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Helmann, John D.
Cornell Faculty Member
Positions
- Professor, Microbiology (BIOMI), College of Agriculture and Life Sciences (CALS)
- Department Chairperson, Microbiology (BIOMI), College of Agriculture and Life Sciences (CALS)
John Helmann earned bachelor`s degrees in Chemistry and Biology (University of California, Santa Cruz) in 1982. He then joined the Department of Biochemistry at the University of California at Berkeley where he studied bacterial RNA polymerase with Dr. Michael Chamberlin and earned a Ph.D. in 1987. From 1987 to 1990, Dr. Helmann worked as a post-doctoral fellow with Dr. Christopher T. Walsh at the Harvard Medical School. His post-doctoral research, on the regulation of bacterial mercuric ion resistance determinants, was supported by the Jane Coffin Childs Memorial Medical Research Foundation. Dr. Helmann joined the Section of Microbiology at Cornell as an Assistant Professor in 1990 and joined the graduate field of Biochemistry, Molecular, and Cell Biology in 1991. He was promoted to Associate Professor in 1996 and Professor in 2002.
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Affiliations
member of graduate field
Research
research overview
- Our laboratory studies Bacillus subtilis, a Gram-positive soil bacterium and genetic model system. Major research efforts address the stress responses elicited by (i) antibiotics that affect the cell envelope, (ii) reactive oxygen species, or (iii) deficiency or excess of nutrient metal ions. For each stress response, we are interested in the global patterns of transcriptional control, the mechanisms of the corresponding regulatory proteins, and the roles of the induced pathways.
research activities
principal investigator on
- BACILLITHIOL AND THE REDOX BIOLOGY OF BACILLUS SUBTILIS awarded by DIRECTORATE FOR BIOLOGICAL SCIENCES NSF 2010 - 2013
- ECF SIGMA FACTORS AND CELL ENVELOPE STRESS IN BACILLUS SUBTILIS awarded by NATL INST OF HEALTH DHHS 2009 - 2012
- METAL ION HOMEOSTASIS IN BACILLUS SUBTILIS awarded by NATL INST OF HEALTH DHHS 2009 - 2013
area(s) of concentration/expertise
keywords
- Antibiotics
- Bacillus subtilis
- Bacterial gene regulation
- Genomics
- Metal homeostasis
- Oxidative stress
- RNA Polymerase
- Transcription
- sigma factors
submitted impact statement
Publications
individual publications
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academic article
- A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism. Journal of Bacteriology. 194:2594-605. 2012
- A mutation of the RNA polymerase β' -subunit (rpoC) that confers cephalosporin resistance in Bacillus subtilis.. Antimicrobial Agents and Chemotherapy. 2012
- A σD-dependent antisense transcript modulates expression of the cyclic-di-AMP hydrolase GdpP in Bacillus subtilis.. Microbiology. 158:2732-2741. 2012
- Analysis of the role of Bacillus subtilis σ(M) in β-lactam resistance reveals an essential role for c-di-AMP in peptidoglycan homeostasis.. Molecular Microbiology. 83:623-639. 2012
- Changes to the editorial team at Molecular Microbiology.. Molecular Microbiology. 86:1283-1284. 2012
- Derepression of the Bacillus subtilis PerR peroxide stress response leads to iron deficiency. Journal of Bacteriology. 194:1266-1235. 2012
- Direct substitution and assisted dissociation pathways for turning off transcription by a MerR-family metalloregulator.. Proceedings of the National Academy of Sciences of the United States of America. 109:15121-15126. 2012
- Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation. Advances in Microbial Physiology. 60:91-210. 2012
- Glutamate Dehydrogenase Affects Resistance to Cell Wall Antibiotics in Bacillus subtilis. Journal of Bacteriology. 194:993-1001. 2012
- Origins of specificity and cross-talk in metal ion sensing by Bacillus subtilis Fur.. Molecular Microbiology. 86:1144-1155. 2012
- The FsrA sRNA and FbpB protein mediate the iron-dependent induction of the Bacillus subtilis lutABC iron-sulfur-containing oxidases.. Journal of Bacteriology. 194:2586-93. 2012
- Transcription activation by the siderophore sensor Btr is mediated by ligand-dependent stimulation of promoter clearance. Nucleic Acids Research. 40:3585-95. 2012
- A σW-dependent stress response in Bacillus subtilis that reduces membrane fluidity. Molecular Microbiology. 81:69-79. 2011
- Bacillus subtilis Fur represses one of two paralogous haem-degrading monooxygenases. Microbiology. 157:3221-3231. 2011
- Bacillus subtilis σ(V) confers lysozyme resistance by activation of two cell wall modification pathways, peptidoglycan O-acetylation and D-alanylation of teichoic acids. Journal of Bacteriology. 193:6223-6232. 2011
- Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. Journal of Bacteriology. 193:4598-4611. 2011
- DNA-binding properties of the Bacillus subtilis and Aeribacillus pallidus AC6 σD proteins. . Journal of Bacteriology. 193:575-9. 2011
- Identification of altered function alleles that affect Bacillus subtilis PerR metal ion selectivity. Nucleic Acids Research. 39:5036-5044. 2011
- New dimensions at Molecular Microbiology: 3D graphics and the Wiley Online Library. Molecular Microbiology. 81:295-296. 2011
- Reduction in membrane phosphatidylglycerol content leads to daptomycin resistance in Bacillus subtilis. Antimicrobial Agents and Chemotherapy. 55:4326-4337. 2011
- Sequential binding and sensing of Zn(II) by Bacillus subtilis Zur. Nucleic Acids Research. 1:9130-9138. 2011
- The Bacillus subtilis GntR family repressor YtrA responds to cell wall antibiotics. Journal of Bacteriology. 193:5793-5801. 2011
- Biosynthesis and functions of bacillithiol, a major low-molecular-weight thiol in Bacilli. Proceedings at the National Academy of Science USA. 107:6482-6486. 2010
- Transcriptomic and phenotypic characterization of a Bacillus subtilis strain without extracytoplasmic function σ factors. Journal of Bacteriology. 192:5736-45. 2010
- A two-subunit bacterial sigma-factor activates transcription in Bacillus subtillis.. Proceedings at the National Academy of Science USA. 106:21323-23328. 2009
- Bacillithiol is an antioxidant thiol produced in Bacilli. Nature Chemical Biology. 5:625-627. 2009
- Contributions of Zur-controlled ribosomal proteins to growth under zinc starvation conditions.. Journal of Bacteriology. 191:6116-6122. 2009
- Direct stimulus perception and transcription activation by a membrane-bound DNA binding protein.. Molecular Microbiology. 73:482-491. 2009
- Extracytoplasmic function sigma factors regulate expression of the Bacillus subtilis yabE gene via a cis-acting antisense RNA. Journal of Bacteriology. 191:1101-1105. 2009
- Genetic Analysis of Factors Affecting Susceptibility of Bacillus subtilis to Daptomycin. Annual Reviews of Microbiology. 53:1598-1609. 2009
- Genome-wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol-dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR-family regulator YraB (AdhR). Molecular Microbiology. 74:876-94. 2009
- Oxidation of a single active site suffices for the functional inactivation of the dimeric Bacillus subtilis OhrR repressor in vitro. Nucleic Acids Research. 37:1174-1181. 2009
- RNA polymerase: a nexus of gene regulation. Methods. 47:1-5. 2009
- ROMA: an in vitro approach to defining target genes for transcription regulators. Methods. 47:73-77. 2009
- The YvrI alternative sigma factor is essential for acid stress induction of oxalate decarboxylase in Bacillus subtilis. Journal of Bacteriology. 191:931-939. 2009
- Zinc-Independent Folate Biosynthesis: Genetic, Biochemical, and Structural Investigations Reveal New Metal Dependence for GTP Cyclohydrolase IB.. Journal of Bacteriology. 191:6936-6949. 2009
- A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis. Molecular Microbiology. 69:954-967. 2008
- Conversion of Bacillus subtilis OhrR from a 1-Cys to a 2-Cys peroxide sensor. Journal of Bacteriology. 190:5738-5745. 2008
- In vitro mutagenesis of Bacillus subtilis by using a modified Tn7 transposon with an outward-facing inducible promoter. Applied and Environmental Microbiology. 74:3419-25. 2008
- In vitro mutagenesis of Bacillus subtilis by using a modified Tn7 transposon with an outward-facing inducible promoter. Applied and Environmental Microbiology. 74:3419-25. 2008
- Oxidant-dependent switching between reversible and sacrificial oxidation pathways for Bacillus subtilis OhrR. Molecular Microbiology. 68:978-986. 2008
- Phenotypic and transcriptomic characterization of Bacillus subtilis mutants with grossly altered membrane composition. Journal of Bacteriology. 190:7797-7807. 2008
- Regulation of the Bacillus subtilis yciC gene and insights into the DNA-binding specificity of the zinc-sensing metalloregulator Zur. Journal of Bacteriology. 190:3482-3488. 2008
- The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. Proceedings of the National Academy of Sciences of the United States of America. 105:11927-32. 2008
- The Bacillus subtilis sigma(M) regulon and its contribution to cell envelope stress responses. Molecular Microbiology. 67:830-48. 2008
- A complex thiolate switch regulates the Bacillus subtilis organic peroxide sensor OhrR. Proceedings at the National Academy of Science USA. 104:8743-8. 2007
