Jay Keasling

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Kinetics of phosphomevalonate kinase from Saccharomyces cerevisiae
    David E Garcia
    Joint BioEnergy Institute, Emeryville, California, United States of America Department of Chemistry, University of California, Berkeley, California, United States of America Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 9:e87112. 2014
  2. pmc Functional Characterization of the Origin of Replication of pRN1 from Sulfolobus islandicus REN1H1
    Chijioke J Joshua
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America Joint BioEnergy Institute, Emeryville, California, United States of America
    PLoS ONE 8:e84664. 2013
  3. pmc Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity
    James M Carothers
    California Institute for Quantitative Biosciences and Berkeley Center for Synthetic Biology, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:2736-47. 2010
  4. pmc Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli
    Aymerick Eudes
    Joint BioEnergy Institute, Emeryville, CA 94608, USA
    Microb Cell Fact 12:62. 2013
  5. pmc Versatile synthesis of probes for high-throughput enzyme activity screening
    Tristan de Rond
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Anal Bioanal Chem 405:4969-73. 2013
  6. doi request reprint Synthetic biology and the development of tools for metabolic engineering
    Jay D Keasling
    Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, USA
    Metab Eng 14:189-95. 2012
  7. pmc Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars
    Dan Groff
    Joint BioEnergy Institute, Emeryville, California, USA
    Appl Environ Microbiol 78:2221-9. 2012
  8. pmc BglBricks: A flexible standard for biological part assembly
    J Christopher Anderson
    Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    J Biol Eng 4:1. 2010
  9. pmc Central metabolism in Mycobacterium smegmatis during the transition from O2-rich to O2-poor conditions as studied by isotopomer-assisted metabolite analysis
    Yinjie J Tang
    Department of Energy, Environmental and Chemical Engineering, Washington University, St Louis, MO 63130, USA
    Biotechnol Lett 31:1233-40. 2009
  10. pmc Global analysis of host response to induction of a latent bacteriophage
    Robin E Osterhout
    Department of Bioengineering and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
    BMC Microbiol 7:82. 2007

Research Grants

  1. Biosensors for metabolic engineering
    Jay Keasling; Fiscal Year: 2004
  2. Biosensors for metabolic engineering
    Jay Keasling; Fiscal Year: 2005
  3. Biosensors for metabolic engineering
    Jay Keasling; Fiscal Year: 2006

Collaborators

Detail Information

Publications96

  1. pmc Kinetics of phosphomevalonate kinase from Saccharomyces cerevisiae
    David E Garcia
    Joint BioEnergy Institute, Emeryville, California, United States of America Department of Chemistry, University of California, Berkeley, California, United States of America Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 9:e87112. 2014
    ..Maximum activity was observed at pH = 7.2. PMK was not found to be substrate inhibited, nor feedback inhibited by FPP at concentrations up to 10 µM FPP...
  2. pmc Functional Characterization of the Origin of Replication of pRN1 from Sulfolobus islandicus REN1H1
    Chijioke J Joshua
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America Joint BioEnergy Institute, Emeryville, California, United States of America
    PLoS ONE 8:e84664. 2013
    ..Detailed knowledge of the pRN1 origin of replication will broaden the application of the plasmid as a genetic tool for Sulfolobus species. ..
  3. pmc Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity
    James M Carothers
    California Institute for Quantitative Biosciences and Berkeley Center for Synthetic Biology, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:2736-47. 2010
    ..We suggest that it may be possible to estimate aptamer-ligand affinities and predict whether a particular aptamer-based design goal is achievable before performing the selection...
  4. pmc Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli
    Aymerick Eudes
    Joint BioEnergy Institute, Emeryville, CA 94608, USA
    Microb Cell Fact 12:62. 2013
    ..Using engineering strategies to overproduce anthranilate and hydroxycinnamates, we describe here an entire pathway for the microbial synthesis of two Avns from glucose in Escherichia coli...
  5. pmc Versatile synthesis of probes for high-throughput enzyme activity screening
    Tristan de Rond
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Anal Bioanal Chem 405:4969-73. 2013
    ..The simplified synthetic approach presented here may help advance the application of mass spectrometry to high-throughput enzyme activity determination...
  6. doi request reprint Synthetic biology and the development of tools for metabolic engineering
    Jay D Keasling
    Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, USA
    Metab Eng 14:189-95. 2012
    ..The development of these tools significantly reduced the costs and time to develop the antimalarial drug artemisinin, but the availability of more tools could have reduced these costs substantially...
