Clostridium acetobutylicum M 5 for highly selective butanol production , 2009 .

[19]  Jian-Zhong Liu,et al.  Chromosomal evolution of Escherichia coli for the efficient production of lycopene , 2013, BMC Biotechnology.

[20]  Sha Li,et al.  Optimization of medium for one-step fermentation of inulin extract from Jerusalem artichoke tubers using Paenibacillus polymyxa ZJ-9 to produce R,R-2,3-butanediol. , 2010, Bioresource technology.

[21]  V. Wendisch,et al.  Putrescine production by engineered Corynebacterium glutamicum , 2010, Applied Microbiology and Biotechnology.

[22]  Sang Yup Lee,et al.  Escherichia coli W as a new platform strain for the enhanced production of L‐Valine by systems metabolic engineering , 2011, Biotechnology and bioengineering.

[23]  Brian F Pfleger,et al.  A process for microbial hydrocarbon synthesis: Overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes , 2010, Biotechnology and bioengineering.

[24]  J. Liao,et al.  Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels , 2008, Nature.

[25]  F. Srienc,et al.  Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses , 2008, Applied and Environmental Microbiology.

[26]  M. Oh,et al.  Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering , 2011, Microbial Cell Factories.

[27]  Matthew D. Smith,et al.  Expanding the product profile of a microbial alkane biosynthetic pathway. , 2013, ACS synthetic biology.

[28]  J. Liao,et al.  Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. , 2008, Metabolic engineering.

[29]  Xiao-Xia Xia,et al.  Direct biosynthesis of adipic acid from a synthetic pathway in recombinant Escherichia coli. , 2014, Biotechnology and bioengineering.

[30]  Chao Huang,et al.  Engineering Clostridium acetobutylicum for alcohol production. , 2013, Journal of biotechnology.

[31]  Jian Chen,et al.  Fumaric Acid Production in Saccharomyces cerevisiae by In Silico Aided Metabolic Engineering , 2012, PloS one.

[32]  Cuiqing Ma,et al.  Systematic metabolic engineering of Escherichia coli for high-yield production of fuel bio-chemical 2,3-butanediol. , 2014, Metabolic engineering.

[33]  J. Liao,et al.  Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli , 2011, Applied and Environmental Microbiology.

[34]  Christoph Wittmann,et al.  Systems and synthetic metabolic engineering for amino acid production - the heartbeat of industrial strain development. , 2012, Current opinion in biotechnology.

[35]  L. Eggeling,et al.  Pushing product formation to its limit: metabolic engineering of Corynebacterium glutamicum for L-leucine overproduction. , 2014, Metabolic engineering.

[36]  S. Lee,et al.  Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation , 2005, Applied and Environmental Microbiology.

[37]  James C Liao,et al.  Synergy as design principle for metabolic engineering of 1-propanol production in Escherichia coli. , 2013, Metabolic engineering.

[38]  Dae-Hyuk Kim,et al.  Identification and characterization of Klebsiella pneumoniae aldehyde dehydrogenases increasing production of 3-hydroxypropionic acid from glycerol , 2013, Bioprocess and Biosystems Engineering.

[39]  K. Prather,et al.  Engineering alternative butanol production platforms in heterologous bacteria. , 2009, Metabolic engineering.

[40]  C. Wittmann,et al.  From zero to hero--design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. , 2011, Metabolic engineering.

[41]  Tae Seok Moon,et al.  Production of Glucaric Acid from a Synthetic Pathway in Recombinant Escherichia coli , 2009, Applied and Environmental Microbiology.

[42]  Xuefeng Lu,et al.  De novo Biosynthesis of Biodiesel by Escherichia coli in Optimized Fed-Batch Cultivation , 2011, PloS one.

[43]  J. W. Frost,et al.  Benzene‐Free Synthesis of Adipic Acid , 2002, Biotechnology progress.

[44]  Gregory Stephanopoulos,et al.  Characterization of lycopene-overproducing E. coli strains in high cell density fermentations , 2006, Applied Microbiology and Biotechnology.

[45]  James C. Liao,et al.  Engineering of an Escherichia coli Strain for the Production of 3-Methyl-1-Butanol , 2008, Applied and Environmental Microbiology.