- An antibiotic-inducible cell wall-associated protein that protects Bacillus subtilis from autolysis. Journal of Bacteriology. 189:4671-80. 2007
- CsoR regulates the copper efflux operon copZA in Bacillus subtilis. Microbiology. 153:4123-8. 2007
- LiaRS-dependent gene expression is embedded in transition state regulation in Bacillus subtilis. Microbiology. 153:2530-40. 2007
- Measuring metals with RNA. Mol Cell. 27:859-60. 2007
- Mutational analysis of active site residues essential for sensing of organic hydroperoxides by Bacillus subtilis OhrR. Journal of Bacteriology. 189:7069-76. 2007
- Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function sigma factors. Journal of Bacteriology. 189:6919-27. 2007
- S-cysteinylation is a general mechanism for thiol protection of Bacillus subtilis proteins after oxidative stress. Journal of Biological Chemistry. 282:25981-5. 2007
- Substrate induction of siderophore transport in Bacillus subtilis mediated by a novel one-component regulator. Molecular Microbiology. 66:164-73. 2007
- The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state. J Mol Biol. 365:1257-65. 2007
- The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRS two-component system. Journal of Bacteriology. 189:8616-25. 2007
- Assessing the impact of denitrifier-produced nitric oxide on other bacteria. Applied and Environmental Microbiology. 77:2200-2205. 2006
- Biochemical characterization of the structural Zn2+ site in the Bacillus subtilis peroxide sensor PerR. Journal of Biological Chemistry. 281:23567-78. 2006
- Deciphering a complex genetic regulatory network: the Bacillus subtilis sigmaW protein and intrinsic resistance to antimicrobial compounds. Sci Prog. 89:243-66. 2006
- Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli. Molecular Microbiology. 60:765-82. 2006
- Regulation of LiaRS-dependent gene expression in bacillus subtilis: identification of inhibitor proteins, regulator binding sites, and target genes of a conserved cell envelope stress-sensing two-component system. Journal of Bacteriology. 188:5153-66. 2006
- Role of the Fur regulon in iron transport in Bacillus subtiliS. Journal of Bacteriology. 188:3664-73. 2006
- Stimulus perception in bacterial signal-transducing histidine kinases. Microbiol Mol Biol Rev. 70:910-38. 2006
- Structural basis for the metal-selective activation of the manganese transport regulator of Bacillus subtilis. Biochemistry. 45:3493-505. 2006
- The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation. Nature. 440:363-7. 2006
- A novel DNA modification by sulphur. Molecular Microbiology. 57:1428-38. 2005
- Bacillus subtilis paraquat resistance is directed by sigmaM, an extracytoplasmic function sigma factor, and is conferred by YqjL and BcrC. Journal of Bacteriology. 187:2948-56. 2005
- Genetic and physiological responses of Bacillus subtilis to metal ion stress. Molecular Microbiology. 57:27-40. 2005
- Metal ion homeostasis in Bacillus subtilis. Current Opinion in Microbiology. 8:188-95. 2005
- Metal-induced structural organization and stabilization of the metalloregulatory protein MntR. Biochemistry. 44:3380-9. 2005
- Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Mol Cell. 20:131-41. 2005
- Antibiotic-inducible promoter regulated by the cell envelope stress-sensing two-component system LiaRS of Bacillus subtilis. Annual Reviews of Microbiology. 48:2888-96. 2004
- Response of Bacillus subtilis to nitric oxide and the nitrosating agent sodium nitroprusside. Journal of Bacteriology. 186:4655-64. 2004
- The Bacillus subtilis extracytoplasmic-function sigmaX factor regulates modification of the cell envelope and resistance to cationic antimicrobial peptides. Journal of Bacteriology. 186:1136-46. 2004
- Bacillus subtilis CPx-type ATPases: characterization of Cd, Zn, Co and Cu efflux systems. Biometals. 16:497-505. 2003
- Cell wall stress responses in Bacillus subtilis: the regulatory network of the bacitracin stimulon. Molecular Microbiology. 50:1591-604. 2003
- DNA-binding and oligomerization studies of the manganese(II) metalloregulatory protein MntR from Bacillus subtilis. Biochemistry. 42:12634-42. 2003
- Origins of metal ion selectivity in the DtxR/MntR family of metalloregulators. Molecular Microbiology. 48:495-506. 2003
- Purification of Bacillus subtilis RNA polymerase and associated factors. Methods in Enzymology. 370:10-24. 2003
- Recognition of DNA by three ferric uptake regulator (Fur) homologs in Bacillus subtilis. Journal of Bacteriology. 185:6348-57. 2003
- Regulation of the Bacillus subtilis extracytoplasmic function protein sigma(Y) and its target promoters. Journal of Bacteriology. 185:4883-90. 2003