  7. pmc Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars
    Dan Groff
    Joint BioEnergy Institute, Emeryville, California, USA
    Appl Environ Microbiol 78:2221-9. 2012
    ..This strain is a useful starting point for the development of an E. coli biocatalyst that can simultaneously convert all biomass sugars...
  8. pmc BglBricks: A flexible standard for biological part assembly
    J Christopher Anderson
    Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    J Biol Eng 4:1. 2010
    ..These tools will provide a foundation from which to transform genetic engineering from a technically intensive art into a purely design-based discipline...
  9. pmc Central metabolism in Mycobacterium smegmatis during the transition from O2-rich to O2-poor conditions as studied by isotopomer-assisted metabolite analysis
    Yinjie J Tang
    Department of Energy, Environmental and Chemical Engineering, Washington University, St Louis, MO 63130, USA
    Biotechnol Lett 31:1233-40. 2009
    ....
  10. pmc Global analysis of host response to induction of a latent bacteriophage
    Robin E Osterhout
    Department of Bioengineering and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
    BMC Microbiol 7:82. 2007
    ..To address this question, we collected transcriptional profiles of Escherichia coli and bacteriophage lambda throughout lysogenic induction by UV light...
  11. pmc Induction of multiple pleiotropic drug resistance genes in yeast engineered to produce an increased level of anti-malarial drug precursor, artemisinic acid
    Dae Kyun Ro
    Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
    BMC Biotechnol 8:83. 2008
    ..annua. In order to develop an industrially competent yeast strain, detailed analyses of microbial physiology and development of gene expression strategies are required...
  12. pmc A rapid and inexpensive labeling method for microarray gene expression analysis
    Mario Ouellet
    The Joint Bioenergy Institute, Lawrence Berkeley National Laboratory, Emeryville, USA
    BMC Biotechnol 9:97. 2009
    ....
  13. pmc Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol
    Eric J Steen
    Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA 94608, USA
    Microb Cell Fact 7:36. 2008
    ..coli. Using metabolite analysis, we were able to determine which steps in the n-butanol biosynthetic pathway were the most problematic and ripe for future improvement...
  14. pmc A framework and model system to investigate linear system behavior in Escherichia coli
    Meghdad Hajimorad
    Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, USA
    J Biol Eng 5:3. 2011
    ..abstract:..
  15. doi request reprint Manufacturing molecules through metabolic engineering
    Jay D Keasling
    Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
    Science 330:1355-8. 2010
    ..In any future, metabolic engineering will soon rival and potentially eclipse synthetic organic chemistry...
  16. doi request reprint Synthetic biology for synthetic chemistry
    Jay D Keasling
    Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720, USA
    ACS Chem Biol 3:64-76. 2008
    ..Some of the most important tools for engineering bacterial metabolism and their use for production of the antimalarial drug artemisinin are reviewed...
  17. pmc Modular engineering of L-tyrosine production in Escherichia coli
    Darmawi Juminaga
    California Institute for Quantitative Biosciences and Berkeley Center for Synthetic Biology, University of California, Berkeley, California, USA
    Appl Environ Microbiol 78:89-98. 2012
    ..This work demonstrates the utility of targeted proteomics and metabolite profiling in pathway construction and optimization, which should be applicable to other metabolic pathways...
  18. ncbi request reprint Engineering Escherichia coli for production of functionalized terpenoids using plant P450s
    Michelle C Y Chang
    California Institute for Quantitative Biomedical Research, University of California, Berkeley, Berkeley, California 94720 3224, USA
    Nat Chem Biol 3:274-7. 2007
    ..coli at high titer using native plant P450s...
  19. ncbi request reprint Engineering a mevalonate pathway in Escherichia coli for production of terpenoids
    Vincent J J Martin
    Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, California 94720 1462, USA
    Nat Biotechnol 21:796-802. 2003
    ....
  20. ncbi request reprint Production of the antimalarial drug precursor artemisinic acid in engineered yeast
    Dae Kyun Ro
    California Institute of Quantitative Biomedical Research, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
    Nature 440:940-3. 2006
    ..annua, yield optimization and industrial scale-up will be required to raise artemisinic acid production to a level high enough to reduce artemisinin combination therapies to significantly below their current prices...
  21. ncbi request reprint Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli
    Douglas J Pitera
    Department of Chemical Engineering, University of California, Berkeley, CA 94720 1462, USA
    Metab Eng 9:193-207. 2007
    ..These results demonstrate that balancing carbon flux through the heterologous pathway is a key determinant in optimizing isoprenoid biosynthesis in microbial hosts...
