JOHN HELMANN

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. pmc Glutamate dehydrogenase affects resistance to cell wall antibiotics in Bacillus subtilis
    Yong Heon Lee
    Department of Microbiology, Cornell University, Ithaca, New York, USA
    J Bacteriol 194:993-1001. 2012
  2. pmc Derepression of the Bacillus subtilis PerR peroxide stress response leads to iron deficiency
    Melinda J Faulkner
    Department of Microbiology, Cornell University, Ithaca, New York, USA
    J Bacteriol 194:1226-35. 2012
  3. ncbi request reprint Anti-sigma factors
    J D Helmann
    Section of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    Curr Opin Microbiol 2:135-41. 1999
  4. ncbi request reprint OxyR: a molecular code for redox sensing?
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Sci STKE 2002:pe46. 2002
  5. pmc Global transcriptional response of Bacillus subtilis to heat shock
    J D Helmann
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 183:7318-28. 2001
  6. pmc RNA polymerase: a nexus of gene regulation
    John D Helmann
    Department of Microbiology, Cornell University, 327 Wing Hall, Ithaca, NY 14853 8101, USA
    Methods 47:1-5. 2009
  7. pmc The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 185:243-53. 2003
  8. pmc Measuring metals with RNA
    John D Helmann
    Department of Microbiology, Cornell University, Wing Hall, Ithaca, NY 14853 8101, USA
    Mol Cell 27:859-60. 2007
  9. pmc Bacillithiol, a new player in bacterial redox homeostasis
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    Antioxid Redox Signal 15:123-33. 2011
  10. ncbi request reprint Deciphering a complex genetic regulatory network: the Bacillus subtilis sigmaW protein and intrinsic resistance to antimicrobial compounds
    John D Helmann
    Cornell University in Ithaca, NY 14853 8101, USA
    Sci Prog 89:243-66. 2006

Collaborators

  • Mayuree Fuangthong
  • M Wilson
  • S Mongkolsuk
  • Peter Setlow
  • Z Wang
  • Thorsten Mascher
  • F J Lopez de Saro
  • R W Ye
  • Arthur Glasfeld
  • Sumarin Soonsanga
  • Michiko M Nakano
  • Mark Strauch
  • Haike Antelmann
  • Michael Hecker
  • M S Paget
  • Jörg Mostertz
  • Ahmed Gaballa
  • Min Cao
  • Jin Won Lee
  • Charles M Moore
  • Bronwyn G Butcher
  • Anna Barbara Hachmann
  • Letal I Salzberg
  • Tao Wang
  • Elif Sevim
  • Gregory T Smaldone
  • Emmanuel Guedon
  • Joseph I Kliegman
  • Noel Baichoo
  • Richard G Brennan
  • Melinda J Faulkner
  • Yong Heon Lee
  • Veronica Guariglia-Oropeza
  • L Chen
  • Scott E Gabriel
  • Warawan Eiamphungporn
  • Christophe Bordi
  • Shawn R MacLellan
  • Mark A DeWitt
  • Kyung Bok Song
  • Falko Hochgräfe
  • Sina Jordan
  • Peter S Choi
  • Juliane Ollinger
  • Misha V Golynskiy
  • Minsun Hong
  • Xiufen Zhou
  • Talib C Davis
  • N Bsat
  • Seth M Cohen
  • Scot A Lieser
  • Qiang Qian
  • J Qiu
  • Anthony W Kingston
  • Zhen Ma
  • A F Herbig
  • M Cao
  • A Osman Beldüz
  • David L Popham
  • Yun Luo
  • Q Que
  • Sukhjit K Khakh
  • Faith Miyagi
  • Claudio Aguilar
  • Joseph E Peters
  • Qiaojuan Shi
  • Tina Wecke
  • Eva Rietkötter
  • David L Farrens
  • Dörte Becher
  • Yi Pin Lin
  • Dierk Christoph Pöther
  • Falk Kalamorz
  • A Gaballa
  • Zeki Naal
  • Charles Moore
  • James P Shapleigh
  • Emerilis Casado-Rivera
  • Héctor D Abruña
  • Sarah L Griner
  • Tiegang Xu
  • Tobias Kieser
  • Jingdan Liang
  • Xinyi He
  • Monica Hui
  • Zixin Deng
  • Aiying Li
  • K Fredrick
  • Leticia Márquez-Magaña
  • Ching Sung Tsai

Detail Information

Publications89

  1. pmc Glutamate dehydrogenase affects resistance to cell wall antibiotics in Bacillus subtilis
    Yong Heon Lee
    Department of Microbiology, Cornell University, Ithaca, New York, USA
    J Bacteriol 194:993-1001. 2012
    ..We conclude that glutamate dehydrogenase activity affects the expression of the σ(W) regulon, by pathways that are yet unclear, and thereby influences resistance to CEF and other antibiotics...
