Microbial engineering strategies to improve cell viability for biochemical production.

Efficient production of biochemicals using engineered microbes as whole-cell biocatalysts requires robust cell viability. Robust viability leads to high productivity and improved bioprocesses by allowing repeated cell recycling. However, cell viability is negatively affected by a plethora of stresses, namely chemical toxicity and metabolic imbalances, primarily resulting from bio-synthesis pathways. Chemical toxicity is caused by substrates, intermediates, products, and/or by-products, and these compounds often interfere with important metabolic processes and damage cellular infrastructures such as cell membrane, leading to poor cell viability. Further, stresses on engineered cells are accentuated by metabolic imbalances, which are generated by heavy metabolic resource consumption due to enzyme overexpression, redistribution of metabolic fluxes, and impaired intracellular redox state by co-factor imbalance. To address these challenges, herein, we discuss a range of key microbial engineering strategies, substantiated by recent advances, to improve cell viability for commercially sustainable production of biochemicals from renewable resources.

[1]  G. Stephanopoulos,et al.  Global transcription machinery engineering: a new approach for improving cellular phenotype. , 2007, Metabolic engineering.

[2]  W. V. van Zyl,et al.  The metabolic burden of the PGK1 and ADH2 promoter systems for heterologous xylanase production by Saccharomyces cerevisiae in defined medium. , 2001, Biotechnology and bioengineering.

[3]  L. Hou,et al.  Improved Production of Ethanol by Novel Genome Shuffling in Saccharomyces cerevisiae , 2010, Applied biochemistry and biotechnology.

[4]  D. Rees,et al.  ABC transporters: the power to change , 2009, Nature Reviews Molecular Cell Biology.

[5]  Mojca Benčina,et al.  DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency , 2011, Nucleic acids research.

[6]  G. Church,et al.  Analysis of optimality in natural and perturbed metabolic networks , 2002 .

[7]  Paul V. Attfield,et al.  Stress tolerance: The key to effective strains of industrial baker's yeast , 1997, Nature Biotechnology.

[8]  Jun Hyoung Lee,et al.  Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli , 2008, Nucleic acids research.

[9]  Jay D. Keasling,et al.  A model for improving microbial biofuel production using a synthetic feedback loop , 2010, Systems and Synthetic Biology.

[10]  Alfonso Jaramillo,et al.  DESHARKY: automatic design of metabolic pathways for optimal cell growth , 2008, Bioinform..

[11]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[12]  G. Stephanopoulos,et al.  Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production , 2006, Science.

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

[14]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[15]  Colin Hughes,et al.  Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export , 2000, Nature.

[16]  J. Keasling Manufacturing Molecules Through Metabolic Engineering , 2010, Science.

[17]  Kate Thodey,et al.  Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. , 2012, Metabolic engineering.

[18]  Claudia Schmidt-Dannert,et al.  Engineered Protein Nano-Compartments for Targeted Enzyme Localization , 2012, PloS one.

[19]  M. Chang,et al.  Identification and reconstitution of genetic regulatory networks for improved microbial tolerance to isooctane. , 2012, Molecular bioSystems.

[20]  Ryan T Gill,et al.  Genes restoring redox balance in fermentation-deficient E. coli NZN111. , 2009, Metabolic engineering.

[21]  Alan Villalobos,et al.  Designing genes for successful protein expression. , 2011, Methods in enzymology.

[22]  R. Aono,et al.  Entry into and Release of Solvents byEscherichia coli in an Organic-Aqueous Two-Liquid-Phase System and Substrate Specificity of the AcrAB-TolC Solvent-Extruding Pump , 2000, Journal of bacteriology.

[23]  M. Dunlop Engineering microbes for tolerance to next-generation biofuels , 2011, Biotechnology for biofuels.

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

[25]  Harvey W Blanch,et al.  Escherichia coli for biofuel production: bridging the gap from promise to practice. , 2012, Trends in biotechnology.

[26]  E. Papoutsakis,et al.  A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation. , 2010, Metabolic engineering.

[27]  Chueh Loo Poh,et al.  Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen , 2011, Molecular systems biology.

[28]  Jay D. Keasling,et al.  Engineering Static and Dynamic Control of Synthetic Pathways , 2010, Cell.