  22. ncbi request reprint Biosynthesis of plant isoprenoids: perspectives for microbial engineering
    James Kirby
    California Institute of Quantitative Biomedical Research, University of California, Berkeley, California 94720, USA
    Annu Rev Plant Biol 60:335-55. 2009
    ..Here, we review investigations into isoprenoid function and gene discovery in plants as well as the latest advances in isoprenoid pathway engineering in both plant and microbial hosts...
  23. ncbi request reprint Effect of glucose or glycerol as the sole carbon source on gene expression from the Salmonella prpBCDE promoter in Escherichia coli
    Sung Kuk Lee
    Department of Chemical Engineering, University of California, USA
    Biotechnol Prog 22:1547-51. 2006
    ..The expression system is comparable to the widely used T7 promoter-driven expression systems in glucose or glycerol minimal medium...
  24. ncbi request reprint High-throughput metabolic engineering: advances in small-molecule screening and selection
    Jeffrey A Dietrich
    UCSF UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720, USA
    Annu Rev Biochem 79:563-90. 2010
    ..We conclude by providing our prospectus for the future, focusing on transcription factor-based detection systems as a natural microbial mode of small-molecule detection...
  25. doi request reprint Synthetic protein scaffolds provide modular control over metabolic flux
    John E Dueber
    California Institute of Quantitative Biomedical Research QB3, University of California, Berkeley, California, USA
    Nat Biotechnol 27:753-9. 2009
    ..5 g/l) without the synthetic complex. These strategies should prove generalizeable to other metabolic pathways and programmable for fine-tuning pathway flux...
  26. pmc Identification of isopentenol biosynthetic genes from Bacillus subtilis by a screening method based on isoprenoid precursor toxicity
    Sydnor T Withers
    Department of Chemical Engineering, University of California, Berkeley, California, USA
    Appl Environ Microbiol 73:6277-83. 2007
    ..Expression of nudF in E. coli engineered with the mevalonate-based isopentenyl pyrophosphate biosynthetic pathway resulted in the production of isopentenol...
  27. ncbi request reprint Effects of the sequence and size of non-polar residues on self-assembly of amphiphilic peptides
    Kai Wang
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Int J Biol Macromol 36:232-40. 2005
    ..The sequence and steric size of non-polar residues are shown to cause variations in peptide secondary structures and create significant differences in the matrix morphology of self-assembled peptides...
  28. pmc Heterologous protein production in Escherichia coli using the propionate-inducible pPro system by conventional and auto-induction methods
    Sung Kuk Lee
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Protein Expr Purif 61:197-203. 2008
    ..These results strongly indicate that the pPro system is well-suited for overproduction of recombinant proteins...
  29. ncbi request reprint Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids
    Yoichiro Shiba
    Berkeley Center for Synthetic Biology, Department of Chemical Engineering, University of California, 717 Potter Street, Building 977, Mail code 3224, Berkeley, CA 94720 3224, USA
    Metab Eng 9:160-8. 2007
    ..This work will be generally applicable to the production of a broad range of isoprenoids in yeast...
  30. ncbi request reprint High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineered Escherichia coli
    Jack D Newman
    Department of Chemical Engineering, University of California, Berkeley, California, USA
    Biotechnol Bioeng 95:684-91. 2006
    ..5 g/L of culture medium. A standard of amorphadiene collected from the off-gas showed that the caryophyllene standard overestimated amorphadiene production by approximately 30%...
  31. doi request reprint Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene
    Jennifer R Anthony
    California Institute for Quantitative Biomedical Research, University of California, Berkeley, CA 94720, USA
    Metab Eng 11:13-9. 2009
    ..The methods demonstrated here are applicable for identifying and eliminating rate-limiting steps in other constructed biosynthetic pathways...
  32. ncbi request reprint Mono and diterpene production in Escherichia coli
    K Kinkead Reiling
    Department of Chemical Engineering, The University of California Berkeley, California 94720 1462, USA
    Biotechnol Bioeng 87:200-12. 2004
    ..Construction and functional expression of GGPP and GPP operons provides an in vivo precursor platform host for the future engineering of di- and monoterpene cyclases and the overproduction of terpenes in bacteria...
  33. ncbi request reprint Production of isoprenoid pharmaceuticals by engineered microbes
    Michelle C Y Chang
    California Institute for Quantitative Biomedical Research, University of California Berkeley, Berkeley, CA 94720, USA
    Nat Chem Biol 2:674-81. 2006
    ..In this Perspective, we discuss ongoing research aimed toward the production of terpenoid natural products in genetically engineered Escherichia coli and Saccharomyces cerevisiae...