  2. pmc Derepression of the Bacillus subtilis PerR peroxide stress response leads to iron deficiency
    Melinda J Faulkner
    Department of Microbiology, Cornell University, Ithaca, New York, USA
    J Bacteriol 194:1226-35. 2012
    ..Strains containing perR991 are peroxide resistant but grow nearly as well as the wild type. Unlike a perR null allele, the perR991 allele (F51S) derepresses KatA, but not Fur, which likely accounts for its comparatively rapid growth...
  3. ncbi request reprint Anti-sigma factors
    J D Helmann
    Section of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    Curr Opin Microbiol 2:135-41. 1999
    ....
  4. ncbi request reprint OxyR: a molecular code for redox sensing?
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Sci STKE 2002:pe46. 2002
    ....
  5. pmc Global transcriptional response of Bacillus subtilis to heat shock
    J D Helmann
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 183:7318-28. 2001
    ..Since many different conditions elicit both specific and general stress responses, knowledge of the heat-induced general stress response reported here will be helpful for interpreting future microarray studies of other stress responses...
  6. pmc RNA polymerase: a nexus of gene regulation
    John D Helmann
    Department of Microbiology, Cornell University, 327 Wing Hall, Ithaca, NY 14853 8101, USA
    Methods 47:1-5. 2009
    ....
  7. pmc The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 185:243-53. 2003
    ..This gene, controlled by the peroxide-sensing repressor OhrR, was not induced by any of the other conditions tested...
  8. pmc Measuring metals with RNA
    John D Helmann
    Department of Microbiology, Cornell University, Wing Hall, Ithaca, NY 14853 8101, USA
    Mol Cell 27:859-60. 2007
    ..In a recent issue of Cell, Winkler and coworkers (Dann et al., 2007) describe in atomic detail the structural changes that allow a specific RNA aptamer (the M box) to regulate transcription in response to changing cellular magnesium levels...
  9. pmc Bacillithiol, a new player in bacterial redox homeostasis
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    Antioxid Redox Signal 15:123-33. 2011
    ..BSH also is predicted to chelate metals avidly, in part due to the appended malate moiety, although the implications of BSH for metal ion homeostasis have yet to be explored in detail...
  10. ncbi request reprint Deciphering a complex genetic regulatory network: the Bacillus subtilis sigmaW protein and intrinsic resistance to antimicrobial compounds
    John D Helmann
    Cornell University in Ithaca, NY 14853 8101, USA
    Sci Prog 89:243-66. 2006
    ..These genes encode proteins that inactivate, sequester, or eliminate toxic compounds from the cell...
  11. pmc Mutation of the Bacillus subtilis alkyl hydroperoxide reductase (ahpCF) operon reveals compensatory interactions among hydrogen peroxide stress genes
    N Bsat
    Section of Microbiology, Cornell University, Ithaca, New York 14853, USA
    J Bacteriol 178:6579-86. 1996
    ..Since the peroxide regulon is activated in the absence of AhpCF, which degrades alkyl hydroperoxides, we propose that organic hydroperoxides may be physiologically relevant inducers in vivo...
  12. ncbi request reprint Bacillus subtilis MrgA is a Dps(PexB) homologue: evidence for metalloregulation of an oxidative-stress gene
    L Chen
    Section of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    Mol Microbiol 18:295-300. 1995
    ..These results indicate a complex interplay between metal ions and the expression of the B. subtilis oxidative stress response...
  13. pmc Identification of a zinc-specific metalloregulatory protein, Zur, controlling zinc transport operons in Bacillus subtilis
    A Gaballa
    Section of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 180:5815-21. 1998
    ..Thus, Fur-like regulators control zinc homeostasis in addition to their previously characterized roles in regulating iron homeostasis, acid tolerance responses, and oxidative stress functions...
  14. pmc Metalloregulation in Bacillus subtilis: isolation and characterization of two genes differentially repressed by metal ions
    L Chen
    Section of Microbiology, Cornell University, Ithaca, New York 14853
    J Bacteriol 175:5428-37. 1993
    ..Mutation of the putative iron box for gene mrgC leads to partial derepression in iron-replete medium...