- Structure of the manganese-bound manganese transport regulator of Bacillus subtilis. Nature Structural and Molecular Biology. 10:652-7. 2003
- The global transcriptional response of Bacillus subtilis to manganese involves the MntR, Fur, TnrA and sigmaB regulons. Molecular Microbiology. 49:1477-91. 2003
- The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors. Journal of Bacteriology. 185:243-53. 2003
- Two MerR homologues that affect copper induction of the Bacillus subtilis copZA operon. Microbiology. 149:3413-21. 2003
- A peroxide-induced zinc uptake system plays an important role in protection against oxidative stress in Bacillus subtilis. Molecular Microbiology. 45:997-1005. 2002
- AbrB is a regulator of the sigma(W) regulon in Bacillus subtilis. FEMS Microbiology Letters. 211:219-23. 2002
- Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons. Molecular Microbiology. 45:1267-76. 2002
- Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. Journal of Molecular Biology. 316:443-57. 2002
- Functional analysis of the Bacillus subtilis Zur regulon. Journal of Bacteriology. 184:6508-14. 2002
- Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon. Molecular Microbiology. 45:1613-29. 2002
- OxyR: a molecular code for redox sensing?. Sci STKE. 157. 2002
- Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence. Journal of Bacteriology. 184:5826-32. 2002
- Regulation of inducible peroxide stress responses. Molecular Microbiology. 45:9-15. 2002
- Regulation of the Bacillus subtilis bcrC bacitracin resistance gene by two extracytoplasmic function sigma factors. Journal of Bacteriology. 184:6123-9. 2002
- Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible. Journal of Bacteriology. 184:3276-86. 2002
- Sensing nickel. NikRs with two pockets. Chemistry and Biology. 9:1055-7. 2002
- The OhrR repressor senses organic hydroperoxides by reversible formation of a cysteine-sulfenic acid derivative. Proceedings at the National Academy of Science USA. 99:6690-5. 2002
- The extracytoplasmic function (ECF) sigma factors. Advances in Microbial Physiology. 46:47-110. 2002
- Bacterial Ohr and OsmC paralogues define two protein families with distinct functions and patterns of expression. Microbiology. 147:1775-82. 2001
- FosB, a cysteine-dependent fosfomycin resistance protein under the control of sigma(W), an extracytoplasmic-function sigma factor in Bacillus subtilis. Journal of Bacteriology. 183:2380-3. 2001
- Global transcriptional response of Bacillus subtilis to heat shock. Journal of Bacteriology. 183:7318-28. 2001
- OhrR is a repressor of ohrA, a key organic hydroperoxide resistance determinant in Bacillus subtilis. Journal of Bacteriology. 183:4134-41. 2001
- Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. Molecular Microbiology. 41:849-59. 2001
- The -10 region is a key promoter specificity determinant for the Bacillus subtilis extracytoplasmic-function sigma factors sigma(X) and sigma(W). Journal of Bacteriology. 183:1921-7. 2001
- Identification of the Escherichia coli K-12 Nramp orthologue (MntH) as a selective divalent metal ion transporter. Molecular Microbiology. 35:1065-78. 2000
- Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins. Molecular Microbiology. 35:1454-68. 2000
- Mutations in multidrug efflux homologs, sugar isomerases, and antimicrobial biosynthesis genes differentially elevate activity of the sigma(X) and sigma(W) factors in Bacillus subtilis. Journal of Bacteriology. 182:5202-10. 2000
- Adenines at -11, -9 and -8 play a key role in the binding of Bacillus subtilis Esigma(A) RNA polymerase to -10 region single-stranded DNA. Nucleic Acids Research. 27:4541-6. 1999
- Anti-sigma factors. Current Opinion in Microbiology. 2:135-41. 1999
- Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis. Journal of Biological Chemistry. 274:15953-8. 1999
- Identification of target promoters for the Bacillus subtilis extracytoplasmic function sigma factor, sigma W. Molecular Microbiology. 31:361-71. 1999
- Interaction of Bacillus subtilis Fur (ferric uptake repressor) with the dhb operator in vitro and in vivo. Journal of Bacteriology. 181:4299-307. 1999
- Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners. Biochemistry. 38:5959-67. 1999
- Bacillus subtilis contains multiple Fur homologues: identification of the iron uptake (Fur) and peroxide regulon (PerR) repressors. Molecular Microbiology. 29:189-98. 1998
- Identification of a zinc-specific metalloregulatory protein, Zur, controlling zinc transport operons in Bacillus subtilis. Journal of Bacteriology. 180:5815-21. 1998
