Virgil A Rhodius

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Predicting the strength of UP-elements and full-length E. coli σE promoters
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California at San Francisco, 600 16th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 40:2907-24. 2012
  2. pmc Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California, 600 16th Street, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 107:2854-9. 2010
  3. pmc Technical considerations in using DNA microarrays to define regulons
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
    Methods 47:63-72. 2009
  4. doi request reprint Dissection of recognition determinants of Escherichia coli sigma32 suggests a composite -10 region with an 'extended -10' motif and a core -10 element
    Byoung Mo Koo
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
    Mol Microbiol 72:815-29. 2009
  5. pmc Convergence of molecular, modeling, and systems approaches for an understanding of the Escherichia coli heat shock response
    Eric Guisbert
    Department of Biochemistry, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    Microbiol Mol Biol Rev 72:545-54. 2008
  6. pmc Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition
    Byoung Mo Koo
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158, USA
    Genes Dev 23:2426-36. 2009
  7. pmc Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress
    Gen Nonaka
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94143, USA
    Genes Dev 20:1776-89. 2006
  8. pmc Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli
    Eric Guisbert
    Department of Biochemistry, University of California at San Francisco, San Francisco, CA 94158, USA
    J Bacteriol 189:1963-73. 2007
  9. pmc Promoter strength properties of the complete sigma E regulon of Escherichia coli and Salmonella enterica
    Vivek K Mutalik
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    J Bacteriol 191:7279-87. 2009
  10. pmc Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element
    Byoung Mo Koo
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
    Mol Microbiol 72:830-43. 2009

Collaborators

Detail Information

Publications15

  1. pmc Predicting the strength of UP-elements and full-length E. coli σE promoters
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California at San Francisco, 600 16th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 40:2907-24. 2012
    ..Our findings provide important insights into the sequence requirements for the strength and function of full-length promoters and establish guidelines for promoter prediction and for forward engineering promoters of specific strengths...
  2. pmc Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California, 600 16th Street, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 107:2854-9. 2010
    ..These results provide valuable insights into sequences that govern promoter strength, distinguish active and inactive promoters for the first time, and are applicable to both in vivo and in vitro measures of promoter strength...
  3. pmc Technical considerations in using DNA microarrays to define regulons
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
    Methods 47:63-72. 2009
    ..Together they can provide detailed information on transcriptional regulatory systems...
  4. doi request reprint Dissection of recognition determinants of Escherichia coli sigma32 suggests a composite -10 region with an 'extended -10' motif and a core -10 element
    Byoung Mo Koo
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
    Mol Microbiol 72:815-29. 2009
    ..This result supports the idea that K130 mediates extended -10 recognition. Sigma32 is the first Group 3 sigma shown to use the 'extended -10' recognition motif...
  5. pmc Convergence of molecular, modeling, and systems approaches for an understanding of the Escherichia coli heat shock response
    Eric Guisbert
    Department of Biochemistry, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    Microbiol Mol Biol Rev 72:545-54. 2008
    ..coli and discuss how these additional components contribute to regulation. Finally, we discuss recent genomic experiments that reveal additional functional aspects of the HSR...
  6. pmc Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition
    Byoung Mo Koo
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158, USA
    Genes Dev 23:2426-36. 2009
    ..Divergent sigmas may generally use a nonoptimal Region 2.3 to increase promoter stringency, enabling them to mount a focused response to altered conditions...
  7. pmc Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress
    Gen Nonaka
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94143, USA
    Genes Dev 20:1776-89. 2006
    ..The intimate connection of the response to the membrane rationalizes why a major regulator of the response resides in that cellular compartment...
  8. pmc Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli
    Eric Guisbert
    Department of Biochemistry, University of California at San Francisco, San Francisco, CA 94158, USA
    J Bacteriol 189:1963-73. 2007
    ..Together, our results indicate that Hfq may play a general role in stress response regulation in E. coli...
  9. pmc Promoter strength properties of the complete sigma E regulon of Escherichia coli and Salmonella enterica
    Vivek K Mutalik
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    J Bacteriol 191:7279-87. 2009
    ....
  10. pmc Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element
    Byoung Mo Koo
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
    Mol Microbiol 72:830-43. 2009
    ..Sigma28 is the second Group 3 sigma shown to use an extended -10 region in promoter recognition, raising the possibility that other Group 3 sigmas will do so as well...
  11. pmc Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon
    Emily B Gogol
    Department of Microbiology and Immunology, and Department of Cell and Tissue Biology, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 108:12875-80. 2011
    ....
  12. pmc Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
    Mol Syst Biol 9:702. 2013
    ..This represents a genome-scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well-characterized regulatory parts will enable the construction of sophisticated gene expression programs...
  13. pmc Conserved and variable functions of the sigmaE stress response in related genomes
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California, San Francisco, California, USA
    PLoS Biol 4:e2. 2006
    ..The success of our promoter prediction model for sigmaE suggests that it will be applicable for the prediction of promoter elements for many alternative sigma factors...
  14. ncbi request reprint Uses and pitfalls of microarrays for studying transcriptional regulation
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California, Genentech Hall, 600 16th Street, San Francisco, CA 94143 2200, USA
    Curr Opin Microbiol 6:114-9. 2003
    ..High-density oligonucleotide arrays have enabled the identification of many new transcripts, including small RNAs and antisense RNAs...
  15. doi request reprint Using DNA microarrays to assay part function
    Virgil A Rhodius
    Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
    Methods Enzymol 497:75-113. 2011
    ..The aim of this chapter is to provide the reader with the information necessary to be able to systematically catalog the impact of genetic parts on the host and also to optimize the operation of fully engineered genetic circuits...