[29]  Jin-Ho Seo,et al.  Analysis of E. coli phoA‐lacZ fusion gene expression inserted into a multicopy plasmid and host cell's chromosome , 1990, Biotechnology and bioengineering.

[30]  E. Bokma,et al.  Directed evolution of a bacterial efflux pump: Adaptation of the E. coli TolC exit duct to the Pseudomonas MexAB translocase , 2006, FEBS letters.

[31]  M. Oldiges,et al.  Metabolic impact of redox cofactor perturbations in Saccharomyces cerevisiae. , 2009, Metabolic engineering.

[32]  W. R. Farmer,et al.  Improving lycopene production in Escherichia coli by engineering metabolic control , 2000, Nature Biotechnology.

[33]  Terence Hwa,et al.  Bacterial growth laws and their applications. , 2011, Current opinion in biotechnology.

[34]  V. Price,et al.  Expression of heterologous proteins in Saccharomyces cerevisiae using the ADH2 promoter. , 1990, Methods in enzymology.

[35]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[36]  Alan Villalobos,et al.  Gene Designer: a synthetic biology tool for constructing artificial DNA segments , 2006, BMC Bioinformatics.

[37]  D. Oh,et al.  Directing vanillin production from ferulic acid by increased acetyl‐CoA consumption in recombinant Escherichia coli , 2009, Biotechnology and bioengineering.

[38]  William C. Deloache,et al.  Spatial organization of enzymes for metabolic engineering. , 2012, Metabolic engineering.

[39]  Yan Zhu,et al.  Engineering the robustness of industrial microbes through synthetic biology. , 2012, Trends in microbiology.

[40]  T. Nyström The glucose‐starvation stimulon of Escherichia coli: induced and repressed synthesis of enzymes of central metabolic pathways and role of acetyl phosphate in gene expression and starvation survival , 1994, Molecular microbiology.

[41]  Rainer Breitling,et al.  Computational tools for the synthetic design of biochemical pathways , 2012, Nature Reviews Microbiology.

[42]  Rongrong Jiang,et al.  Random mutagenesis of global transcription factor cAMP receptor protein for improved osmotolerance , 2012, Biotechnology and bioengineering.

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

[44]  Vassily Hatzimanikatis,et al.  Computational framework for predictive biodegradation , 2009, Biotechnology and bioengineering.

[45]  Zhanglin Lin,et al.  Significant Rewiring of the Transcriptome and Proteome of an Escherichia coli Strain Harboring a Tailored Exogenous Global Regulator IrrE , 2012, PloS one.

[46]  J. Gancedo Yeast Carbon Catabolite Repression , 1998, Microbiology and Molecular Biology Reviews.

[47]  Jens Nielsen,et al.  Combined metabolic engineering of precursor and co-factor supply to increase α-santalene production by Saccharomyces cerevisiae , 2012, Microbial Cell Factories.

[48]  E. Duque,et al.  Three Efflux Pumps Are Required To Provide Efficient Tolerance to Toluene in Pseudomonas putidaDOT-T1E , 2001, Journal of bacteriology.

[49]  Fuzhong Zhang,et al.  Biosensors and their applications in microbial metabolic engineering. , 2011, Trends in microbiology.

[50]  Faisal A. Aldaye,et al.  Organization of Intracellular Reactions with Rationally Designed RNA Assemblies , 2011, Science.

[51]  Ana Segura,et al.  Mechanisms of solvent tolerance in gram-negative bacteria. , 2002, Annual review of microbiology.

[52]  Hal S. Alper,et al.  Promoter engineering: Recent advances in controlling transcription at the most fundamental level , 2013, Biotechnology journal.

[53]  Gabriel C. Wu,et al.  Synthetic protein scaffolds provide modular control over metabolic flux , 2009, Nature Biotechnology.

[54]  E. Papoutsakis,et al.  Dynamics of Genomic-Library Enrichment and Identification of Solvent Tolerance Genes for Clostridium acetobutylicum , 2007, Applied and Environmental Microbiology.

[55]  W. R. Cluett,et al.  Dynamic metabolic engineering for increasing bioprocess productivity. , 2008, Metabolic engineering.

[56]  Bernhard O. Palsson,et al.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions , 2010, BMC Bioinformatics.

