Importance of systems biology in engineering microbes for biofuel production
Open accessAbstract
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.
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Systems metabolic engineering has proven very successful for the design and implementation of biotechnological production processes.
“Synthetic biology is a new emerging field [10,11] and systems metabolic engineering has proven very successful for the design and implementation of biotechnological production processes [12-14].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [13]
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Cites
Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd
Fleischmann, R. D., Adams, M. D., White, O. R., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J.-F., Dougherty, B. A., Merrick, J. M., et al. (1995) · Science · doi:10.1126/science.7542800 · Cited by 5,641 · see citing works
Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401 · see citing works
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316 · see citing works
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., et al. (2001) · Nature Genetics · doi:10.1038/ng1201-365 · Cited by 4,109 · see citing works
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925 · see citing works
Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Ro, D.-K., Paradise, E. M., Ouellet, M., Fisher, K. J., Newman, K. L., Ndungu, J. M., Ho, K. A., Eachus, R. A., Ham, T. S., Kirby, J., et al. (2006) · Nature · doi:10.1038/nature04640 · Cited by 2,805 · see citing works
Self-citationMechanisms of membrane toxicity of hydrocarbons
Sikkema, J., de Bont, J. A., & Poolman, B. (1995) · Microbiological Reviews · doi:10.1128/mr.59.2.201-222.1995 · Cited by 2,685 · see citing works
Mass Spectrometry and Protein Analysis
Domon, B., & Aebersold, R. H. (2006) · Science · doi:10.1126/science.1124619 · Cited by 2,188 · see citing works
Direct multiplexed measurement of gene expression with color-coded probe pairs
Geiss, G. K., Bumgarner, R. E., Birditt, B., Dahl, T., Dowidar, N., Dunaway, D. L., Fell, H. P., Ferree, S., George, R. D., Grogan, T., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1385 · Cited by 2,066 · see citing works
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
Atsumi, S., Hanai, T., & Liao, J. C. (2008) · Nature · doi:10.1038/nature06450 · Cited by 1,945 · see citing works
A N <scp>EW</scp> A <scp>PPROACH TO</scp> D <scp>ECODING</scp> L <scp>IFE</scp> : Systems Biology
Ideker, T., Galitski, T., & Hood, L. (2001) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.2.1.343 · Cited by 1,664 · see citing works
Ethanol fermentation from biomass resources: current state and prospects
Lin, Y., & Tanaka, S. (2005) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-005-0229-x · Cited by 1,622 · see citing works
Codon bias and heterologous protein expression
Gustafsson, C., Govindarajan, S., & Minshull, J. (2004) · Trends in Biotechnology · doi:10.1016/j.tibtech.2004.04.006 · Cited by 1,330 · see citing works
Quantitative Metabolome Analysis Using Capillary Electrophoresis Mass Spectrometry
Soga, T., Ohashi, Y., Ueno, Y., Naraoka, H., Tomita, M., & Nishioka, T. (2003) · Journal of Proteome Research · doi:10.1021/pr034020m · Cited by 975 · see citing works
Metabolic engineering for the microbial production of 1,3-propanediol.