- Identification of target promoters for the Bacillus subtilis sigma X factor using a consensus-directed search. Journal of Molecular Biology. 279:165-73. 1998
- Interactions between the promoter regions of nitrogenase structural genes (nifHDK2) and DNA-binding proteins from N2- and ammonium-grown cells of the archaeon Methanosarcina barkeri 227. Journal of Bacteriology. 180:2723-8. 1998
- Promoter recognition by Bacillus subtilis sigmaW: autoregulation and partial overlap with the sigmaX regulon. Journal of Bacteriology. 180:3765-70. 1998
- DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally. Journal of Molecular Biology. 267:47-59. 1997
- RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates. Proceedings at the National Academy of Science USA. 94:4982-7. 1997
- The Bacillus subtilis sigma(X) protein is an extracytoplasmic function sigma factor contributing to survival at high temperature. Journal of Bacteriology. 179:2915-21. 1997
- sigma factor mutations affecting the sequence-selective interaction of RNA polymerase with -10 region single-stranded DNA. Nucleic Acids Research. 25:2603-9. 1997
- FlgM is a primary regulator of sigmaD activity, and its absence restores motility to a sinR mutant. Journal of Bacteriology. 178:7010-3. 1996
- Mutation of the Bacillus subtilis alkyl hydroperoxide reductase (ahpCF) operon reveals compensatory interactions among hydrogen peroxide stress genes. Journal of Bacteriology. 178:6579-86. 1996
- Bacillus subtilis MrgA is a Dps(PexB) homologue: evidence for metalloregulation of an oxidative-stress gene. Molecular Microbiology. 18:295-300. 1995
- Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Research. 23:2351-60. 1995
- Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions. Proceedings at the National Academy of Science USA. 92:8190-4. 1995
- Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Molecular Microbiology. 16:817-24. 1995
- Pathway of promoter melting by Bacillus subtilis RNA polymerase at a stable RNA promoter: effects of temperature, delta protein, and sigma factor mutations. Biochemistry. 34:8465-73. 1995
- Promoter architecture in the flagellar regulon of Bacillus subtilis: high-level expression of flagellin by the sigma D RNA polymerase requires an upstream promoter element. Proceedings at the National Academy of Science USA. 92:2582-6. 1995
- Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase. Journal of Molecular Biology. 252:189-202. 1995
- The Bacillus subtilis flagellar regulatory protein sigma D: overproduction, domain analysis and DNA-binding properties. Journal of Molecular Biology. 249:743-53. 1995
- A mismatch bubble in double-stranded DNA suffices to direct precise transcription initiation by Escherichia coli RNA polymerase. Journal of Biological Chemistry. 269:13179-84. 1994
- A promoter melting region in the primary sigma factor of Bacillus subtilis. Identification of functionally important aromatic amino acids. Journal of Molecular Biology. 235:1470-88. 1994
- Chemotaxis in Bacillus subtilis requires either of two functionally redundant CheW homologs. Journal of Bacteriology. 176:2736-9. 1994
- Dual chemotaxis signaling pathways in Bacillus subtilis: a sigma D-dependent gene encodes a novel protein with both CheW and CheY homologous domains. Journal of Bacteriology. 176:2727-35. 1994
- Genetic and physiological studies of Bacillus subtilis sigma A mutants defective in promoter melting. Journal of Bacteriology. 176:5218-24. 1994
- Mutations in sigma factor that affect the temperature dependence of transcription from a promoter, but not from a mismatch bubble in double-stranded DNA. Biochemistry. 33:11501-6. 1994
- The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT. Journal of Bacteriology. 176:3093-101. 1994
- The delta subunit of Bacillus subtilis RNA polymerase. An allosteric effector of the initiation and core-recycling phases of transcription. Journal of Molecular Biology. 239:1-14. 1994
- Metalloregulation in Bacillus subtilis: isolation and characterization of two genes differentially repressed by metal ions. Journal of Bacteriology. 175:5428-37. 1993
- Restoration of motility to an Escherichia coli fliA flagellar mutant by a Bacillus subtilis sigma factor. Proceedings at the National Academy of Science USA. 89:5123-7. 1992
- The A. tumefaciens transcriptional activator OccR causes a bend at a target promoter, which is partially relaxed by a plant tumor metabolite. Cell. 69:659-67. 1992
- Alternative sigma factors and the regulation of flagellar gene expression. Molecular Microbiology. 5:2875-82. 1991
- Regulation of gene expression by mercury. Advances in Inorganic Biochemistry. 8:33-61. 1990