[57]  L. Blank,et al.  Selected Pseudomonas putida Strains Able To Grow in the Presence of High Butanol Concentrations , 2009, Applied and Environmental Microbiology.

[58]  J. Liao,et al.  An integrated network approach identifies the isobutanol response network of Escherichia coli , 2009, Molecular systems biology.

[59]  M. Oldiges,et al.  Metabolic Impact of Increased NADH Availability in Saccharomyces cerevisiae , 2009, Applied and Environmental Microbiology.

[60]  H. Sahm,et al.  Improving d-mannitol productivity of Escherichia coli: impact of NAD, CO2 and expression of a putative sugar permease from Leuconostoc pseudomesenteroides. , 2009, Metabolic engineering.

[61]  R. Montange,et al.  Riboswitches: emerging themes in RNA structure and function. , 2008, Annual review of biophysics.

[62]  David P. Clark,et al.  The IdhA Gene Encoding the Fermentative Lactate Dehydrogenase of Escherichia Coli , 1997 .

[63]  G. Bennett,et al.  The effect of NAPRTase overexpression on the total levels of NAD, the NADH/NAD+ ratio, and the distribution of metabolites in Escherichia coli. , 2002, Metabolic engineering.

[64]  Pamela A Silver,et al.  Designing biological compartmentalization. , 2012, Trends in cell biology.

[65]  M. Kleerebezem,et al.  Cofactor Engineering: a Novel Approach to Metabolic Engineering in Lactococcus lactis by Controlled Expression of NADH Oxidase , 1998, Journal of bacteriology.

[66]  D. Schnappinger,et al.  Biosynthesis and Recycling of Nicotinamide Cofactors in Mycobacterium tuberculosis , 2008, Journal of Biological Chemistry.

[67]  Ka-Yiu San,et al.  Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD(+)-dependent formate dehydrogenase. , 2002, Metabolic engineering.

[68]  S. Dequin,et al.  Cofactor engineering in Saccharomyces cerevisiae: Expression of a H2O-forming NADH oxidase and impact on redox metabolism. , 2006, Metabolic engineering.

[69]  Sara Hooshangi,et al.  Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli. , 2010, Metabolic engineering.

[70]  V. Hatzimanikatis,et al.  Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3‐hydroxypropanoate , 2010, Biotechnology and bioengineering.

[71]  C. Higgins,et al.  Multiple molecular mechanisms for multidrug resistance transporters , 2007, Nature.

[72]  Julie A. Dickerson,et al.  Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities , 2011, BMC Bioinformatics.

[73]  Jack T Pronk,et al.  Physiological and genetic engineering of cytosolic redox metabolism in Saccharomyces cerevisiae for improved glycerol production. , 2006, Metabolic engineering.

[74]  A. Burgard,et al.  Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.

[75]  M. Futai Stimulation of Transport into Escherichia coli Membrane Vesicles by Internally Generated Reduced Nicotinamide Adenine Dinucleotide , 1974, Journal of bacteriology.

[76]  Vassily Hatzimanikatis,et al.  A computational framework for the design of optimal protein synthesis , 2012, Biotechnology and bioengineering.

[77]  Pamela A Silver,et al.  Natural strategies for the spatial optimization of metabolism in synthetic biology. , 2012, Nature chemical biology.

[78]  S. Günther,et al.  Structural basis of enzyme encapsulation into a bacterial nanocompartment , 2008, Nature Structural &Molecular Biology.

[79]  P. Rogers,et al.  Generation and characterisation of stable ethanol-tolerant mutants of Saccharomyces cerevisiae , 2010, Journal of Industrial Microbiology & Biotechnology.

[80]  J. Collado-Vides,et al.  Regulation by transcription factors in bacteria: beyond description , 2008, FEMS microbiology reviews.

[81]  J. Keasling,et al.  High-throughput metabolic engineering: advances in small-molecule screening and selection. , 2010, Annual review of biochemistry.

[82]  Santiago Garcia-Vallvé,et al.  Working toward a new NIOSH. , 1996, Nucleic Acids Res..

[83]  I. Mannazzu,et al.  Behaviour of Saccharomyces cerevisiae wine strains during adaptation to unfavourable conditions of fermentation on synthetic medium: cell lipid composition, membrane integrity, viability and fermentative activity. , 2008, International journal of food microbiology.