  15. ncbi request reprint Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA
    A F Herbig
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 41:849-59. 2001
    ..These results are consistent with the idea that the intracellular form of the PerR metalloprotein, and therefore its hydrogen peroxide sensitivity, can be altered by growth conditions...
  16. pmc Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions
    L Chen
    Section of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Proc Natl Acad Sci U S A 92:8190-4. 1995
    ..These data indicate that the peroxide stress response of B. subtilis is regulated by a repressor that senses both metal ion levels and H2O2...
  17. ncbi request reprint Bacillus subtilis contains multiple Fur homologues: identification of the iron uptake (Fur) and peroxide regulon (PerR) repressors
    N Bsat
    Section of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 29:189-98. 1998
    ..Thus, ygaG encodes the peroxide regulon repressor and is allelic with perR...
  18. ncbi request reprint Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins
    Q Que
    Section of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 35:1454-68. 2000
    ..Biochemical studies demonstrate that MntR binding to the mntH control region requires Mn(II), while interaction with the mntABCD control region does not depend on Mn(II)...
  19. pmc The -10 region is a key promoter specificity determinant for the Bacillus subtilis extracytoplasmic-function sigma factors sigma(X) and sigma(W)
    J Qiu
    Department of Microbiology, Cornell University, Ithaca, New York 14853-8101, USA
    J Bacteriol 183:1921-7. 2001
    ..However, we were unable to alter promoter selectivity by replacements of two candidate recognition residues in sigma(W)...
  20. ncbi request reprint Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis
    F J Lopez de Saro
    Section of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Biol Chem 274:15953-8. 1999
    ..5 x 10(6) M-1, but we are unable to demonstrate the formation of a ternary complex containing core enzyme, delta, and sigmaA...
  21. pmc The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT
    L Chen
    Section of Microbiology, Cornell University, Ithaca, New York 14853
    J Bacteriol 176:3093-101. 1994
    ..Expression from the fliD operon promoter, but not the hag promoter, is repressed by iron, which suggests that the target of metalloregulation is the promoter rather than the sigma D protein...
  22. pmc OhrR is a repressor of ohrA, a key organic hydroperoxide resistance determinant in Bacillus subtilis
    M Fuangthong
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 183:4134-41. 2001
    ..Thus, B. subtilis contains at least three regulons (sigma(B), PerR, and OhrR) that contribute to peroxide stress responses...
  23. pmc FosB, a cysteine-dependent fosfomycin resistance protein under the control of sigma(W), an extracytoplasmic-function sigma factor in Bacillus subtilis
    M Cao
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 183:2380-3. 2001
    ..FosB is a metallothiol transferase related to the FosA class of Mn(2+)-dependent glutathione transferases but with a preference for Mg(2+) and L-cysteine as cofactors...
  24. pmc Dual chemotaxis signaling pathways in Bacillus subtilis: a sigma D-dependent gene encodes a novel protein with both CheW and CheY homologous domains
    K L Fredrick
    Section of Microbiology, Cornell University, Ithaca, New York 14853
    J Bacteriol 176:2727-35. 1994
    ..W. Hanlon, L. Márques-Magaña, P. B. Carpenter, M. J. Chamberlin, and G. W. Ordal, J. Biol. Chem. 267:12055-12060, 1992)...
  25. ncbi request reprint Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase
    F J Lopez de Saro
    Section of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Mol Biol 252:189-202. 1995
    ..This suggests that the function of the amino-terminal domain is to bind and orient the carboxyl-terminal region on the surface of RNA polymerase...
  26. ncbi request reprint The Bacillus subtilis flagellar regulatory protein sigma D: overproduction, domain analysis and DNA-binding properties
    Y F Chen
    Section of Microbiology, Cornell University, Ithaca, New York 14853, USA
    J Mol Biol 249:743-53. 1995
    ....
  27. pmc RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates
    K Fredrick
    Section of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Proc Natl Acad Sci U S A 94:4982-7. 1997
    ..Thus, sigmaA appears to recognize the -10 region even in a single-stranded state. We propose that in addition to its described roles in promoter recognition and start-site melting, sigma also localizes the transcription start site...