Nakamura, C. E., & Whited, G. (2003) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2003.08.005 · Cited by 801 · see citing works
Bacteria engineered for fuel ethanol production: current status
Dien, B. S., Cotta, M. A., & Jeffries, T. W. (2003) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-003-1444-y · Cited by 796 · see citing works
Quantification of protein half-lives in the budding yeast proteome
Belle, A., Tanay, A., Bitincka, L., Shamir, R., & O’Shea, E. K. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605420103 · Cited by 678 · see citing works
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., et al. (2007) · Science · doi:10.1126/science.1132067 · Cited by 668 · see citing works
Bajad, S. U., Lu, W., Kimball, E., Yuan, J., Peterson, C. N., & Rabinowitz, J. D. (2006) · Journal of Chromatography A · doi:10.1016/j.chroma.2006.05.019 · Cited by 593 · see citing works
He, Z., Gentry, T. J., Schadt, C. W., Wu, L., Liebich, J., Chong, S. C., Huang, Z., Wu, W., Gu, B., Jardine, P. M., et al. (2007) · The ISME Journal · doi:10.1038/ismej.2007.2 · Cited by 584 · see citing works
Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes
Pfleger, B. F., Pitera, D. J., Smolke, C. D., & Keasling, J. D. (2006) · Nature Biotechnology · doi:10.1038/nbt1226 · Cited by 535 · see citing works
Self-citationDeSantis, T. Z., Brodie, E., Parker, J. M., Zubieta, I. X., Piceno, Y. M., & Andersen, G. L. (2007) · Microbial Ecology · doi:10.1007/s00248-006-9134-9 · Cited by 509 · see citing works
Microdiesel: Escherichia coli engineered for fuel production
Kalscheuer, R., Stölting, T., & Steinbüchel, A. (2006) · Microbiology · doi:10.1099/mic.0.29028-0 · Cited by 490 · see citing works
Mueller, L. N., Brusniak, M., Mani, D. R., & Aebersold, R. H. (2008) · Journal of Proteome Research · doi:10.1021/pr700758r · Cited by 450 · see citing works
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
Alper, H. S., Jin, Y., Moxley, J. F., & Stephanopoulos, G. N. (2005) · Metabolic Engineering · doi:10.1016/j.ymben.2004.12.003 · Cited by 450 · see citing works
The genomics of yeast responses to environmental stress and starvation
Gasch, A. P., & Werner‐Washburne, M. (2002) · Functional & Integrative Genomics · doi:10.1007/s10142-002-0058-2 · Cited by 448 · see citing works
Global transcription machinery engineering: A new approach for improving cellular phenotype
Alper, H. S., & Stephanopoulos, G. N. (2007) · Metabolic Engineering · doi:10.1016/j.ymben.2006.12.002 · Cited by 448 · see citing works
Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli
Pitera, D. J., Paddon, C. J., Newman, J. D., & Keasling, J. D. (2006) · Metabolic Engineering · doi:10.1016/j.ymben.2006.11.002 · Cited by 440 · see citing works
Self-citationProduction of isoprenoid pharmaceuticals by engineered microbes
Chang, M. C. Y., & Keasling, J. D. (2006) · Nature Chemical Biology · doi:10.1038/nchembio836 · Cited by 388 · see citing works
Self-citationVemuri, G. N., Altman, E., Sangurdekar, D. P., Khodursky, A. B., & Eiteman, M. A. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3653-3661.2006 · Cited by 369 · see citing works
Biofuel alternatives to ethanol: pumping the microbial well
Fortman, J. L., Chhabra, S. R., Mukhopadhyay, A., Chou, H. H., Lee, T. S., Steen, E. J., & Keasling, J. D. (2008) · Trends in biotechnology · doi:10.1016/j.tibtech.2008.03.008 · Cited by 365 · see citing works
Self-citationChoe, L. H., D'Ascenzo, M. D., Relkin, N. R., Pappin, D., Ross, P. L., Williamson, B., Guertin, S., Pribil, P. A., & Lee, K. H. (2007) · PROTEOMICS · doi:10.1002/pmic.200700316 · Cited by 326 · see citing works
Guidelines for the next 10 years of proteomics
Wilkins, M. R., Appel, R. D., Eyk, J. E. V., Chung, M. C. M., Görg, A., Hecker, M., Huber, L. A., Langen, H., Link, A. J., Paik, Y., et al. (2006) · PROTEOMICS · doi:10.1002/pmic.200500856 · Cited by 302 · see citing works
A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
Bonneau, R., Facciotti, M. T., Reiss, D. J., Schmid, A., Pan, M., Kaur, A., Thórsson, V., Shannon, P. T., Johnson, M. H., Bare, J. C., et al. (2007) · Cell · doi:10.1016/j.cell.2007.10.053 · Cited by 298 · see citing works
