Importance of systems biology in engineering microbes for biofuel production.

Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.

[1]  Gary L. Andersen,et al.  High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment , 2007, Microbial Ecology.

[2]  Jay D Keasling,et al.  Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. , 2007, Metabolic engineering.

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

[4]  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.

[5]  S. Carr,et al.  Reporting Protein Identification Data , 2006, Molecular & Cellular Proteomics.

[6]  H. Harmsen,et al.  Mapping the Pathways to StaphylococcalPathogenesis by Comparative Secretomics , 2006, Microbiology and Molecular Biology Reviews.

[7]  R. Aebersold,et al.  Mass Spectrometry and Protein Analysis , 2006, Science.

[8]  A. Khodursky,et al.  Overflow Metabolism in Escherichia coli during Steady-State Growth: Transcriptional Regulation and Effect of the Redox Ratio , 2006, Applied and Environmental Microbiology.

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

[10]  Rick Stevens,et al.  Essential genes on metabolic maps. , 2006, Current opinion in biotechnology.

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

[12]  Lucy Shapiro,et al.  Getting organized — how bacterial cells move proteins and DNA , 2008, Nature Reviews Microbiology.

[13]  Peter D. Karp,et al.  The EcoCyc and MetaCyc databases , 2000, Nucleic Acids Res..

[14]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[15]  Lukas N. Mueller,et al.  An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. , 2008, Journal of proteome research.

[16]  Wenyun Lu,et al.  Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. , 2006, Journal of chromatography. A.

[17]  S. Herrera Bonkers about biofuels , 2006, Nature Biotechnology.

[18]  Yijia Xiong,et al.  Remodeling of the bacterial RNA polymerase supramolecular complex in response to environmental conditions. , 2007, Biochemistry.

[19]  Amy K. Schmid,et al.  A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell , 2007, Cell.

[20]  L. Wackett Biomass to fuels via microbial transformations. , 2008, Current opinion in chemical biology.

[21]  Ming Dong,et al.  A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking. , 2008, Journal of proteome research.

[22]  Jennifer L. Osborn,et al.  Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.

[23]  Swapnil Chhabra,et al.  Biofuel alternatives to ethanol: pumping the microbial well. , 2008, Trends in biotechnology.

[24]  Yan Lin,et al.  Ethanol fermentation from biomass resources: current state and prospects , 2006, Applied Microbiology and Biotechnology.

[25]  Pei Yee Ho,et al.  Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations , 2007, Science.

[26]  M. Adams,et al.  Posttranslational Protein Modification in Archaea , 2005, Microbiology and Molecular Biology Reviews.

[27]  David J. Reiss,et al.  The Gaggle: An open-source software system for integrating bioinformatics software and data sources , 2006, BMC Bioinformatics.

[28]  S. Govindarajan,et al.  Codon bias and heterologous protein expression. , 2004, Trends in biotechnology.

[29]  B. Poolman,et al.  Mechanisms of membrane toxicity of hydrocarbons. , 1995, Microbiological reviews.

[30]  Jay D Keasling,et al.  Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. , 2008, ACS chemical biology.

[31]  Mark D'Ascenzo,et al.  8‐Plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease , 2007, Proteomics.

[32]  E. O’Shea,et al.  Quantification of protein half-lives in the budding yeast proteome , 2006, Proceedings of the National Academy of Sciences.

[33]  T. W. Jeffries,et al.  Bacteria engineered for fuel ethanol production: current status , 2003, Applied Microbiology and Biotechnology.

[34]  G. Stephanopoulos,et al.  Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. , 2005, Metabolic engineering.

[35]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[36]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[37]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[38]  Rainer Kalscheuer,et al.  Microdiesel: Escherichia coli engineered for fuel production. , 2006, Microbiology.

[39]  Ralf Takors,et al.  Metabolic flux analysis at ultra short time scale: isotopically non-stationary 13C labeling experiments. , 2007, Journal of biotechnology.

[40]  Seon-Won Kim,et al.  An update on microbial carotenoid production: application of recent metabolic engineering tools , 2007, Applied Microbiology and Biotechnology.

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

[42]  R. Overbeek,et al.  Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover , 2006, Journal of Bacteriology.

[43]  Sunia A Trauger,et al.  Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile , 2022 .

[44]  M. Kumar,et al.  The commercial production of chemicals using pathway engineering. , 2000, Biochimica et biophysica acta.

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

[46]  Edward L Huttlin,et al.  Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. , 2007, Journal of proteome research.

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

[48]  T. Mascher,et al.  Cell Envelope Stress Response in Bacillus licheniformis: Integrating Comparative Genomics, Transcriptional Profiling, and Regulon Mining To Decipher a Complex Regulatory Network , 2006, Journal of bacteriology.

[49]  L. Jønson,et al.  Genome‐wide identification of genes required for growth of Saccharomyces cerevisiae under ethanol stress , 2006, Yeast.

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

[51]  Katherine H. Huang,et al.  The MicrobesOnline Web site for comparative genomics. , 2005, Genome research.

[52]  R. Appel,et al.  Guidelines for the next 10 years of proteomics , 2009, Proteomics.

[53]  Sang Yup Lee,et al.  The Escherichia coli Proteome: Past, Present, and Future Prospects , 2006, Microbiology and Molecular Biology Reviews.

[54]  Marco Oldiges,et al.  Metabolomics: current state and evolving methodologies and tools , 2007, Applied Microbiology and Biotechnology.

[55]  Jay D Keasling,et al.  Production of isoprenoid pharmaceuticals by engineered microbes , 2006, Nature chemical biology.

[56]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[57]  G. Reid,et al.  Emerging methods in proteomics: top-down protein characterization by multistage tandem mass spectrometry. , 2007, The Analyst.

[58]  M. Tomita,et al.  Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. , 2003, Journal of proteome research.

[59]  Michael I. Jordan,et al.  Toward a protein profile of Escherichia coli: Comparison to its transcription profile , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Yinjie J. Tang,et al.  Pathway Confirmation and Flux Analysis of Central Metabolic Pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry , 2006, Journal of bacteriology.

[61]  Margaret Werner-Washburne,et al.  The genomics of yeast responses to environmental stress and starvation , 2002, Functional & Integrative Genomics.

[62]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[63]  Baohua Gu,et al.  GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes , 2007, The ISME Journal.

[64]  Brian F. Pfleger,et al.  Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes , 2006, Nature Biotechnology.