Metabolomics-assisted Synthetic Biology This Review Comes from a Themed Issue on Analytical Biotechnology Edited Metabolite and Metabolic Engineering

As the world progresses from a fossil-fuel based economy to a more sustainable one, synthetic biology will become increasingly important for the production of high-value fine chemicals as well as low-value commodities in bulk. The integration of metabolomics and fluxomics within synthetic biology projects will be vital at all levels, including the initial design of the pathways to be generated, through to the optimisation of those pathways so that more efficient conversion of low-cost starting materials into highly desirable products can be achieved. This review highlights these areas and details the most important and exciting advances being made in this area.

[1]  Brian F. Pfleger,et al.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production , 2008, Applied and Environmental Microbiology.

[2]  D. Kell Metabolomics, modelling and machine learning in systems biology – towards an understanding of the languages of cells , 2006, The FEBS journal.

[3]  D. Kell,et al.  Metabolic footprinting and systems biology: the medium is the message , 2005, Nature Reviews Microbiology.

[4]  R. Goodacre,et al.  Global Metabolic Profiling of Escherichia Coli Cultures: an Evaluation of Methods for Quenching and Extraction of Intracellular Metabolites , 2022 .

[5]  Age K. Smilde,et al.  Metabolic network discovery through reverse engineering of metabolome data , 2009, Metabolomics.

[6]  Jens Nielsen,et al.  Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology. , 2008, Trends in biotechnology.

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

[8]  Douglas B. Kell,et al.  Functional Genomics Via Metabolic Footprinting: Monitoring Metabolite Secretion by Escherichia Coli Tryptophan Metabolism Mutants Using FT–IR and Direct Injection Electrospray Mass Spectrometry , 2003, Comparative and functional genomics.

[9]  Age K Smilde,et al.  Reverse engineering of metabolic networks, a critical assessment. , 2011, Molecular bioSystems.

[10]  R. Goodacre,et al.  Metabolite profiling of recombinant CHO cells: designing tailored feeding regimes that enhance recombinant antibody production. , 2011, Biotechnology and bioengineering.

[11]  J. Nielsen,et al.  Industrial systems biology. , 2010, Biotechnology and bioengineering.

[12]  Jian-Guo Jiang,et al.  The metabolomics of carotenoids in engineered cell factory , 2009, Applied Microbiology and Biotechnology.

[13]  Yinjie J. Tang,et al.  Advances in analysis of microbial metabolic fluxes via (13)C isotopic labeling. , 2009, Mass spectrometry reviews.

[14]  A. Ishihara,et al.  Metabolic profiling analysis of genetically modified rice seedlings that overproduce tryptophan reveals the occurrence of its inter-tissue translocation , 2010 .

[15]  K. Rumbold,et al.  Microbial production host selection for converting second-generation feedstocks into bioproducts , 2009, Microbial cell factories.

[16]  David I. Ellis,et al.  Metabolomics: Current analytical platforms and methodologies , 2005 .

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

[18]  Gregory Stephanopoulos,et al.  Nontargeted elucidation of metabolic pathways using stable-isotope tracers and mass spectrometry. , 2010, Analytical chemistry.

[19]  Jens Nielsen,et al.  Systems biology of industrial microorganisms. , 2010, Advances in biochemical engineering/biotechnology.

[20]  Royston Goodacre,et al.  TARDIS-based microbial metabolomics: time and relative differences in systems. , 2011, Trends in microbiology.

[21]  Ningning Ma,et al.  A single nutrient feed supports both chemically defined NS0 and CHO fed‐batch processes: Improved productivity and lactate metabolism , 2009, Biotechnology progress.

[22]  Nicholas R. Abu-Absi,et al.  NMR-based metabolomics of mammalian cell and tissue cultures , 2011, Journal of biomolecular NMR.

[23]  David I. Ellis,et al.  Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy. , 2006, The Analyst.

[24]  T. Hasunuma,et al.  Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae , 2011, Microbial cell factories.

[25]  Jane Tang,et al.  Microbial Metabolomics , 2011, Current genomics.

[26]  G. Dismukes,et al.  Redirecting Reductant Flux into Hydrogen Production via Metabolic Engineering of Fermentative Carbon Metabolism in a Cyanobacterium , 2010, Applied and Environmental Microbiology.

[27]  Royston Goodacre,et al.  Metabolic fingerprinting as a tool to monitor whole-cell biotransformations , 2011, Analytical and bioanalytical chemistry.

[28]  Dong-Yup Lee,et al.  Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II. , 2010, Journal of biotechnology.

[29]  Royston Goodacre,et al.  Effective quenching processes for physiologically valid metabolite profiling of suspension cultured Mammalian cells. , 2009, Analytical chemistry.

[30]  Jack T Pronk,et al.  Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae. , 2010, Metabolic engineering.

[31]  M. Pátek,et al.  Tools for genetic manipulations in Corynebacterium glutamicum and their applications , 2011, Applied Microbiology and Biotechnology.

[32]  P. Fraser,et al.  Genetic engineering of carotenoid formation in tomato fruit and the potential application of systems and synthetic biology approaches. , 2009, Archives of biochemistry and biophysics.

[33]  P Mendes,et al.  Modelling and simulation for metabolomics data analysis. , 2005, Biochemical Society transactions.

[34]  Royston Goodacre,et al.  Rapid monitoring of recombinant antibody production by mammalian cell cultures using fourier transform infrared spectroscopy and chemometrics , 2010, Biotechnology and bioengineering.

[35]  H. J. Woerdenbag,et al.  Metabolic engineering strategies for the optimization of medicinal and aromatic plants: realities and expectations , 2010 .

[36]  N. Kruger,et al.  Insights into plant metabolic networks from steady-state metabolic flux analysis. , 2009, Biochimie.

[37]  Royston Goodacre,et al.  Evaluation of extraction processes for intracellular metabolite profiling of mammalian cells: matching extraction approaches to cell type and metabolite targets , 2010, Metabolomics.

[38]  Royston Goodacre,et al.  Metabolic fingerprinting as a diagnostic tool. , 2007, Pharmacogenomics.