The EcoCyc and MetaCyc databases
Karp, P. D. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.56 · Cited by 296 · see citing works
Anderson, K. L., Roberts, C., Disz, T. L., Vonstein, V., Hwang, K., Overbeek, R., Olson, P. D., Projan, S. J., & Dunman, P. M. (2006) · Journal of Bacteriology · doi:10.1128/jb.00609-06 · Cited by 271 · see citing works
Mapping the Pathways to StaphylococcalPathogenesis by Comparative Secretomics
Sibbald, M. J. J. B., Ziebandt, A., Engelmann, S., Hecker, M., de Jong, A., Harmsen, H. J. M., Raangs, G. C., Stokroos, I., Arends, J. P., Dubois, J. Y. F., et al. (2006) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00008-06 · Cited by 267 · see citing works
Metabolomics: current state and evolving methodologies and tools
Oldiges, M., Lütz, S., Pflug, S., Schroer, K., Stein, N., & Wiendahl, C. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-007-1029-2 · Cited by 235 · see citing works
The commercial production of chemicals using pathway engineering
Chotani, G., Dodge, T., Hsu, A., Kumar, M., LaDuca, R., Trimbur, D., Weyler, W., & Sanford, K. (2000) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/s0167-4838(00)00234-x · Cited by 234 · see citing works
Reporting Protein Identification Data
Bradshaw, R. A., Burlingame, A. L., Carr, S. A., et al. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.e600005-mcp200 · Cited by 222 · see citing works
Antoniewicz, M. R., Kraynie, D. F., Laffend, L. A., González‐Lergier, J., Kelleher, J. K., & Stephanopoulos, G. N. (2007) · Metabolic Engineering · doi:10.1016/j.ymben.2007.01.003 · Cited by 221 · see citing works
An update on microbial carotenoid production: application of recent metabolic engineering tools
Das, A., Yoon, S., Lee, S.-H., Kim, J., Oh, D., & Kim, S.-W. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-007-1206-3 · Cited by 215 · see citing works
Posttranslational Protein Modification inArchaea
Eichler, J., & Adams, M. W. W. (2005) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.69.3.393-425.2005 · Cited by 211 · see citing works
The MicrobesOnline Web site for comparative genomicsPreprint
Alm, E. J., Huang, K. H., Price, M. N., et al. (2005) · Genome Research · doi:10.1101/gr.3844805 · Cited by 205 · see citing works
Nöh, K., Grönke, K., Luo, B., Takors, R., Oldiges, M., & Wiechert, W. (2006) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2006.11.015 · Cited by 200 · see citing works
TheEscherichia coliProteome: Past, Present, and Future Prospects
Han, M., & Lee, S. Y. (2006) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-05 · Cited by 179 · see citing works
Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production
Kizer, L., Pitera, D. J., Pfleger, B. F., & Keasling, J. D. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02750-07 · Cited by 178 · see citing works
Self-citationToward a protein profile of Escherichia coli : Comparison to its transcription profile
Corbin, R. W., Paliy, O., Yang, F., Shabanowitz, J., Platt, M., Lyons, C. E., Root, K. E., McAuliffe, J., Jordan, M. I., Kustu, S. G., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1533294100 · Cited by 177 · see citing works
van Voorst, F., Houghton‐Larsen, J., Jønson, L., Kielland‐Brandt, M. C., & Brandt, A. (2006) · Yeast · doi:10.1002/yea.1359 · Cited by 156 · see citing works
The Gaggle: An open-source software system for integrating bioinformatics software and data sources
Shannon, P. T., Reiss, D. J., Bonneau, R., & Baliga, N. S. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-176 · Cited by 155 · see citing works
Getting organized — how bacterial cells move proteins and DNA
Thanbichler, M. R., & Shapiro, L. (2007) · Nature Reviews Microbiology · doi:10.1038/nrmicro1795 · Cited by 129 · see citing works
Biomass to fuels via microbial transformations
Wackett, L. P. (2008) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2008.01.025 · Cited by 114 · see citing works
Essential genes on metabolic maps
Gerdes, S., Edwards, R. A., Kubal, M., Fonstein, M., Stevens, R. L., & Osterman, A. L. (2006) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2006.08.006 · Cited by 112 · see citing works