[46]  Xin Li,et al.  Fumaric Acid Production from Alkali-Pretreated Corncob by Fed-Batch Simultaneous Saccharification and Fermentation Combined with Separated Hydrolysis and Fermentation at High Solids Loading , 2017, Applied Biochemistry and Biotechnology.

[47]  Chikara Furusawa,et al.  Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli , 2014, Microbial Cell Factories.

[48]  Guocheng Du,et al.  Pathway engineering of Bacillus subtilis for microbial production of N-acetylglucosamine. , 2013, Metabolic engineering.

[49]  Jiangang Yang,et al.  Metabolic engineering of Escherichia coli and in silico comparing of carboxylation pathways for high succinate productivity under aerobic conditions. , 2014, Microbiological research.

[50]  S. Lee,et al.  Metabolic engineering of Escherichia coli for the production of cadaverine: A five carbon diamine , 2011, Biotechnology and bioengineering.

[51]  S. Lee,et al.  Metabolic engineering of Escherichia coli for the production of 5-aminovalerate and glutarate as C5 platform chemicals. , 2013, Metabolic engineering.

[52]  Rob Lee,et al.  Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli , 2013, Proceedings of the National Academy of Sciences.

[53]  Gregory Stephanopoulos,et al.  Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli , 2012, Proceedings of the National Academy of Sciences.

[54]  S. M. Raj,et al.  Production of 3-hydroxypropionic acid via malonyl-CoA pathway using recombinant Escherichia coli strains. , 2012, Journal of biotechnology.

[55]  Donovan S. Layton,et al.  Engineering modular ester fermentative pathways in Escherichia coli. , 2014, Metabolic engineering.

[56]  J. Altenbuchner,et al.  Genetic engineering of Pseudomonas putida KT2440 for rapid and high-yield production of vanillin from ferulic acid , 2013, Applied Microbiology and Biotechnology.

[57]  J. Martínez,et al.  Natural Antibiotic Resistance and Contamination by Antibiotic Resistance Determinants: The Two Ages in the Evolution of Resistance to Antimicrobials , 2012, Front. Microbio..

[58]  K. Prather,et al.  Metabolic Engineering of Escherichia coli for Enhanced Production of (R)- and (S)-3-Hydroxybutyrate , 2009, Applied and Environmental Microbiology.

[59]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[60]  Melissa Straffon,et al.  Metabolic production of a novel polymer feedstock, 3-carboxy muconate, from vanillin , 2011, Applied Microbiology and Biotechnology.

[61]  W. Grajek,et al.  Biotechnological production of 2,3-butanediol--current state and prospects. , 2009, Biotechnology advances.

[62]  Yong-Su Jin,et al.  Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation , 2010, Proceedings of the National Academy of Sciences.

[63]  Yinjie J. Tang,et al.  Photoautotrophic production of D-lactic acid in an engineered cyanobacterium , 2013, Microbial Cell Factories.

[64]  Jeong Wook Lee,et al.  Microbial production of building block chemicals and polymers. , 2011, Current opinion in biotechnology.

[65]  H. Chang,et al.  Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence , 2008, Applied Microbiology and Biotechnology.

[66]  S. Lee,et al.  Systems Metabolic Engineering for Chemicals and Materials , 2010 .

[67]  Yajun Yan,et al.  Dehydratase mediated 1-propanol production in metabolically engineered Escherichia coli , 2011, Microbial cell factories.

[68]  Susana Vinga,et al.  From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria. , 2013, Biotechnology advances.

[69]  Alyssa M. Redding,et al.  Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol , 2008, Microbial cell factories.

[70]  D. Nielsen,et al.  Microbial production of the aromatic building-blocks (S)-styrene oxide and (R)-1,2-phenylethanediol from renewable resources. , 2013, Biotechnology journal.

[71]  Y. Choi,et al.  Metabolic engineering of Escherichia coli for the production of 1-propanol. , 2012, Metabolic engineering.

[72]  Tae Yong Kim,et al.  Metabolic engineering of Escherichia coli for the production of malic acid , 2008 .

[73]  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.

[74]  E. Papoutsakis,et al.  Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance. , 2008, Metabolic engineering.

[75]  P. van Dijck,et al.  Metabolic engineering of Kluyveromyces lactis for L-ascorbic acid (vitamin C) biosynthesis , 2013, Microbial Cell Factories.

[76]  P. Ouyang,et al.  Microbial 2,3-butanediol production: a state-of-the-art review. , 2011, Biotechnology advances.

