archaeal gene expression regulation

Summary

Summary: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.

Top Publications

  1. ncbi Mechanism and regulation of transcription in archaea
    S D Bell
    Wellcome Trust and Cancer Research Campaign Institute of Cancer and Developmental Biology and Department of Zoology, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK
    Curr Opin Microbiol 4:208-13. 2001
  2. pmc Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome
    Yunwei Xie
    Department of Microbiology, Ohio State University, Columbus, Ohio 43210 1292, USA
    J Bacteriol 186:3492-8. 2004
  3. ncbi Ss-LrpB, a novel Lrp-like regulator of Sulfolobus solfataricus P2, binds cooperatively to three conserved targets in its own control region
    Eveline Peeters
    Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, B 1050 Brussels, Belgium
    Mol Microbiol 54:321-36. 2004
  4. ncbi The many faces of the helix-turn-helix domain: transcription regulation and beyond
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N50, Bethesda, MD 20894, USA
    FEMS Microbiol Rev 29:231-62. 2005
  5. pmc Genome-wide transcription map of an archaeal cell cycle
    Magnus Lundgren
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE 752 36 Uppsala, Sweden
    Proc Natl Acad Sci U S A 104:2939-44. 2007
  6. ncbi Ss-LrpB from Sulfolobus solfataricus condenses about 100 base pairs of its own operator DNA into globular nucleoprotein complexes
    Eveline Peeters
    Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel VUB, Pleinlaan 2, B 1050 Brussels, Belgium
    J Biol Chem 281:11721-8. 2006
  7. ncbi Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences
    Thomas J Santangelo
    Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 355:196-210. 2006
  8. ncbi Archaeal chromatin and transcription
    John N Reeve
    Department of Microbiology, Ohio State University, Columbus, OH 43210 1292, USA
    Mol Microbiol 48:587-98. 2003
  9. ncbi Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii
    Alexander Zaigler
    J W Goethe Universitat, Biozentrum Niederursel, Institut fur Mikrobiologie, Marie Curie Str 9, D 60439 Frankfurt, Germany
    Mol Microbiol 48:1089-105. 2003
  10. ncbi The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri
    Andrei L Brioukhanov
    Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob evy Hills 1 12, 119992 Moscow, Russia
    Microbiology 152:1671-7. 2006