- Studies of sigma D-dependent functions in Bacillus subtilis. Journal of Bacteriology. 172:3435-43. 1990
- The MerR metalloregulatory protein binds mercuric ion as a tricoordinate, metal-bridged dimer. Science. 247:946-8. 1990
- Homologous metalloregulatory proteins from both gram-positive and gram-negative bacteria control transcription of mercury resistance operons. Journal of Bacteriology. 171:222-9. 1989
- The developmental fate of S. coelicolor hyphae depends upon a gene product homologous with the motility sigma factor of B. subtilis. Cell. 59:133-43. 1989
- Transcriptional switching by the MerR protein: activation and repression mutants implicate distinct DNA and mercury(II) binding domains. Biochemistry. 28:2340-4. 1989
- Cloning, sequencing, and disruption of the Bacillus subtilis sigma 28 gene. Journal of Bacteriology. 170:1568-74. 1988
- Isolation and characterization of the Bacillus subtilis sigma 28 factor. Journal of Bacteriology. 170:1560-7. 1988
- Structure and function of bacterial sigma factors. Annual Review of Biochemistry. 57:839-72. 1988
- DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor. Proceedings at the National Academy of Science USA. 84:6422-4. 1987
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booksection
- Iron Uptake in Gram-positive (Bacillus). 2009
- Effects of Metal Ions and Reactive Oxygen Species on Gene Regulation. Vol. 405-414. 2002
- Gene Expression and Its Regulation 2002
- RNA Polymerase and Sigma Factors 2002
- Promoters, sigma factors, and variant RNA polymerases 1999
- Sigma Factors in Gene Expression 1999
- Metal Cation Regulation in Gram Positive Bacteria 1997
- Bacterial Sigma Factors 1994
- The Agrobacterium tumefaciens Transcriptional Activator OccR Causes a Bend at a Target Promoter, Which is Partially Relaxed by a Plant Tumor Metabolite. Vol. 2. 1993
- A Mercury Regulated Transcriptional Activator from Bacillus sp. RC607. Vol. 3. 1990
- Regulation of Gene Expression by Mercury. Vol. 8. 1990
- Separation of the Mercury Binding and DNA-Binding Activities of the MerR Regulatory Protein 1989
- Cloning and Characterization of the Bacillus subtilis Sigma-28 Gene. Vol. 2. 1987
- Isolation of Genomic Segments from Bacillus subtilis that Contain Promoters for 28 RNA Polymerase, and Studies on Regulation of Their Transcription in B. subtilis and Escherichia coli 1985
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chapter
- Prokaryotic Redox Switches.. Oxidative Stress and Redox Regulation. 2013
- Environmental sensing and the role of extracytoplasmic function (ECF) sigma factors . Bacterial Physiology- A Molecular Approach. 233-261. 2008
- Metalloregulators: Arbiters of Metal Sufficiency. How Bacteria Handle Heavy Metals (Microbiology Monographs). 2007
- Regulation of Bacterial MntH genes. The NRAMP Family. 2004
- Sigma Factors. Encyclopedia of Biological Chemistry. 2004
- The Agrobacterium tumefaciens transcriptional activator OccR causes a bend at a target promoter that is partially relaxed by a plant tumor metabolite. Advances in Molecular Genetics of Plant-Microbe Interactions. Vol 2. 125-129. 1993
- The Agrobacterium tumefaciens transcriptional activator OccR causes a bend at a target promoter that is partially relaxed by a plant tumor metabolite. Current Plant Science and Biotechnology in Agriculture. 125-129. 1993
- Regulation of Transcription by Mercuric Ion in a Marine Bacillus. Journal of Cellular Biochemistry Supplement. 1990
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conference paper
- Modulation of Bacillus subtilis membrane composition and resistance to cell envelope stress. Abstracts of the General Meeting of the American Society for Microbiology. 2007
- The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces expression of the LiaRS two-component system. Abstracts of the General Meeting of the American Society for Microbiology. 107. 2007
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document part
- The Transcriptional Response to Daptomycin: Defining the Mechanisms of Resistance in Bacillus subtilis. 47. 2007
- The PerR transcription factor senses hydrogen peroxide by metalcatalyzed histidine oxidation. 106. 2006
- Global analysis of the nitric oxide stress stimulon of Bacillus subtilis 2003
- The Bacillus subtilis Zur regulon 2003
- Gene regulation by fur and iron in B. subtilis 2002
- Origins of metal selectivity within the DtxR metalloregulatory family 2002
- From Gene to Genome: Studies on the ECF Sigma Factors of Bacillus subtilis 2001
- Global Regulation by manganese in Bacillus subtilis 2001
- Manganese Homeostasis in Bacillus subtilis 2001