  34. pmc A propionate-inducible expression system for enteric bacteria
    Sung Kuk Lee
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Appl Environ Microbiol 71:6856-62. 2005
    ..Since the prpBCDE promoter has CAP-dependent activation, the prpR-P(prpB) system exhibited negligible basal expression by addition of glucose to the medium...
  35. ncbi request reprint Optimization of DsRed production in Escherichia coli: effect of ribosome binding site sequestration on translation efficiency
    Brian F Pfleger
    Department of Chemical Engineering, University of California Berkeley, California, USA
    Biotechnol Bioeng 92:553-8. 2005
    ..The new DsRed, designated here as RFP(EC) for E. coli optimized red fluorescent protein, fluoresces 2.5 times greater than DsRed-Express when expressed from the same vector...
  36. doi request reprint Metabolic engineering of microorganisms for isoprenoid production
    James Kirby
    California Institute of Quantitative Biomedical Research, University of California, Berkeley, CA 94720, USA
    Nat Prod Rep 25:656-61. 2008
    ..Here we review recent advances in the metabolic engineering of microbes for isoprenoid production as well as some novel approaches to gene discovery and expression...
  37. pmc Genes involved in long-chain alkene biosynthesis in Micrococcus luteus
    Harry R Beller
    Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
    Appl Environ Microbiol 76:1212-23. 2010
    ....
  38. doi request reprint Expression of a synthetic Artemesia annua amorphadiene synthase in Aspergillus nidulans yields altered product distribution
    David Lubertozzi
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    J Ind Microbiol Biotechnol 35:1191-8. 2008
    ..In contrast, expression of ADS in Escherichia coli produced almost exclusively amorpha-4,11-diene. These results indicate that the host environment can greatly impact the terpenes produced from terpene synthases...
  39. ncbi request reprint Importance of systems biology in engineering microbes for biofuel production
    Aindrila Mukhopadhyay
    Joint BioEnergy Institute, Emeryville, CA 95608, United States
    Curr Opin Biotechnol 19:228-34. 2008
    ....
  40. pmc Application of functional genomics to pathway optimization for increased isoprenoid production
    Lance Kizer
    Department of Chemical Engineering, University of California, Berkeley, California 94720 1462, USA
    Appl Environ Microbiol 74:3229-41. 2008
    ..This work demonstrates the utility of using transcriptomic and metabolomic methods to optimize synthetic biological systems...
  41. doi request reprint Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support
    Wesley D Marner
    Dept of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Biotechnol Prog 25:417-23. 2009
    ..Under certain circumstances, the enzymatically-active biosilica displayed improved stability relative to free enzyme at elevated temperatures...
  42. ncbi request reprint Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels
    Sung Kuk Lee
    Joint BioEnergy Institute, Emeryville, CA 95608, USA
    Curr Opin Biotechnol 19:556-63. 2008
    ....
  43. doi request reprint A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3)
    Jeffrey A Dietrich
    UCSF UCB Joint Graduate Group in Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA
    ACS Chem Biol 4:261-7. 2009
    ..coli. We also demonstrate high-yielding, selective transformations to dihydroartemisinic acid, the immediate precursor to the high-value antimalarial drug artemisinin...
  44. pmc Directed evolution of AraC for improved compatibility of arabinose- and lactose-inducible promoters
    Sung Kuk Lee
    Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
    Appl Environ Microbiol 73:5711-5. 2007
    ..Detailed studies indicate that the AraC dimerization domain and C terminus are important for the increased sensitivity of AraC to arabinose...
  45. ncbi request reprint Effect of lacY expression on homogeneity of induction from the P(tac) and P(trc) promoters by natural and synthetic inducers
    Artem Khlebnikov
    Department of Chemical Engineering, University of California, Berkeley, California 94720 1462, USA
    Biotechnol Prog 18:672-4. 2002
    ..In contrast, induction with IPTG gave rise to a single population of cells at all inducer concentrations in both lacY and lacY(+) strains...
  46. ncbi request reprint Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae
    James Kirby
    California Institute for Quantitative Biosciences QB3, University of California, Berkeley, CA 94720, USA
    Phytochemistry 71:1466-73. 2010
    ..Casbene production levels of 31 mg/L were achieved in S. cerevisiae and we discuss strategies to further increase production by maximizing flux through the mevalonate pathway...
  47. ncbi request reprint Propionate-regulated high-yield protein production in Escherichia coli
    Sung Kuk Lee
    Department of Chemical Engineering and Bioengineering, University of California, Synthetic Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Biotechnol Bioeng 93:912-8. 2006
    ..In addition, propionate is an inexpensive, simple-to-use, nontoxic inducer that is attractive for large-scale protein production. Hence, this new system is highly complementary to the widely used T7 promoter-driven expression systems...