  28. pmc Bacillus subtilis σ(V) confers lysozyme resistance by activation of two cell wall modification pathways, peptidoglycan O-acetylation and D-alanylation of teichoic acids
    Veronica Guariglia-Oropeza
    Department of Microbiology, 370 Wing Hall, Cornell University, Ithaca, NY 14853, USA
    J Bacteriol 193:6223-32. 2011
    ..Thus, we suggest that σ(V) confers lysozyme resistance by the activation of two cell wall modification pathways: O-acetylation of peptidoglycan catalyzed by OatA and D-alanylation of teichoic acids by DltABCDE...
  29. pmc The Bacillus subtilis GntR family repressor YtrA responds to cell wall antibiotics
    Letal I Salzberg
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101 14853 8101, USA
    J Bacteriol 193:5793-801. 2011
    ..Repression of both operons requires YtrA, which recognizes an inverted repeat in front of its own operon and in front of ywoB. These results suggest that YtrA is an additional regulator of cell envelope stress responses...
  30. pmc Reduction in membrane phosphatidylglycerol content leads to daptomycin resistance in Bacillus subtilis
    Anna Barbara Hachmann
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    Antimicrob Agents Chemother 55:4326-37. 2011
    ..These results suggest a resistance mechanism by which reduced levels of phosphatidylglycerol decrease the net negative charge of the membrane, thereby weakening interaction with the positively charged Ca(2+)-DAP complex...
  31. pmc DNA-binding properties of the Bacillus subtilis and Aeribacillus pallidus AC6 σ(D) proteins
    Elif Sevim
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 193:575-9. 2011
    ..Binding required a conserved CG motif within the -10 element, and this motif is known to be recognized by σ region 2.4 and critical for promoter activity...
  32. ncbi request reprint Biochemical characterization of the structural Zn2+ site in the Bacillus subtilis peroxide sensor PerR
    Jin Won Lee
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Biol Chem 281:23567-78. 2006
    ..This model is supported by metal ion affinity measurements demonstrating that PerR bound Fe2+ with higher affinity than Mn2+...
  33. ncbi request reprint Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family
    Minsun Hong
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, USA
    Mol Cell 20:131-41. 2005
    ..The structure of the OhrR-ohrA operator complex reveals the DNA binding mechanism of the entire MarR family and suggests a common inducer binding pocket...
  34. ncbi request reprint The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation
    Jin Won Lee
    Department of Microbiology, Cornell University, Ithaca, New York 14853, USA
    Nature 440:363-7. 2006
    ....
  35. pmc A complex thiolate switch regulates the Bacillus subtilis organic peroxide sensor OhrR
    Jin Won Lee
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Proc Natl Acad Sci U S A 104:8743-8. 2007
    ..subtilis identifies three distinct S-thiolated species, including mixed disulfides with a novel 398-Da thiol, cysteine, and CoASH. Evidence for in vivo formation of the sulfenamide derivative is also presented...
  36. pmc An antibiotic-inducible cell wall-associated protein that protects Bacillus subtilis from autolysis
    Letal I Salzberg
    Department of Microbiology, 370 Wing Hall, Cornell University, Ithaca, NY 14853, USA
    J Bacteriol 189:4671-80. 2007
    ..subtilis. These results support a model in which induction of YoeB in response to cell envelope stress decreases the activity of autolysins and thereby reduces the rate of antibiotic-dependent cell death...
  37. pmc Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function sigma factors
    Thorsten Mascher
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 189:6919-27. 2007
    ..In several cases, these antibiotic-sensitive phenotypes are significantly enhanced in the triple mutant strain relative to strains lacking only one or two sigma factors...
  38. ncbi request reprint Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli
    Bronwyn G Butcher
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 60:765-82. 2006
    ....
  39. ncbi request reprint Functional specialization within the Fur family of metalloregulators
    Jin Won Lee
    Department of Microbiology, Cornell University, Wing Hall, Ithaca, NY 14853 8101, USA
    Biometals 20:485-99. 2007
    ..Despite numerous studies, the mechanism of metal ion sensing by Fur family proteins is still controversial. Other family members use metal catalyzed oxidation reactions to sense peroxide-stress (PerR) or the availability of heme (Irr)...
  40. pmc Role of the Fur regulon in iron transport in Bacillus subtilis
    Juliane Ollinger
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 188:3664-73. 2006
    ..We have also investigated the effects of a fur mutation on the proteome and documented the derepression of 11 Fur-regulated proteins, including a newly identified thioredoxin reductase homolog, YcgT...
