Construction of microbial cell factories for industrial bioprocesses

The development of industrial microbial processes is gaining unprecedented momentum. Increased concern for environmental issues and the prospect of declining petroleum resources has shifted the industrial focus increasingly to microorganisms as biocatalysts. At the same time systems biology and synthetic biology supply industry and academia with new tools to design optimal microbial cell factories. Among the tools are systems biology approaches allowing the modelling of cellular networks for rational strain design, single cell analyses methods for gaining insight into population hetereogeneity, and an exciting combination of tools from structural biology and synthetic biology, permitting the catalysis of new (unnatural) enzymatic reactions or the production of new (unnatural) chemicals. This perspective article outlines recent advances and new developments within the field of microbial cell factory design. Copyright © 2012 Society of Chemical Industry

[1]  T. Szyperski.  Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. , 1995, European journal of biochemistry.

[2]  A. Zeng,et al.  Bulk chemicals from biotechnology: the case of 1,3-propanediol production and the new trends. , 2002, Advances in biochemical engineering/biotechnology.

[3]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

[4]  George H. McArthur,et al.  Toward Engineering Synthetic Microbial Metabolism , 2009, Journal of biomedicine & biotechnology.

[5]  Bas Teusink,et al.  Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model* , 2006, Journal of Biological Chemistry.

[6]  Hyun Uk Kim,et al.  Metabolic engineering of microorganisms: general strategies and drug production. , 2009, Drug discovery today.

[7]  M. Sauer,et al.  Microbial production of 1,3-propanediol. , 2008, Recent patents on biotechnology.

[8]  Giang-Huong Duong,et al.  Catalase Overexpression Reduces Lactic Acid-Induced Oxidative Stress in Saccharomyces cerevisiae , 2009, Applied and Environmental Microbiology.

[9]  Alvis Brazma,et al.  Current approaches to gene regulatory network modelling , 2007, BMC Bioinformatics.

[10]  Jason A. Papin,et al.  Genome-scale microbial in silico models: the constraints-based approach. , 2003, Trends in biotechnology.

[11]  Jens Nielsen,et al.  Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis , 2011, Proceedings of the National Academy of Sciences.

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

[13]  James C. Liao,et al.  Expanding metabolism for biosynthesis of nonnatural alcohols , 2008, Proceedings of the National Academy of Sciences.

[14]  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.

[15]  Manor Askenazi,et al.  Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains , 2003, Nature Biotechnology.

[16]  U. Sauer.  Evolutionary engineering of industrially important microbial phenotypes. , 2001, Advances in biochemical engineering/biotechnology.

[17]  Nathan E Lewis,et al.  Microbial laboratory evolution in the era of genome-scale science , 2011, Molecular systems biology.

[18]  Andreas Schmid,et al.  Chemical and biological single cell analysis. , 2010, Current opinion in biotechnology.

[19]  Christoph Wittmann,et al.  Metabolic Engineering of the Tricarboxylic Acid Cycle for Improved Lysine Production by Corynebacterium glutamicum , 2009, Applied and Environmental Microbiology.

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

[21]  Christoph Wittmann,et al.  Metabolic fluxes and beyond—systems biology understanding and engineering of microbial metabolism , 2010, Applied Microbiology and Biotechnology.

[22]  Andreas Schmid,et al.  Single cell analytics: an overview. , 2011, Advances in biochemical engineering/biotechnology.

[23]  David Baker,et al.  Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. , 2010, Journal of molecular biology.

[24]  J. Bailey,et al.  Toward a science of metabolic engineering , 1991, Science.

[25]  Roland Somogyi,et al.  Reverse engineers map the molecular switching yards. , 2002, Trends in biotechnology.

[26]  M. Sauer,et al.  Microbial production of organic acids: expanding the markets. , 2008, Trends in biotechnology.

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

[28]  A. V. Vliet.  Next generation sequencing of microbial transcriptomes: challenges and opportunities. , 2010 .

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

[30]  C. Maranas,et al.  An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. , 2006, Metabolic engineering.