  48. pmc Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: evidence for involvement of the cyclic AMP receptor protein
    Sung Kuk Lee
    Department of Chemical Engineering, University of California, Berkeley, CA 94720 1462, USA
    J Bacteriol 187:2793-800. 2005
    ....
  49. ncbi request reprint Amplification of HMG-CoA reductase production enhances carotenoid accumulation in Neurospora crassa
    Guang Yi Wang
    Department of Chemical Engineering, University of California at Berkeley, Berkeley, California 94720 1462, USA
    Metab Eng 4:193-201. 2002
    ..5-fold, respectively, relative to the wild-type strain. Over-expression of cHMG1 under control of the alcA promoter increased production of lycopene and neurosporaxanthin 3- and 2-fold, respectively...
  50. ncbi request reprint Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon
    Christina D Smolke
    Department of Chemical Engineering, University of California, Berkeley 94720 1462, USA
    Biotechnol Bioeng 80:762-76. 2002
    ..By changing gene location and incorporating secondary structures and RNase E sites the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 100-fold and 750-fold, respectively...
  51. pmc Metabolic engineering of a novel propionate-independent pathway for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in recombinant Salmonella enterica serovar typhimurium
    Ilana S Aldor
    Department of Chemical Engineering, University of California, Berkeley, California 94720 1462, USA
    Appl Environ Microbiol 68:3848-54. 2002
    ..It was possible to vary the average HV fraction in the copolymer by adjusting the arabinose or cyanocobalamin (precursor of coenzyme B12) concentration in the medium...
  52. ncbi request reprint Improved assembly of multimeric genes for the biosynthetic production of protein polymers
    Nichole L Goeden-Wood
    Department of Chemical Engineering, University of California at Berkeley, Berkeley, California 94720 1462, USA
    Biomacromolecules 3:874-9. 2002
    ..Circular dichroism studies on the artificial protein poly-EAK9 demonstrate the formation of a beta-sheet structure in aqueous solution...
  53. ncbi request reprint Modulation of gene expression from the arabinose-inducible araBAD promoter
    A Khlebnikov
    Department of Chemical Engineering, University of California, Berkeley, CA 94720 1462, USA
    J Ind Microbiol Biotechnol 29:34-7. 2002
    ....
  54. ncbi request reprint A Salmonella-based, propionate-inducible, expression system for Salmonella enterica
    Sung Kuk Lee
    Department of Chemical Engineering, University of California, Berkeley, 94720, USA
    Gene 377:6-11. 2006
    ..In contrast, the prpB(-) strain showed very high background expression in both culture tubes and shake flasks...
  55. ncbi request reprint Biosynthesis and engineering of isoprenoid small molecules
    Sydnor T Withers
    Department of Chemical Engineering, University of California, Berkeley, CA, USA
    Appl Microbiol Biotechnol 73:980-90. 2007
    ..Finally, we will describe the efforts to produce to commercial terpenoids, paclitaxel and artemisinin...
  56. ncbi request reprint Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes
    Brian F Pfleger
    Department of Chemical Engineering, University of California Berkeley, Berkeley, CA 94720 1462, USA
    Nat Biotechnol 24:1027-32. 2006
    ..This technology should be useful for optimizing the expression of multiple genes in synthetic operons, both in prokaryotes and eukaryotes...
  57. ncbi request reprint Microbioreactor arrays with parametric control for high-throughput experimentation
    Michel M Maharbiz
    Berkeley Sensor and Actuator Center BSAC, Dept of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, California 94720, USA
    Biotechnol Bioeng 86:485-90. 2004
    ..Growth data are presented for Escherichia coli cultured in the array with varying microaerobic conditions using electrochemically generated oxygen. Additionally, we present data on carbon dioxide generation for pH dosing...
  58. doi request reprint Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
    Eric J Steen
    Joint BioEnergy Institute, Emeryville, California 94608, USA
    Nature 463:559-62. 2010
    ..Furthermore, we show engineering of the biodiesel-producing cells to express hemicellulases, a step towards producing these compounds directly from hemicellulose, a major component of plant-derived biomass...
  59. ncbi request reprint Microbial sensors for small molecules: development of a mevalonate biosensor
    Brian F Pfleger
    Department of Chemical Engineering, University of California Berkeley, Berkeley, CA 94720 1462, USA
    Metab Eng 9:30-8. 2007
    ....