[77]  Dong In Kim,et al.  Metabolic engineering of Escherichia coli for the production of fumaric acid , 2013, Biotechnology and bioengineering.

[78]  S. Haynie,et al.  Functional expression of prokaryotic and eukaryotic genes in Escherichia coli for conversion of glucose to p-hydroxystyrene. , 2007, Metabolic engineering.

[79]  J. Keasling,et al.  Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids , 2012, Nature Biotechnology.

[80]  Jeong Wook Lee,et al.  Systems metabolic engineering of microorganisms for natural and non-natural chemicals. , 2012, Nature chemical biology.

[81]  Gregory Stephanopoulos,et al.  Melanin-Based High-Throughput Screen for l-Tyrosine Production in Escherichia coli , 2007, Applied and Environmental Microbiology.

[82]  F. Blattner,et al.  In silico design and adaptive evolution of Escherichia coli for production of lactic acid. , 2005, Biotechnology and bioengineering.

[83]  Wei Liu,et al.  Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels , 2013, Biotechnology for Biofuels.

[84]  Stephen S Fong,et al.  Metabolic engineering of Thermobifida fusca for direct aerobic bioconversion of untreated lignocellulosic biomass to 1-propanol. , 2011, Metabolic engineering.

[85]  S. Lee,et al.  Metabolic engineering of Escherichia coli for the production of putrescine: a four carbon diamine. , 2009, Biotechnology and bioengineering.

[86]  C. Wittmann,et al.  Systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane. , 2010, Metabolic engineering.

[87]  Daoyi Guo,et al.  Metabolic engineering of Escherichia coli for production of fatty acid short-chain esters through combination of the fatty acid and 2-keto acid pathways. , 2014, Metabolic engineering.

[88]  G. Bennett,et al.  Novel pathway engineering design of the anaerobic central metabolic pathway in Escherichia coli to increase succinate yield and productivity. , 2005, Metabolic engineering.

[89]  Guocheng Du,et al.  Spatial modulation of key pathway enzymes by DNA-guided scaffold system and respiration chain engineering for improved N-acetylglucosamine production by Bacillus subtilis. , 2014, Metabolic engineering.

[90]  Alexander Steinbüchel,et al.  β-Carotene production by Saccharomyces cerevisiae with regard to plasmid stability and culture media , 2011, Applied Microbiology and Biotechnology.

[91]  Y. Jang,et al.  Enhanced Butanol Production Obtained by Reinforcing the Direct Butanol-Forming Route in Clostridium acetobutylicum , 2012, mBio.

[92]  James C. Liao,et al.  Production of 2-methyl-1-butanol in engineered Escherichia coli , 2008, Applied Microbiology and Biotechnology.

[93]  Dong-Woo Lee,et al.  Genome-wide analysis of redox reactions reveals metabolic engineering targets for D-lactate overproduction in Escherichia coli. , 2013, Metabolic engineering.

[94]  M. Eiteman,et al.  Homolactate Fermentation by Metabolically Engineered Escherichia coli Strains , 2006, Applied and Environmental Microbiology.

[95]  Hyohak Song,et al.  Genome-Based Metabolic Engineering of Mannheimia succiniciproducens for Succinic Acid Production , 2006, Applied and Environmental Microbiology.

[96]  Xueli Zhang,et al.  Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate , 2008, Biotechnology and bioengineering.

[97]  C. Trinh,et al.  Enhancing fatty acid ethyl ester production in Saccharomyces cerevisiae through metabolic engineering and medium optimization , 2014, Biotechnology and bioengineering.

[98]  Xueli Zhang,et al.  Engineering central metabolic modules of Escherichia coli for improving β-carotene production. , 2013, Metabolic engineering.

[99]  Kristala L. J. Prather,et al.  Biosynthesis of chiral 3-hydroxyvalerate from single propionate-unrelated carbon sources in metabolically engineered E. coli , 2010, Microbial cell factories.

[100]  J. Chu,et al.  Microbial production of 2,3-butanediol by a mutagenized strain of Serratia marcescens H30. , 2010, Bioresource technology.

[101]  Masayuki Inui,et al.  An efficient succinic acid production process in a metabolically engineered Corynebacterium glutamicum strain , 2008, Applied Microbiology and Biotechnology.