  41. pmc Mutational analysis of active site residues essential for sensing of organic hydroperoxides by Bacillus subtilis OhrR
    Sumarin Soonsanga
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 189:7069-76. 2007
    ..Oxidative modification of C15 likely disrupts the C15-Y29'-Y40' hydrogen bond network and thereby initiates conformational changes that reduce the ability of OhrR to bind to its operator site...
  42. ncbi request reprint LiaRS-dependent gene expression is embedded in transition state regulation in Bacillus subtilis
    Sina Jordan
    Department of General Microbiology, Georg August University, 37077 Gottingen, Germany
    Microbiology 153:2530-40. 2007
    ..The activity of the liaI promoter is therefore tightly regulated by at least five regulators to ensure an appropriate level of liaIH expression...
  43. pmc Conversion of Bacillus subtilis OhrR from a 1-Cys to a 2-Cys peroxide sensor
    Sumarin Soonsanga
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 190:5738-45. 2008
    ..Rapid formation of intersubunit disulfide bonds protects OhrR against irreversible overoxidation in the presence of strong oxidants much more efficiently than do the endogenous low-molecular-weight thiols...
  44. pmc A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis
    Shawn R MacLellan
    Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
    Mol Microbiol 69:954-67. 2008
    ..A yvrL deletion results in the upregulation of YvrI activity suggesting that YvrL is a negative regulator of YvrI-dependent transcription, possibly functioning as an anti-sigma factor...
  45. ncbi request reprint S-cysteinylation is a general mechanism for thiol protection of Bacillus subtilis proteins after oxidative stress
    Falko Hochgräfe
    Institute for Microbiology, Ernst Moritz Arndt University Greifswald, D 17487 Greifswald, Germany
    J Biol Chem 282:25981-5. 2007
    ..By means of multidimensional shotgun proteomics, the sites of S-cysteinylation for six proteins could be identified, three of which are known to be S-glutathionylated in other organisms...
  46. doi request reprint Oxidant-dependent switching between reversible and sacrificial oxidation pathways for Bacillus subtilis OhrR
    Sumarin Soonsanga
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 68:978-86. 2008
    ..Thus, depending on the oxidant, OhrR can be either reversibly oxidized or can instead function as a sacrificial regulator...
  47. pmc Regulation of the Bacillus subtilis yciC gene and insights into the DNA-binding specificity of the zinc-sensing metalloregulator Zur
    Scott E Gabriel
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 190:3482-8. 2008
    ..Unlike Fur and PerR, which bind efficiently to sequences containing a core 7-1-7 repeat element, Zur requires a 9-1-9 inverted repeat for high-affinity binding...
  48. pmc The Bacillus subtilis sigma(M) regulon and its contribution to cell envelope stress responses
    Warawan Eiamphungporn
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 67:830-48. 2008
    ..Activation of the sigma(M) regulon increases expression of proteins functioning in transcriptional control, cell wall synthesis and shape determination, cell division, DNA damage monitoring, recombinational repair and detoxification...
  49. pmc CsoR regulates the copper efflux operon copZA in Bacillus subtilis
    Gregory T Smaldone
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Microbiology 153:4123-8. 2007
    ..As previously described, the YhdQ (CueR) protein also binds to the copZA regulatory region, but genetic experiments indicate that this protein is not responsible for the copper-dependent regulation of this operon...
  50. pmc The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRS two-component system
    Bronwyn G Butcher
    Department of Microbiology, 370 Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 189:8616-25. 2007
    ..These results suggest that this operon is involved in the synthesis and export of a modified peptide (YydF*) that elicits cell envelope stress sensed by the LiaRS TCS...
  51. pmc Substrate induction of siderophore transport in Bacillus subtilis mediated by a novel one-component regulator
    Ahmed Gaballa
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 66:164-73. 2007
    ..Thus, the FeuABC transporter is optimally expressed under conditions of iron starvation, when Fur-mediated repression is relieved, and in the presence of its cognate substrate...
  52. pmc The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins
    Ahmed Gaballa
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Proc Natl Acad Sci U S A 105:11927-32. 2008
    ..Thus, iron deprivation in B. subtilis activates pathways to remodel the proteome to preserve iron for the most critical cellular functions...
  53. pmc Regulation of the Bacillus subtilis extracytoplasmic function protein sigma(Y) and its target promoters
    Min Cao
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 185:4883-90. 2003
    ..This was supported by analysis of direct targets for sigma(Y) transcription with whole-genome runoff transcription followed by macroarray analysis...