  60. pmc Functional genomic study of exogenous n-butanol stress in Escherichia coli
    Becky J Rutherford
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Appl Environ Microbiol 76:1935-45. 2010
    ..Cellular engineering based on these cues may assist in developing a high-titer, n-butanol-producing host...
  61. doi request reprint Biosensors and their applications in microbial metabolic engineering
    Fuzhong Zhang
    Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
    Trends Microbiol 19:323-9. 2011
    ..This review will focus on recent developments in biosensor design, and their applications for controlling microbial behavior...
  62. doi request reprint Engineering static and dynamic control of synthetic pathways
    William J Holtz
    Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA 94720, USA
    Cell 140:19-23. 2010
    ..The next frontier is to create synthetic pathways that adapt to changing environments...
  63. ncbi request reprint A tightly regulated inducible expression system utilizing the fim inversion recombination switch
    Timothy S Ham
    Department of Bioengineering, University of California, Berkeley, 94720, USA
    Biotechnol Bioeng 94:1-4. 2006
    ..These characteristics make our system suitable for large-scale expression or for production of toxic proteins...
  64. ncbi request reprint Rationally engineered biotransformation of p-nitrophenol
    Matthew de la Peña Mattozzi
    Dept of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Biotechnol Prog 26:616-21. 2010
    ..Although P. putida harboring the refactored construct was incapable of growing exclusively on PNP as a carbon source, evidence that the engineered pathway was functional was demonstrated by the induced expression of chromosomal pcaIJF...
  65. doi request reprint Advanced biofuel production in microbes
    Pamela P Peralta-Yahya
    Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
    Biotechnol J 5:147-62. 2010
    ..We concentrate on the metabolic engineering of genetically tractable organisms such as Escherichia coli and Saccharomyces cerevisiae for the production of these advanced biofuels...
  66. pmc Design and construction of a double inversion recombination switch for heritable sequential genetic memory
    Timothy S Ham
    Department of Bioengineering, University of California, Berkeley, California, United States of America
    PLoS ONE 3:e2815. 2008
    ..Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence...
  67. ncbi request reprint Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates
    Ilana S Aldor
    Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, CA 94720 1462, USA
    Curr Opin Biotechnol 14:475-83. 2003
    ..In addition, mathematical models and molecular methods can be used to elucidate metabolically engineered systems and to identify targets for performance improvement...
  68. ncbi request reprint Metabolic engineering for drug discovery and development
    Chaitan Khosla
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    Nat Rev Drug Discov 2:1019-25. 2003
  69. ncbi request reprint Microbioreactor arrays with parametric control for high-throughput experimentation
    Michel M Maharbiz
    Berkeley Sensor and Actuator Center BSAC, Dept of Electrical Engineering and Computer Science, 497 Cory Hall, University of California at Berkeley, Berkeley, California 94720, USA
    Biotechnol Bioeng 85:376-81. 2004
    ..Growth data are presented for Escherichia coli cultured in the array with varying microaerobic conditions using electrochemically generated oxygen. Additionally, we present data on carbon dioxide generation for pH dosing...
  70. ncbi request reprint Programming cellular function
    Christopher A Voigt
    Department of Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research QB3, University of California, San Francisco, San Francisco, California 94143 2540, USA
    Nat Chem Biol 1:304-7. 2005
    ..A meeting was held in August 2005 to present progress in the field and to discuss topics in ethics, safety and security...
  71. ncbi request reprint Designed divergent evolution of enzyme function
    Yasuo Yoshikuni
    UCSF UCB Joint Graduate Group in Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, USA
    Nature 440:1078-82. 2006
    ..Creation of these enzymes demonstrates the feasibility of exploiting the underlying evolvability of this scaffold, and provides evidence that rational approaches based on these ideas are useful for enzyme design...
  72. pmc Chlorxanthomycin, a fluorescent, chlorinated, pentacyclic pyrene from a Bacillus sp
    Andrew Magyarosy
    Department of Chemical Engineering, University of California, Berkeley, California 94720 1462, USA
    Appl Environ Microbiol 68:4095-101. 2002
    ..7865. Chlorxanthomycin appears to be located in the cytoplasm, does not diffuse out of the cells into the culture medium, and has selective antibiotic activity...
  73. ncbi request reprint Manipulation of intracellular magnesium levels in Saccharomyces cerevisiae with deletion of magnesium transporters
    Bernardo M T da Costa
    Department of Chemical Engineering, University of California, Berkeley, CA 94720 3224, USA
    Appl Microbiol Biotechnol 77:411-25. 2007
    ..cerevisiae and overexpression of magnesium transporters from A. thaliana also affected the intracellular concentrations of a range of metal ions, which suggests that cells use non-specific transporters to help regulate metal homeostasis...