[102]  Shangtian Yang,et al.  Metabolic engineering of Clostridium tyrobutyricum for n-butanol production from sugarcane juice , 2017, Applied Microbiology and Biotechnology.

[103]  J. Keasling,et al.  Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals. , 2014, Metabolic engineering.

[104]  H. Sahm,et al.  Isolation and prominent characteristics of an L-lysine hyperproducing strain of Corynebacterium glutamicum , 1992, Applied Microbiology and Biotechnology.

[105]  V. Zverlov,et al.  Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis , 2010, Applied Microbiology and Biotechnology.

[106]  Jing Wang,et al.  High-Level Production of Beta-Carotene in Saccharomyces cerevisiae by Successive Transformation with Carotenogenic Genes from Xanthophyllomyces dendrorhous , 2007, Applied and Environmental Microbiology.

[107]  Shangtian Yang,et al.  Effects of different replicons in conjugative plasmids on transformation efficiency, plasmid stability, gene expression and n-butanol biosynthesis in Clostridium tyrobutyricum , 2011, Applied Microbiology and Biotechnology.

[108]  G. Stephanopoulos,et al.  Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. , 2007, Metabolic engineering.

[109]  F. Sato,et al.  A bacterial platform for fermentative production of plant alkaloids , 2011, Nature communications.

[110]  Shang-Tian Yang,et al.  Metabolic engineering of Propionibacterium freudenreichii for n-propanol production , 2013, Applied Microbiology and Biotechnology.

[111]  Kathleen A. Curran,et al.  Expanding the chemical palate of cells by combining systems biology and metabolic engineering. , 2012, Metabolic engineering.

[112]  D. Na,et al.  Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli , 2013, Nature Protocols.

[113]  A. Zeng,et al.  Production of 2,3-butanediol in a membrane bioreactor with cell recycle , 2004, Applied Microbiology and Biotechnology.

[114]  J. Park,et al.  Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs , 2013, Nature Biotechnology.

[115]  Kristala L J Prather,et al.  A platform pathway for production of 3-hydroxyacids provides a biosynthetic route to 3-hydroxy-γ-butyrolactone , 2013, Nature Communications.

[116]  Ana Rita Brochado,et al.  Improved vanillin production in baker's yeast through in silico design , 2010, Microbial cell factories.

[117]  S. Lee,et al.  Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation , 2007, Proceedings of the National Academy of Sciences.

[118]  Y. Choi,et al.  Microbial production of short-chain alkanes , 2013, Nature.

[119]  Farren J. Isaacs,et al.  Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement , 2011, Science.

[120]  L. Jarboe,et al.  Development of ethanologenic bacteria. , 2007, Advances in biochemical engineering/biotechnology.

[121]  Vinod Kumar,et al.  Recent advances in biological production of 3-hydroxypropionic acid. , 2013, Biotechnology advances.

[122]  Jens Nielsen,et al.  Improved production of fatty acid ethyl esters in Saccharomyces cerevisiae through up-regulation of the ethanol degradation pathway and expression of the heterologous phosphoketolase pathway , 2014, Microbial Cell Factories.

[123]  Yong‐Su Jin,et al.  Production of 2,3-butanediol by engineered Saccharomyces cerevisiae. , 2013, Bioresource technology.

[124]  D. Nielsen,et al.  Styrene biosynthesis from glucose by engineered E. coli. , 2011, Metabolic engineering.

[125]  D. Nielsen,et al.  Engineering microbial chemical factories to produce renewable “biomonomers” , 2012, Front. Microbio..

[126]  James C. Liao,et al.  Directed Evolution of Methanococcus jannaschii Citramalate Synthase for Biosynthesis of 1-Propanol and 1-Butanol by Escherichia coli , 2008, Applied and Environmental Microbiology.

[127]  A. Schirmer,et al.  Microbial Biosynthesis of Alkanes , 2010, Science.

[128]  Kazuyuki Shimizu,et al.  Modification of metabolic pathways of Saccharomyces cerevisiae by the expression of lactate dehydrogenase and deletion of pyruvate decarboxylase genes for the lactic acid fermentation at low pH value , 1998 .

[129]  Vinod Kumar,et al.  Effect of puuC overexpression and nitrate addition on glycerol metabolism and anaerobic 3-hydroxypropionic acid production in recombinant Klebsiella pneumoniae ΔglpKΔdhaT. , 2013, Metabolic engineering.