  54. pmc Recognition of DNA by three ferric uptake regulator (Fur) homologs in Bacillus subtilis
    Mayuree Fuangthong
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 185:6348-57. 2003
    ..Together, our results identify two nucleotide positions that are important for the ability of PerR, Fur, and Zur to distinguish among the many closely related operator sites present in the B. subtilis genome...
  55. ncbi request reprint The global transcriptional response of Bacillus subtilis to manganese involves the MntR, Fur, TnrA and sigmaB regulons
    Emmanuel Guedon
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 49:1477-91. 2003
    ....
  56. ncbi request reprint Regulation of inducible peroxide stress responses
    Skorn Mongkolsuk
    Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
    Mol Microbiol 45:9-15. 2002
    ..Peroxide sensing in this system requires a single conserved cysteine, which is oxidized to form a cysteine-sulphenic acid derivative...
  57. ncbi request reprint Structure of the manganese-bound manganese transport regulator of Bacillus subtilis
    Arthur Glasfeld
    Department of Chemistry, Reed College, 3203 SE Woodstock Blvd, Portland, Oregon 97202, USA
    Nat Struct Biol 10:652-7. 2003
    ..D8M binds only a single Mn2+ per monomer, owing to alteration of the metal-binding site. The sole retained metal site adopts pseudo-hexacoordinate geometry rather than the pseudo-heptacoordinate geometry of the MntR metal sites...
  58. ncbi request reprint Bacillus subtilis CPx-type ATPases: characterization of Cd, Zn, Co and Cu efflux systems
    Ahmed Gaballa
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Biometals 16:497-505. 2003
    ..Mutation of either copZ, encoding a metallochaperone, or copA sensitizes the cells to copper but not to other metal ions...
  59. ncbi request reprint Origins of metal ion selectivity in the DtxR/MntR family of metalloregulators
    Emmanuel Guedon
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 48:495-506. 2003
    ..However, the broadened selectivity of DtxR when expressed in B. subtilis, and the effects of a fur mutation, demonstrate that cellular milieu also influences metal responsiveness...
  60. pmc The sigma70 family of sigma factors
    Mark S B Paget
    School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK
    Genome Biol 4:203. 2003
    ..These structural data are starting to illuminate the mechanistic role of sigma factors in transcription initiation...
  61. pmc Functional analysis of the Bacillus subtilis Zur regulon
    Ahmed Gaballa
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 184:6508-14. 2002
    ..Mutant strains lacking all three identified zinc uptake systems (yciABC, ycdHI-yceA, and zosA) are dependent on micromolar levels of added zinc for optimal growth...
  62. ncbi request reprint Sensing nickel. NikRs with two pockets
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
    Chem Biol 9:1055-7. 2002
    ..Recent results suggest that repression is elicited by binding of nickel to a high-affinity site, but a low-affinity binding pocket may also play a role...
  63. pmc Regulation of the Bacillus subtilis bcrC bacitracin resistance gene by two extracytoplasmic function sigma factors
    Min Cao
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 184:6123-9. 2002
    ..A sigX sigM double mutant was similar to a bcrC mutant in sensitivity. These results support the suggestion that one function of B. subtilis ECF sigma factors is to coordinate antibiotic stress responses...
  64. pmc Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence
    Noel Baichoo
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 184:5826-32. 2002
    ....
  65. ncbi request reprint Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon
    Noel Baichoo
    Department of Mirobiology, Cornell University, Ithica, NY 14853 8101, USA
    Mol Microbiol 45:1613-29. 2002
    ....
  66. ncbi request reprint Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons
    Min Cao
    Department of Microbiology, Cornell uhniversity, Ithaca, NY 14853 8101, USA
    Mol Microbiol 45:1267-76. 2002
    ..Our findings are consistent with the idea that one function of ECF sigma factors is to coordinate antibiosis stress responses and cell envelope homeostasis...
  67. ncbi request reprint DNA-binding and oligomerization studies of the manganese(II) metalloregulatory protein MntR from Bacillus subtilis
    Scot A Lieser
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093 0358, USA
    Biochemistry 42:12634-42. 2003
    ....
  68. ncbi request reprint Cell wall stress responses in Bacillus subtilis: the regulatory network of the bacitracin stimulon
    Thorsten Mascher
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Mol Microbiol 50:1591-604. 2003
    ..By comparing the bacitracin and the vancomycin stimulons, we can differentiate between loci induced specifically by bacitracin and those that are induced by multiple cell wall-active antibiotics...