[84]  J. Keasling,et al.  Engineering microbial biofuel tolerance and export using efflux pumps , 2011, Molecular systems biology.

[85]  Miguel C. Teixeira,et al.  Increased expression of the yeast multidrug resistance ABC transporter Pdr18 leads to increased ethanol tolerance and ethanol production in high gravity alcoholic fermentation , 2012, Microbial Cell Factories.

[86]  K. V. van Wijk,et al.  Consequences of Membrane Protein Overexpression in Escherichia coli*S , 2007, Molecular & Cellular Proteomics.

[87]  K. Poole,et al.  Role of the Multidrug Efflux Systems ofPseudomonas aeruginosa in Organic Solvent Tolerance , 1998, Journal of bacteriology.

[88]  Pao-Yang Chen,et al.  Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli , 2010, Molecular systems biology.

[89]  R. Mahadevan,et al.  Estimating optimal profiles of genetic alterations using constraint-based models. , 2005, Biotechnology and bioengineering.

[90]  Christopher A. Voigt,et al.  Automated Design of Synthetic Ribosome Binding Sites to Precisely Control Protein Expression , 2009, Nature Biotechnology.

[91]  D. Yernool,et al.  Restrained expression, a method to overproduce toxic membrane proteins by exploiting operator–repressor interactions , 2011, Protein science : a publication of the Protein Society.

[92]  B. Bassler,et al.  Quorum sensing in bacteria. , 2001, Annual review of microbiology.

[93]  T. Hwa,et al.  Interdependence of Cell Growth and Gene Expression: Origins and Consequences , 2010, Science.

[94]  Marina Lotti,et al.  Laboratory evolution of copper tolerant yeast strains , 2012, Microbial Cell Factories.

[95]  G. Bennett,et al.  Metabolic engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli. , 2002, Metabolic engineering.

[96]  H. Alper,et al.  Global strain engineering by mutant transcription factors. , 2011, Methods in molecular biology.

[97]  Donald Hilvert,et al.  Directed Evolution of a Protein Container , 2011, Science.

[98]  S. Avery,et al.  Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry , 2000, Yeast.

[99]  Jeffrey D Varner,et al.  Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy. , 2008, Current opinion in biotechnology.

[100]  Hal Alper,et al.  Development of systematic and combinatorial approaches for the metabolic engineering of microorganisms , 2006 .

[101]  Joshua K. Michener,et al.  High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. , 2012, Metabolic engineering.

[102]  Z. Deng,et al.  Overexpression of the ABC transporter AvtAB increases avermectin production in Streptomyces avermitilis , 2011, Applied Microbiology and Biotechnology.

[103]  W. Martin,et al.  Evolutionary origins of metabolic compartmentalization in eukaryotes , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[104]  N. Price,et al.  Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae , 2011, PloS one.

[105]  W. Lu,et al.  Improved Osmotic Tolerance and Ethanol Production of Ethanologenic Escherichia coli by IrrE, a Global Regulator of Radiation-Resistance of Deinococcus radiodurans , 2011, Current Microbiology.

[106]  J. Bont,et al.  Solvent-tolerant bacteria in biocatalysis , 1998 .

[107]  J. Keasling,et al.  Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. , 2000, Metabolic engineering.

[108]  Ming Yan,et al.  gTME for Improved Xylose Fermentation of Saccharomyces cerevisiae , 2010, Applied biochemistry and biotechnology.

[109]  K. Vogel,et al.  The yeast phosphatase system , 1990, Molecular microbiology.

[110]  M. Inui,et al.  Improvement of the Redox Balance Increases l-Valine Production by Corynebacterium glutamicum under Oxygen Deprivation Conditions , 2011, Applied and Environmental Microbiology.

[111]  Samuel Wagner,et al.  Tuning Escherichia coli for membrane protein overexpression , 2008, Proceedings of the National Academy of Sciences.

[112]  Anton Glieder,et al.  Engineering the Pichia pastoris methanol oxidation pathway for improved NADH regeneration during whole-cell biotransformation. , 2010, Metabolic engineering.

[113]  R. Weiss,et al.  Programmed population control by cell–cell communication and regulated killing , 2004, Nature.

[114]  R. Patnaik Engineering Complex Phenotypes in Industrial Strains , 2012, Biotechnology progress.