  74. ncbi request reprint Biofuel alternatives to ethanol: pumping the microbial well
    J L Fortman
    Department of Chemical Engineering, University of California, 717 Potter Street, Building 977, Mail code 3224 Berkeley, CA 94720 3224, USA
    Trends Biotechnol 26:375-81. 2008
    ..To highlight additional options, we review advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways...
  75. pmc Absence of diauxie during simultaneous utilization of glucose and Xylose by Sulfolobus acidocaldarius
    Chijioke J Joshua
    Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
    J Bacteriol 193:1293-301. 2011
    ..The mechanism by which the organism utilized a mixture of sugars has yet to be elucidated...
  76. ncbi request reprint Engineering the lycopene synthetic pathway in E. coli by comparison of the carotenoid genes of Pantoea agglomerans and Pantoea ananatis
    Sang Hwal Yoon
    Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660 701, South Korea
    Appl Microbiol Biotechnol 74:131-9. 2007
    ..agglomerans and P. ananatis. As there was no significant difference in lycopene production between E. coli harboring P. agglomerans crtE and A. fulgidus gps, farnesyl diphosphate (FPP) synthesis was not rate-limiting in E. coli...
  77. ncbi request reprint Increased beta-carotene production in recombinant Escherichia coli harboring an engineered isoprenoid precursor pathway with mevalonate addition
    Sang Hwal Yoon
    Division of Applied Life Science BK21, EB NCRC and PMBBRC, and Division of Forest Science, Gyeongsang National University, Jinju 660 701, Korea
    Biotechnol Prog 23:599-605. 2007
    ..5% (w/v) glycerol, beta-carotene production of 503 mg/L in concentration and 49.3 mg/g DCW in content was obtained at 144 h, which was the highest level of carotenoid production in E. coli ever reported in the literature...
  78. ncbi request reprint Identification of genes affecting lycopene accumulation in Escherichia coli using a shot-gun method
    Min Jung Kang
    Amicogen Inc, Jinsung, Jinju 660 852, Korea
    Biotechnol Bioeng 91:636-42. 2005
    ..The co-expression of appY with dxs produced eight times the amount of lycopene (4.7 mg/g DCW) that was produced without expression of both genes (0.6 mg/g DCW)...
  79. doi request reprint Metabolic engineering delivers next-generation biofuels
    Jay D Keasling
    Nat Biotechnol 26:298-9. 2008
  80. doi request reprint Engineering triterpene production in Saccharomyces cerevisiae-beta-amyrin synthase from Artemisia annua
    James Kirby
    California Institute for Quantitative Biomedical Research, University of California, Berkeley, CA 94720, USA
    FEBS J 275:1852-9. 2008
    ..L(-1) culture. As we have observed a 12-fold increase in squalene levels, it appears that this strain has the capacity for even higher beta-amyrin production. Options for further engineering efforts are explored...
  81. pmc Uranyl precipitation by Pseudomonas aeruginosa via controlled polyphosphate metabolism
    Neil Renninger
    Department of Chemical Engineering, University of California at Berkeley, Berkeley, CA 94720 1462, USA
    Appl Environ Microbiol 70:7404-12. 2004
    ..Lethal doses of radiation did not halt phosphate secretion from polyphosphate-filled cells under carbon starvation conditions...
  82. ncbi request reprint Dibenzothiophene biodesulfurization pathway improvement using diagnostic GFP fusions
    David S Reichmuth
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Biotechnol Bioeng 88:94-9. 2004
    ..When cotransformed with the full dszABC operon, the mutant dszB increased the rate of desulfurization ninefold relative to that using the native dszB...
  83. doi request reprint Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins
    Sara P Gaucher
    Sandia National Laboratory, Livermore, California 94550, USA
    J Proteome Res 7:2320-31. 2008
    ..Here, we discuss our methods and implications of potential trimethylation in the D. vulgaris sulfate reduction pathway...
  84. doi request reprint Separation and mass spectrometry in microbial metabolomics
    David E Garcia
    Joint BioEnergy Institute, Emeryville, CA 94608, USA
    Curr Opin Microbiol 11:233-9. 2008
    ....