  69. ncbi request reprint Genetic and physiological responses of Bacillus subtilis to metal ion stress
    Charles M Moore
    Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
    Mol Microbiol 57:27-40. 2005
    ..In addition to systems dedicated to metal homeostasis, specific metal stresses also strongly induced pathways related to cysteine, histidine and arginine metabolism...
  70. ncbi request reprint Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches
    Min Cao
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Mol Biol 316:443-57. 2002
    ..We conclude that in B. subtilis sudden imposition of alkali stress activates the sigma(W) stress response, perhaps by impairing the ability of the cell wall biosynthetic machinery to function...
  71. pmc The OhrR repressor senses organic hydroperoxides by reversible formation of a cysteine-sulfenic acid derivative
    Mayuree Fuangthong
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Proc Natl Acad Sci U S A 99:6690-5. 2002
    ..In the presence of organic hydroperoxides, OhrR is inactivated by the reversible oxidation of a single conserved cysteine residue to the corresponding cysteine-sulfenic acid, and perhaps to higher oxidation states...
  72. pmc Bacillus subtilis paraquat resistance is directed by sigmaM, an extracytoplasmic function sigma factor, and is conferred by YqjL and BcrC
    Min Cao
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    J Bacteriol 187:2948-56. 2005
    ..Expression of yqjL, but not bcrC, from a xylose-inducible promoter restored PQ resistance to the sigM mutant...
  73. ncbi request reprint Metal ion homeostasis in Bacillus subtilis
    Charles M Moore
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    Curr Opin Microbiol 8:188-95. 2005
    ..A Fur homolog, PerR, functions as an Fe(II)-dependent peroxide stress sensor and regulates putative metal transport and storage functions...
  74. ncbi request reprint Metal-induced structural organization and stabilization of the metalloregulatory protein MntR
    Misha V Golynskiy
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0358, USA
    Biochemistry 44:3380-9. 2005
    ..Fluorescence anisotropy experiments on MntR D8M indicate significantly impaired DNA binding, providing additional evidence that MntR D8M is a dysfunctional regulator...
  75. pmc Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible
    Mayuree Fuangthong
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 184:3276-86. 2002
    ..This model is supported by the observation that the metal ion composition of the growth medium can greatly influence the transcriptional response of the various PerR regulon genes to hydrogen peroxide...
  76. ncbi request reprint The extracytoplasmic function (ECF) sigma factors
    John D Helmann
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    Adv Microb Physiol 46:47-110. 2002
    ....
  77. ncbi request reprint AbrB is a regulator of the sigma(W) regulon in Bacillus subtilis
    Qiang Qian
    Department of Oral and Craniofacial Biological Sciences, Dental School, University of Maryland, 666 W Baltimore St, Room 4 C 30, Baltimore, MD 21201, USA
    FEMS Microbiol Lett 211:219-23. 2002
    ..subtilis. Defects in antibiotic resistance properties caused by spo0A mutations are at least partially correlated with AbrB repression of the sigma(W) regulon...
  78. pmc Response of Bacillus subtilis to nitric oxide and the nitrosating agent sodium nitroprusside
    Charles M Moore
    Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
    J Bacteriol 186:4655-64. 2004
    ..This emphasizes that NO and SNP elicit genetically distinct stress responses...
  79. pmc The Bacillus subtilis extracytoplasmic-function sigmaX factor regulates modification of the cell envelope and resistance to cationic antimicrobial peptides
    Min Cao
    Department of Microbiology, Cornell University, Ithaca, New York 14853 8101, USA
    J Bacteriol 186:1136-46. 2004
    ..We conclude that activation of the sigma(X) regulon serves to alter cell surface properties to provide protection against antimicrobial peptides...
  80. pmc Structural basis for the metal-selective activation of the manganese transport regulator of Bacillus subtilis
    Joseph I Kliegman
    Department of Chemistry, Reed College, Portland, Oregon 97202, USA
    Biochemistry 45:3493-505. 2006
    ....
  81. ncbi request reprint Two MerR homologues that affect copper induction of the Bacillus subtilis copZA operon
    Ahmed Gaballa
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    Microbiology 149:3413-21. 2003
    ..The results demonstrate the direct regulation of the B. subtilis copper efflux system by CueR, and indirect regulation by a putative multidrug efflux system...
  82. ncbi request reprint A peroxide-induced zinc uptake system plays an important role in protection against oxidative stress in Bacillus subtilis
    Ahmed Gaballa
    Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
    Mol Microbiol 45:997-1005. 2002
    ..Our results indicate that peroxide stress leads to the upregulation of a dedicated Zn(II) uptake system that plays an important role in H2O2 and disulphide stress resistance...