- Peroxide Stress Responses in Bacillus subtilis 2001
- Regulation of Gene Expression by Fur and Iron in Bacillus subtilis 2001
- Roles of ECF Sigma Factors in Bacillus subtilis 2001
- The Bacillus subtilis peroxide stress response is mediated by the metalloregulatory PerR 2001
- From activation to repression: Regulation of two promoters by MntR protein in Bacillus subtilis 2000
- Mechanistic studies of the PerR-mediated peroxide stress response in Bacillus subtilis 2000
- Modification of the cell wall teichoic acids is regulated by an ECF sigma factor in Bacillus subtilis. 356-357. 2000
- Promoter selectivity of Bacillus subtilis ECF sigma factors is largely determined by the -10 region sequence 2000
- Alternative sigma factors controlling antimicrobial drug resistance functions in Bacillus subtilis 1999
- Biochemical characterization of metal- and peroxide-dependent induction of peroxide stress genes mediated by a Bacillus subtilis fur homolog, PerR 1999
- Fur in Bacillus subtilis: DNA-binding and transcriptional repression of siderophore synthesis are sequence specific and independent of any added metals 1999
- Regulation of manganese uptake in Bacillus subtilis by a bifunctional DNA-binding metalloregulator, MntR 1999
- sigmaW, an antibiotic inducible sigma factor that controls fosfomycin resistance and bacteriocin production in Bacillus subtilis 1999
- An Antibiotic Inducible Sigma Factor that Regulates Antibiotic Resistance and Bacteriocin Producion in Bacillus subtilis 1998
- Bacillus subtilis contains multiple fur homologs: Identification and characterization of the repressor of iron uptake functions 1998
- Manganese transport in Bacillus subtilis is mediated by an NRAMP-like transporter and is regulated by a diphtheria toxin repressor (DtxR) homolog, MntR 1998
- PerR, regulator of Bacillus subtilis peroxide stress genes ferric uptake repressor homolog PerR 1998
- Novel Regulatory Circuits Controlling Oxidative Stress and Iron Homeostasis in Bacillus subtilis 1997
- Regulation of Bacillus subtilis iron uptake genes by Fur protein 1997
- Structural and Functional Analysis of the Delta Subunit of B. subtilis RNA Polymerase 1997
- The Bacillus subtilis Sigma-X protein is an ECF sigma factor contributing to the survival of high temperature stress 1997
- Transcription Initiation by Bacillus subtilis SigD RNA Polymerase. A1375.17th International Congress of Biochemistry and Molecular Biology and 1997 Annual Meeting of ASBMB, San Francisco, CA. Aug. 24-29, 1997 1997
- Transcription initiation by Bacillus subtilis Sigma-D RNA polymerase 1997
- Transcription initiation by Bacillus subtilis sigma-D RNA polymerase 1997
- Interaction between DNA-binding proteins and the promoter region of the nitrogenase structural genes (nifHDK2) in the archaeon Methanosarcina barkeri 227 1996
- Intersecting Regulation of Bacillus subtilis Iron Uptake and Peroxide Stress Genes 1996
- Peroxide Stress Response and Iron Uptake in Bacillus subtilis: Interesecting Regulation 1996
- Regulation of D Activity in B. subtilis 1996
- Structural Analysis of the Bacillus subtilis subunit of RNA Polymerase: Protein Mimicry of Nucleic Acids 1996
- Chemotaxis in Bacillus subtilis Requires Either of Two Functionally Redundant CheW Homologs 1995
- DNA-binding ability of the D subunit of Bacillus subtilis RNA Polymerase 1995
- Identification and Regulation of an H-2O-2-Inducible Operon Encoding Alkyl Hydroperoxide Reductase in Bacillus subtilis 1995
- Promoter Architecture Among D-Dependent (Class III) Flagellar Genes of Bacillus subtilis 1995
- Regulation of the Bacillus subtilis oxidative Stress Response by Metal Ions 1995
- Regulation of the Bacillus subtilis oxidative stress response by metal ions, Keystone Symposium- -Metal Ions and Oxygen in Gene Regulation, 3-23 to 3-28-95, Park City, UT 1995
- The Bacillus subtilis MrgA Protein Is a Dps/PexB Homolog and Protects Against Oxidative Stress, UCLA-Keystone Symposium on Metal Ions and Oygen in Gene Regulation, 3-23 to 3-28, 1995 Park City, UT 1995
- Genetic Analysis of Bacillus subtilis A Mutants Altered in a Putative Promoter Melting Region 1994
- Regulation of gene expression by iron and manganese in Bacillus subtilis 1994
- Regulation of the B. subtilis Oxidative Stress Response by Metal Ions 1994
- Structural Analysis of the B. subtilis Delta Factor: A Protein Polyanion which Displaces RNA from RNA Polymerase 1994
- Alternative Sigma Factors and the Regulation of Flagellar Gene Expression 1993
- Bacillus subtilis RNA Polymerase: Multiple Roles of the and Subunits 1993
- Bacillus subtilis RNA Polymerase: Multiple Roles of and Proteins 1993
