John E Dueber

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay
    Michael E Lee
    The UC Berkeley and UCSF Graduate Program in Bioengineering, Berkeley, CA 94720, USA, Department of Bioengineering, University of California, Berkeley, CA 94720, USA, Energy Biosciences Institute, Berkeley, CA 94720, USA, Department of Industrial Engineering and Operations Research, University of California, Berkeley, CA 94720, USA and Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 41:10668-78. 2013
  2. 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
  3. doi request reprint Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways
    William C Deloache
    UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley UC Berkeley, Berkeley, California 94720, USA
    Nat Commun 7:11152. 2016
  4. doi request reprint Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding sequences
    Weston R Whitaker
    Departments of Bioengineering, University of California, Berkeley, California 94720, United States
    ACS Synth Biol 4:249-57. 2015
  5. doi request reprint Application of a Palladium-Catalyzed C-H Functionalization/Indolization Method to Syntheses of cis-Trikentrin A and Herbindole B
    Raul A Leal
    Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
    Angew Chem Int Ed Engl 55:11824-8. 2016
  6. pmc Selection of chromosomal DNA libraries using a multiplex CRISPR system
    Owen W Ryan
    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    elife 3:. 2014
  7. doi request reprint A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly
    Michael E Lee
    Department of Bioengineering, University of California, Berkeley, California 94720, United States
    ACS Synth Biol 4:975-86. 2015
  8. doi request reprint An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose
    William C Deloache
    Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
    Nat Chem Biol 11:465-71. 2015
  9. pmc Engineering robust control of two-component system phosphotransfer using modular scaffolds
    Weston R Whitaker
    The University of California, Berkeley and University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 109:18090-5. 2012
  10. 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

Collaborators

  • Jay Keasling
  • William C Deloache
  • Michael E Lee
  • Weston R Whitaker
  • Adam P Arkin
  • Zachary N Russ
  • Raul A Leal
  • Owen W Ryan
  • J Christopher Anderson
  • Nathan A Sallee
  • Luke N Latimer
  • Caroline Bischof
  • Christopher C McAtee
  • Youjin V Lee
  • Richmond Sarpong
  • Shota Sawano
  • Jin Quan Yu
  • Bernardo Cervantes
  • Andrew M Gonzales
  • Lauren Narcross
  • Vincent J J Martin
  • Hanson Lee
  • Jeffrey M Skerker
  • Jordan C Tsai
  • Snigdha Poddar
  • Xin Li
  • Matthew J Maurer
  • Will Deloache
  • Jamie H D Cate
  • Claire J Tomlin
  • Anil Aswani
  • Audrey S Han
  • Stephanie A Davis
  • Gabriel C Wu
  • Jonathan A Goler
  • Mariana Leguia
  • R Dyche Mullins
  • Gonzalo M Rivera
  • Wendell A Lim
  • Bruce J Mayer
  • Dan Vasilescu

Detail Information

Publications13

  1. pmc Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay
    Michael E Lee
    The UC Berkeley and UCSF Graduate Program in Bioengineering, Berkeley, CA 94720, USA, Department of Bioengineering, University of California, Berkeley, CA 94720, USA, Energy Biosciences Institute, Berkeley, CA 94720, USA, Department of Industrial Engineering and Operations Research, University of California, Berkeley, CA 94720, USA and Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 41:10668-78. 2013
    ..This generalizable method should prove useful in engineering new pathways for the sustainable production of small molecules. ..
  2. 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...
  3. doi request reprint Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways
    William C Deloache
    UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley UC Berkeley, Berkeley, California 94720, USA
    Nat Commun 7:11152. 2016
    ..This work builds a foundation for using the peroxisome as a synthetic organelle, highlighting both promise and future challenges on the way to realizing this goal. ..
  4. doi request reprint Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding sequences
    Weston R Whitaker
    Departments of Bioengineering, University of California, Berkeley, California 94720, United States
    ACS Synth Biol 4:249-57. 2015
    ..We found that balancing promoter strengths and upstream RBS strengths to intermediate levels can achieve the target protein concentration while avoiding both excessive noise and truncated protein...
  5. doi request reprint Application of a Palladium-Catalyzed C-H Functionalization/Indolization Method to Syntheses of cis-Trikentrin A and Herbindole B
    Raul A Leal
    Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
    Angew Chem Int Ed Engl 55:11824-8. 2016
    ..Key steps include a sterically demanding Buchwald-Hartwig amination as well as a unique C(sp(3) )-H amination/indole formation. Studies toward a selective desymmetrization of the meso-hydroquinone are also reported. ..
  6. pmc Selection of chromosomal DNA libraries using a multiplex CRISPR system
    Owen W Ryan
    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    elife 3:. 2014
    ....
  7. doi request reprint A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly
    Michael E Lee
    Department of Bioengineering, University of California, Berkeley, California 94720, United States
    ACS Synth Biol 4:975-86. 2015
    ..Additionally, by relieving researchers of the burden of technical details, they can focus on higher-level aspects of experimental design. ..
  8. doi request reprint An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose
    William C Deloache
    Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
    Nat Chem Biol 11:465-71. 2015
    ..Future work to improve titers and connect these steps with downstream pathway branches, already demonstrated in S. cerevisiae, will enable low-cost production of many high-value BIAs. ..
  9. pmc Engineering robust control of two-component system phosphotransfer using modular scaffolds
    Weston R Whitaker
    The University of California, Berkeley and University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 109:18090-5. 2012
    ..Thus, we demonstrate that design principles inspired by the complex signal-transduction pathways of eukaryotes may be generalized, abstracted, and applied to prokaryotes using well-characterized parts...
  10. 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
    ..In particular, the system is not suitable for the construction of protein fusions due to an unfavorable scar sequence that encodes an in-frame stop codon...
  11. pmc The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency
    Nathan A Sallee
    Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA
    Nature 454:1005-8. 2008
    ..Thus, this pathogen has used a simple autoinhibitory fragment as a component to build a highly effective actin polymerization machine...
  12. ncbi request reprint Engineering synthetic signaling proteins with ultrasensitive input/output control
    John E Dueber
    Program in Biological Sciences, University of California, San Francisco, California 94158 2517, USA
    Nat Biotechnol 25:660-2. 2007
    ..By systematically altering the number and affinity of modular autoinhibitory interactions, we show that we can predictably convert a simple linear signaling protein into an ultrasensitive switch...
  13. ncbi request reprint Reprogramming control of an allosteric signaling switch through modular recombination
    John E Dueber
    Program in Biological Sciences, University of California, San Francisco, CA 94143 2240, USA
    Science 301:1904-8. 2003
    ..Synthetic switch proteins were created with diverse gating behaviors in response to nonphysiological inputs. Thus, this type of modular framework can facilitate the evolution or engineering of cellular signaling circuits...