  83. ncbi request reprint A novel DNA modification by sulphur
    Xiufen Zhou
    Bio X Life Science Research Centre and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
    Mol Microbiol 57:1428-38. 2005
    ..A coincidence between the Dnd phenotype and DNA modification by sulphur was demonstrated to occur in several representative bacterial genomes by the in vivo(35)S-labelling experiments...
  84. pmc Stimulus perception in bacterial signal-transducing histidine kinases
    Thorsten Mascher
    Department of General Microbiology, Georg August University, Grisebachstr 8, D 37077 Gottingen, Germany
    Microbiol Mol Biol Rev 70:910-38. 2006
    ..This review provides an overview of mechanisms of stimulus perception for members of all three groups of bacterial signal-transducing histidine kinases...
  85. pmc The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state
    Mark A DeWitt
    Department of Chemistry, Reed College, Portland, OR 97202, USA
    J Mol Biol 365:1257-65. 2007
    ....
  86. pmc Antibiotic-inducible promoter regulated by the cell envelope stress-sensing two-component system LiaRS of Bacillus subtilis
    Thorsten Mascher
    Department of Microbiology, Cornell University, Ithaca, New York 14853, USA
    Antimicrob Agents Chemother 48:2888-96. 2004
    ..Thus, the reporter derived from P(liaI) (the liaI promoter) provides a tool for the detection and classification of antimicrobial compounds...
  87. ncbi request reprint Purification of Bacillus subtilis RNA polymerase and associated factors
    John D Helmann
    Department of Microbiology, Cornell University, Ithaca, New York 14853, USA
    Methods Enzymol 370:10-24. 2003
  88. pmc Assessing the impact of denitrifier-produced nitric oxide on other bacteria
    Peter S Choi
    Cornell University, Department of Microbiology, Wing Hall, Ithaca, NY 14853, USA
    Appl Environ Microbiol 72:2200-5. 2006
    ....
  89. pmc In vitro mutagenesis of Bacillus subtilis by using a modified Tn7 transposon with an outward-facing inducible promoter
    Christophe Bordi
    Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853 8101, USA
    Appl Environ Microbiol 74:3419-25. 2008
    ..subtilis genome. The utility of this system was demonstrated by the selection of mutants with increased resistance to the antibiotic fosfomycin or duramycin...

Research Grants27

  1. Extracytoplasmic function sigma factors & cell envelope stress in B. subtilis
    JOHN HELMANN; Fiscal Year: 2007
    ..Finally, we will identify and characterize novel antibiotic resistance mechanisms focusing on genes that are strongly induced as part of the cell envelope stress responses. ..
  2. Metal Ion Homeostasis in Bacillus subtilis
    JOHN HELMANN; Fiscal Year: 2007
    ..abstract_text> ..
  3. ECF Sigma Factors and Cell Envelope Stress in Bacillus subtilis
    John D Helmann; Fiscal Year: 2010
    ..This proposal focuses specifically on the model Gram-positive bacterium Bacillus subtilis, which is related to Staphylococcus aureus and pathogenic streptococcal and enterococcal strains. ..
  4. Metal Ion Homeostasis in Bacillus subtilis
    John D Helmann; Fiscal Year: 2010
    ..g. Staphylococcus aureus, streptococci, and enterococci) to survive in the metal-limited environments encountered in the host. ..
  5. B SUBTILIS ECF SIGMA FACTORS: ROLES AND REGULATION
    JOHN HELMANN; Fiscal Year: 2004
    ..Genetic approaches have been devised to identify components of these signaling pathways. Together, these two aims will provide a unified picture of these two large regulons and their roles in B. subtilis physiology. ..
  6. STRUCTURAL STUDIES OF BACILLUS SUBTILIS SIGMA FACTORS
    JOHN HELMANN; Fiscal Year: 1999
    ..coli RNAP; and (iii) allow insights into the roles of structurally related subunits of eukaryotic RNAP. ..
  7. STRUCTURAL STUDIES OF BACILLUS SUBTILIS SIGMA FACTORS
    JOHN HELMANN; Fiscal Year: 1993
    ....
  8. Metal Ion Homeostasis in Bacillus subtilis
    John D Helmann; Fiscal Year: 2010
    ..g. Staphylococcus aureus, streptococci, and enterococci) to survive in the metal-limited environments encountered in the host. ..