- Biochemical Studies of the Flagellar Factor, D, and Its Role in Bacillus subtilis 1993
- Identification of Amino Acids Essential for Promoter-Melting by the Primary Sigma Factor of Bacillus subtilis Control of Transcription Initiation in Prokaryotes 1993
- Regulation of a Bacillus subtilis flagellar gene by metal ions 1993
- Regulation of gene expression by iron and manganese in Bacillus subtilis 1993
- The Agrobacterium tumefaciens transcriptional activator OccR causes a bend at a target promoter that is partially relaxed by a plant tumor metabolite, in Current Plant Science and Biotechnology in Agriculture. 125-129. 1993
- Regulation of Post-Exponential Gene Expression in Bacillus subtilis 1992
- Restoration of motility to an Escherichia coli fliA flagellar mutant by a Bacillus subtilis sigma factor 1992
- Structure and Function Analysis of Bacillus-Subtilis Sigma Factors 1992
- Structure and Function Analysis of Bacterial Sigma Factors 1992
- Structure and Function Analysis of the Bacillus subtilis Sigma-43 Factor 1992
- The Agrobacterium tumefaciens Transcriptional Activator OccR Causes a Bend at a Target Promoter, Which is Partially Relaxed by a Plant Tumor Metabolite 1992
- STRUCTURAL STUDIES OF Bacillus subtilis SIGMA FACTORS 1991
- A Mercury-Activated Transcriptional Regulator from Bacillus 1989
- Regulation of Transcription by Mercuric Ion in Bacillus 1989
- Regulation of Transcription by Mercuric Ion in Bacillus, Fourth International Conference on Bioinorganic Chemistry, Massachusetts Institute of Technology, Boston, MA. 7-89 1989
- Separation of the Mercury-Binding and DNA-Binding Activities of the Merr Regulatory Protein. 397-406. 1989
- Regulation of Transcription by Mercuric Ion UCLA Colloquium: Metal Ion Homeostasis 1988
- The Bacillus subtilis 28 Factor Controls Genes Involved in Flagellar Morphogenesis 1988
- Cloning and Characterization of the Structural Gene for B. subtilis 28 1987
- Isolation of Genomic Segments from Bacillus-Subtilis That Contain Promoters for Sigma-28 Rna Polymerase and Studies on Regulation of Their Transcription in Bacillus-Subtilis and Escherichia-Coli. 143-8. 1985
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review
- Cysteine-sulfenic acid formation is a novel redox sensing mechanism by the transcription repressor, OhrR 2002
- Review of "Gene Expression in Recombinant Microorganisms" Ed. by Alan Smith. 562-563. 1996
- Review of "What is Life?" by L. Margulis and D. Sagan. 62-63. 1996
- Review of "Essentials of Molecular Biology, 2nd Ed." by Freifelder 1993
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Teaching
teaching overview
- Current teaching efforts include Microbial Genomics (BioMI4200), a graduate level module in Bacterial Genetics (BioMI6904), and an advanced discussion section in conjunction with our large undergraduate core course (BioMI2900-4 credit option).
teaching activities
- BIOMI-6904: Prokaryotic Biology: Bacterial Genetics - Spring 2013
- BIOMI-7980: Graduate Research Seminar in Microbiology - Spring 2013
- BIOMI-7980: Graduate Research Seminar in Microbiology - Fall 2012
- BIOMI-6904: Prokaryotic Biology: Bacterial Genetics - Spring 2012
- BIOMI-7980: Graduate Research Seminar in Microbiology - Spring 2012
- BIOMI-7980: Graduate Research Seminar in Microbiology - Fall 2011
Service
service to the profession
- American Society for Biochemistry and Molecular Biology Member 1992 -
- AMERICAN CHEMICAL SOCIETY Member 1991 -
- America Society for Microbiology Member 1988 -
- American Association for the Advancement of Science Member 1982 -
reviewer or editor for
Background
education and training
- Ph.D. in Biochemistry, University of California 1987
- B.A. in Biology, University of California, Santa Cruz 1982
- B.A. in Chemistry, University of California, Santa Cruz 1982
awards and honors
- Outstanding Accomplishments in Basic Research, 2012
- Fellow American Academy of Microbiology, 2010
- Division J Lecturer, 2007
- Keynote Lecturer, 2006
- Plenary Lecture, 2005
- Ethel S. Tessman memorial lecture, 2004
- Vector Laboratories Young Investigator Award, 1993
- B.A. in Biology with Highest Honors, 1982
- B.A. in Chemistry with Highest Honors, 1982
- Achievement Reward for College Scientists (ARCS), 1982
- University of California Regents Fellowship, 1982
- Elected to Sigma Xi, 1982
- University of California Regents Scholarship, 1980
Other
college
- CALS
research keyword
- Antibiotics
- Bacillus subtilis
- Bacterial gene regulation
- Genomics
- Metal homeostasis
- Oxidative stress
- RNA Polymerase
- Transcription
- sigma factors
name prefix
- Professor