[31]  Michael Sauer,et al.  Improvement of Lactic Acid Production in Saccharomyces cerevisiae by Cell Sorting for High Intracellular pH , 2006, Applied and Environmental Microbiology.

[32]  Sang Yup Lee,et al.  Construction and optimization of synthetic pathways in metabolic engineering. , 2010, Current opinion in microbiology.

[33]  S. Bodovitz,et al.  Single cell analysis: the new frontier in 'omics'. , 2010, Trends in biotechnology.

[34]  N. Allbritton,et al.  Chemical analysis of single cells. , 2008, Annual review of analytical chemistry.

[35]  M. Nowrousian.  Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems , 2010, Eukaryotic Cell.

[36]  Michael Sauer,et al.  Stress in recombinant protein producing yeasts. , 2004, Journal of biotechnology.

[37]  Zhaolei Zhang,et al.  Gene expression variations are predictive for stochastic noise , 2011, Nucleic Acids Res..

[38]  N. Friedman,et al.  Stochastic protein expression in individual cells at the single molecule level , 2006, Nature.

[39]  J. Pronk,et al.  Novel Evolutionary Engineering Approach for Accelerated Utilization of Glucose, Xylose, and Arabinose Mixtures by Engineered Saccharomyces cerevisiae Strains , 2008, Applied and Environmental Microbiology.

[40]  K. Moffat,et al.  Light-activated DNA binding in a designed allosteric protein , 2008, Proceedings of the National Academy of Sciences.

[41]  J. Liao,et al.  Bioengineering of microorganisms for C3 to C5 alcohols production , 2010, Biotechnology journal.

[42]  A J Sinskey,et al.  Metabolic engineering--methodologies and future prospects. , 1993, Trends in biotechnology.

[43]  Christoph Wittmann,et al.  Metabolic flux engineering of L-lysine production in Corynebacterium glutamicum--over expression and modification of G6P dehydrogenase. , 2007, Journal of biotechnology.

[44]  B. Palsson,et al.  Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.

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

[46]  S. Lee,et al.  Application of systems biology for bioprocess development. , 2008, Trends in biotechnology.

[47]  Huimin Zhao,et al.  Engineering microbial factories for synthesis of value-added products , 2011, Journal of Industrial Microbiology & Biotechnology.

[48]  Weiwen Zhang,et al.  Integrating multiple 'omics' analysis for microbial biology: application and methodologies. , 2010, Microbiology.

[49]  Eric A. Althoff,et al.  Kemp elimination catalysts by computational enzyme design , 2008, Nature.

[50]  C. Kiel,et al.  Structures in systems biology. , 2007, Current opinion in structural biology.

[51]  Lars M. Blank,et al.  Metabolic flux distributions: genetic information, computational predictions, and experimental validation , 2010, Applied Microbiology and Biotechnology.

[52]  J. Beekwilder,et al.  Production of Resveratrol in Recombinant Microorganisms , 2006, Applied and Environmental Microbiology.

[53]  I. S. Pretorius,et al.  Metabolic engineering of Saccharomyces cerevisiae for the synthesis of the wine‐related antioxidant resveratrol , 2003 .

[54]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[55]  U. Sauer,et al.  Article number: 62 REVIEW Metabolic networks in motion: 13 C-based flux analysis , 2022 .

[56]  A. Zeng,et al.  Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development. , 2010, Trends in biotechnology.

[57]  Costas D Maranas,et al.  OptStrain: a computational framework for redesign of microbial production systems. , 2004, Genome research.

[58]  Michael Sauer,et al.  Biosynthesis of Vitamin C by Yeast Leads to Increased Stress Resistance , 2007, PloS one.

[59]  T. Szyperski.  Biosynthetically Directed Fractional 13C‐labeling of Proteinogenic Amino Acids , 1995 .

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

[61]  Gabor T. Marth,et al.  Rapid whole-genome mutational profiling using next-generation sequencing technologies. , 2008, Genome research.

[62]  S. Lee,et al.  Metabolic flux analysis and metabolic engineering of microorganisms. , 2008, Molecular bioSystems.