Herrera, S. (2006) · Nature Biotechnology · doi:10.1038/nbt0706-755 · Cited by 111 · see citing works
Tang, Y., Pingitore, F., Mukhopadhyay, A., et al. (2006) · Journal of Bacteriology · doi:10.1128/jb.00948-06 · Cited by 97 · see citing works
Self-citationTrauger, S. A., Kalisak, E., Kalisiak, J., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr700609j · Cited by 79 · see citing works
Huttlin, E. L., Hegeman, A. D., Harms, A. C., et al. (2006) · Journal of Proteome Research · doi:10.1021/pr0603194 · Cited by 76 · see citing works
Dong, M., Yang, L. L., Williams, K., Fisher, S. J., Hall, S. C., Biggin, M. D., Jin, J., & Witkowska, H. E. (2008) · Journal of Proteome Research · doi:10.1021/pr700624e · Cited by 49 · see citing works
Addressing the Need for Alternative Transportation Fuels: The Joint BioEnergy Institute
Blanch, H. W., Adams, P. D., Andrews-Cramer, K. M., et al. (2008) · ACS Chemical Biology · doi:10.1021/cb700267s · Cited by 45 · see citing works
Proteomic Analysis of Saccharomyces cerevisiae under High Gravity Fermentation Conditions
Pham, T. K., Chong, P. K., Gan, C. S., et al. (2006) · Journal of Proteome Research · doi:10.1021/pr060377p · Cited by 44 · see citing works
Wecke, T., Veith, B., Ehrenreich, A., et al. (2006) · Journal of Bacteriology · doi:10.1128/jb.01110-06 · Cited by 37 · see citing works
Scherperel, G., & Reid, G. E. (2007) · The Analyst · doi:10.1039/b618499p · Cited by 30 · see citing works
Verma, S., Xiong, Y., Mayer, M. U., et al. (2007) · Biochemistry · doi:10.1021/bi0621157 · Cited by 23 · see citing works
Flagged first, then by citations
Research works printed but not linked: 4
- Ideker T, Galitski T, Hood L: A new approach to decoding life: systems biology. Annu Rev Genom Hum Genet 2001, 2:343-372.
- Eichler J, Adams MWW: Posttranslational protein modification in Archaea. Microbiol Mol Biol Rev 2005, 69:393-425.
- Jarboe LR, Grabar TB, Yomano LP, Shanmugan KT, Ingram LO: Development of ethanologenic bacteria. Adv Biochem Eng Biotechnol 2007, 108:237-261.
- Han M-J, Lee SY: The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev 2006, 70:362-439.
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Rutherford, B. J., Dahl, R. H., Price, R. E., Szmidt, H. L., Benke, P. I., Mukhopadhyay, A., & Keasling, J. D. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.02323-09 · Cited by 227 · see citing works
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- Authors
- Mukhopadhyay, A., Redding, A. M., Rutherford, B. J., & Keasling, J. D.
- Affiliations
- Joint BioEnergy Institute (US)
- Lawrence Berkeley National Laboratory (US)
- University of California, Berkeley (US)
- Corresponding author
- Keasling, Jay D
- Venue
- Current Opinion in Biotechnology
- Publisher
- Elsevier BV
- Published
- 2008-06
- Volume
- 19
- Issue
- 3
- Pages
- 228-234
- ISSN
- 0958-1669 (ISSN-L)
- OpenAlex
- W1417120179
- Cited by
- 129
- References
- 63
- Citations by year
- 2025: 4 · 2024: 6 · 2022: 3 · 2021: 3 · 2020: 6 · 2019: 10 · 2018: 5 · 2017: 6 · 2016: 5 · 2015: 6 · 2014: 9 · 2013: 11 · 2012: 10
- FWCI
- 1.16
- Type
- journal article
- Language
- en
- Open access
- Locations
- Current Opinion in Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Lawrence Berkeley National Laboratory
- Funders
- National Science Foundation (DEAC02-05CH11231)
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02)
- Basic Energy Sciences (DE-AC02, DE-AC02-05CH11231., AC02–05CH11231)
- Sandia National Laboratories (DE-AC02-05CH11231)
- Lawrence Berkeley National Laboratory (AC02‐05CH11231, DE-AC02-05CH11231, 05CH11231)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Physical Sciences › Engineering › Biomedical Engineering › Biofuel production and bioconversion
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- systems biology, microbial engineering, biofuel production, pathway engineering, metabolic bottlenecks, industrial microorganisms, renewable transportation fuels, metabolic stress
- MeSH terms
- Bioelectric Energy Sources, Biotechnology, Energy-Generating Resources, Escherichia coli, Genetic Engineering, Genomics, Systems Biology
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