  85. ncbi request reprint Microbially derived artemisinin: a biotechnology solution to the global problem of access to affordable antimalarial drugs
    Victoria Hale
    The Institute for OneWorld Health, 50 California Street, San Francisco, CA 94111, USA
    Am J Trop Med Hyg 77:198-202. 2007
    ..By making life-saving ACTs affordable to the people who most need them, the Artemisinin Project hopes to show that the power of biotechnology can be harnessed to provide solutions to global health problems...
  86. ncbi request reprint Metabolic engineering of Pseudomonas putida for the utilization of parathion as a carbon and energy source
    Andy W Walker
    Department of Chemical Engineering, University of California, Berkeley 94720 1462, USA
    Biotechnol Bioeng 78:715-21. 2002
    ..8 mM parathion as a source of carbon and energy. Degradation studies showed that parathion formed a separate dense, non-aqueous phase liquid phase but was still bioavailable...
  87. ncbi request reprint Enhanced lycopene production in Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate
    Sang Hwal Yoon
    Department of Food Science and Nutrition, Gyeongsang National University, Jinju, Korea
    Biotechnol Bioeng 94:1025-32. 2006
    ..6 mM mevalonate for the mevalonate lower pathway, and 0.5% (w/v) Tween 80 to prevent clump formation, lycopene production was 102 mg/L and 22 mg/g dry cell weight, and cell growth had an OD(600) value of 15 for 72 h...
  88. ncbi request reprint Morphology of artificial silica matrices formed via autosilification of a silaffin/protein polymer chimera
    Wesley D Marner
    Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
    Biomacromolecules 9:1-5. 2008
    ....
  89. doi request reprint Redirection of flux through the FPP branch-point in Saccharomyces cerevisiae by down-regulating squalene synthase
    Eric M Paradise
    Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
    Biotechnol Bioeng 100:371-8. 2008
    ..The levels of these three metabolites were dependent not only upon the level of ERG9 repression, but also the timing of its repression relative to the induction of ADS and genes responsible for enhancing flux to FPP...
  90. pmc Metabolic flux elucidation for large-scale models using 13C labeled isotopes
    Patrick F Suthers
    Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
    Metab Eng 9:387-405. 2007
    ..Finally, we discuss the effect of reducing the model, as well as shed light onto the customization of the developed computational framework to other systems...
  91. pmc Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough
    Aindrila Mukhopadhyay
    Berkeley Center for Synthetic Biology, 717 Potter Street, Berkeley, CA 94720, USA
    J Bacteriol 189:5996-6010. 2007
    ..vulgaris and suggest that while exposure to air is highly detrimental to D. vulgaris, this bacterium can successfully cope with periodic exposure to low O(2) levels in its environment...
  92. pmc Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid
    Yinjie J Tang
    Synthetic Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 3224, USA
    Appl Environ Microbiol 73:3859-64. 2007
    ..These findings enable a better understanding of the relationship between genome annotation and extant metabolic pathways in G. metallireducens...
  93. doi request reprint Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein
    Afshan S Shaikh
    Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
    Anal Chem 80:886-90. 2008
    ..This study provides the foundation to extend isotopomer-based flux analysis to study metabolism of individual strains in microbial communities...
  94. ncbi request reprint Coenzyme Q10 production in recombinant Escherichia coli strains engineered with a heterologous decaprenyl diphosphate synthase gene and foreign mevalonate pathway
    Hossein Shahbani Zahiri
    Department of Microbiology, Gyeongsang National University, Gazwa dong 900, Jinju 660 701, Korea
    Metab Eng 8:406-16. 2006
    ..However, it provided CoQ(10) production of up to 1,706+/-86 microg/gDCW, which was roughly 1.9 times higher than that obtained by ddsA alone...
  95. ncbi request reprint Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR-1 in a novel high-throughput mini-bioreactor
    Yinjie J Tang
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Biotechnol Bioeng 95:176-84. 2006
    ..Besides its use for examining parameters of interest to environmental remediation, the device will also allow one to quickly assess parameters for optimal production of recombinant proteins or secondary metabolites...
  96. ncbi request reprint Charge-associated effects of fullerene derivatives on microbial structural integrity and central metabolism
    Yinjie J Tang
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nano Lett 7:754-60. 2007
    ..The results presented here favor the hypothesis that fullerenes cause more membrane stress 4-6 than perturbation to energy metabolism.7...

Research Grants3

  1. Biosensors for metabolic engineering
    Jay Keasling; Fiscal Year: 2004
    ..abstract_text> ..
  2. Biosensors for metabolic engineering
    Jay Keasling; Fiscal Year: 2005
    ..abstract_text> ..
  3. Biosensors for metabolic engineering
    Jay Keasling; Fiscal Year: 2006
    ..abstract_text> ..