Detail Information

Publications152 found, 100 shown here

  1. ncbi Mechanism and regulation of transcription in archaea
    S D Bell
    Wellcome Trust and Cancer Research Campaign Institute of Cancer and Developmental Biology and Department of Zoology, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK
    Curr Opin Microbiol 4:208-13. 2001
    ..The presence of these shared bacterial-archaeal regulators has given insight into the evolution of gene regulatory processes in all three domains of life...
  2. pmc Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome
    Yunwei Xie
    Department of Microbiology, Ohio State University, Columbus, Ohio 43210 1292, USA
    J Bacteriol 186:3492-8. 2004
    ..This inhibited transcription presumably by preventing archaeal TATA-box binding protein, general transcription factor TFB, and RNAP access and thus inhibiting transcription initiation...
  3. ncbi Ss-LrpB, a novel Lrp-like regulator of Sulfolobus solfataricus P2, binds cooperatively to three conserved targets in its own control region
    Eveline Peeters
    Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, B 1050 Brussels, Belgium
    Mol Microbiol 54:321-36. 2004
    ..The latter is based on the concentration-dependent formation of distinct complexes exhibiting different stoichiometries and conformations, which could positively and negatively affect promoter activity...
  4. ncbi The many faces of the helix-turn-helix domain: transcription regulation and beyond
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N50, Bethesda, MD 20894, USA
    FEMS Microbiol Rev 29:231-62. 2005
    ..This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus...
  5. pmc Genome-wide transcription map of an archaeal cell cycle
    Magnus Lundgren
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE 752 36 Uppsala, Sweden
    Proc Natl Acad Sci U S A 104:2939-44. 2007
    ....
  6. ncbi Ss-LrpB from Sulfolobus solfataricus condenses about 100 base pairs of its own operator DNA into globular nucleoprotein complexes
    Eveline Peeters
    Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel VUB, Pleinlaan 2, B 1050 Brussels, Belgium
    J Biol Chem 281:11721-8. 2006
    ..The profound remodeling of the control region is expected to have a strong impact on gene expression and might constitute the key element in the autoregulatory process...
  7. ncbi Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences
    Thomas J Santangelo
    Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 355:196-210. 2006
    ....
  8. ncbi Archaeal chromatin and transcription
    John N Reeve
    Department of Microbiology, Ohio State University, Columbus, OH 43210 1292, USA
    Mol Microbiol 48:587-98. 2003
    ..However, this seems unlikely as it might limit repressor competition at this site to only the first round of transcription initiation...
  9. ncbi Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii
    Alexander Zaigler
    J W Goethe Universitat, Biozentrum Niederursel, Institut fur Mikrobiologie, Marie Curie Str 9, D 60439 Frankfurt, Germany
    Mol Microbiol 48:1089-105. 2003
    ..Analysis of the results revealed that onefold-coverage shotgun DNA microarrays are well suited to characterize the regulation of metabolic pathways as well as protein complexes in response to changes in environmental conditions...
  10. ncbi The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri
    Andrei L Brioukhanov
    Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob evy Hills 1 12, 119992 Moscow, Russia
    Microbiology 152:1671-7. 2006
    ..PQ and to a lesser degree H2O2 induced the expression of superoxide dismutase. The results indicate the regulation of the adaptive response of M. barkeri to different oxidative stresses...
  11. pmc Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus
    Vincenzo Salerno
    Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P Castellino, 80131 Naples, Italy
    Nucleic Acids Res 31:6127-38. 2003
    ..Moreover, several of these genes are also strongly induced by the intercalating agent actinomycin D. Thus, response to DNA damage in S.solfataricus has features essentially conserved in all three domains of life...
  12. ncbi Cell cycle-dependent expression of an essential SMC-like protein and dynamic chromosome localization in the archaeon Halobacterium salinarum
    Ute Herrmann
    J W Goethe Universitat, Biozentrum Niederusel, Institut fur Mikrobiologie, Frankfurt, Germany
    Mol Microbiol 46:395-409. 2002
    ..The Sph1 concentration is elevated when segregation of the new chromosomes is nearly complete; therefore, it is proposed to play a role in a late step of replication, e.g. DNA repair, similar to eukaryotic Rad18 proteins...
  13. ncbi The Lrp family of transcriptional regulators
    Arie B Brinkman
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, NL 6307 CT Wageningen, The Netherlands
    Mol Microbiol 48:287-94. 2003
    ....
  14. ncbi Promoter architecture and response to a positive regulator of archaeal transcription
    Mohamed Ouhammouch
    Division of Biological Sciences and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0634, USA
    Mol Microbiol 56:625-37. 2005
    ....
  15. pmc Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase
    Derek J Richard
    Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
    Nucleic Acids Res 32:1065-74. 2004
    ..The tail forms a stable interaction with RNA polymerase. These data reveal an unexpected role for single-stranded DNA-binding proteins in transcription in archaea...
  16. ncbi Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene
    Andrew Large
    School of Biosciences, The University of Birmingham, Edgbaston B15 2TT, UK
    Mol Microbiol 66:1092-106. 2007
    ..To demonstrate this, we used the promoter to follow the consequences of depletion of the essential chaperonin protein CCT1, and to determine the ability of heterologous CCT proteins to function in H. volcanii...
  17. ncbi A predictive model for transcriptional control of physiology in a free living cell
    Richard Bonneau
    Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, NY 10003, USA
    Cell 131:1354-65. 2007
    ..This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments...
  18. ncbi Archaeal transcriptional regulation--variation on a bacterial theme?
    Stephen D Bell
    MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 2XZ, UK
    Trends Microbiol 13:262-5. 2005
    ..However, little is known about the co-factor requirements, in vivo mechanisms and targets of many of these regulators. It is anticipated that the application of post-genomic technologies will begin to shed light on this fascinating area...
  19. ncbi The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation
    Stephen D Bell
    Medical Research Council MRC Cancer Cell Unit, The Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 2QH, UK
    Science 296:148-51. 2002
    ..These data provide a paradigm for how Sir2 family proteins influence transcription and suggest that modulation of chromatin structure by acetylation arose before the divergence of the archaeal and eukaryotic lineages...
  20. ncbi In vivo analyses of constitutive and regulated promoters in halophilic archaea
    Dagmar Gregor
    Institut fur Mikrobiologie und Genetik, Technische Universitat Darmstadt, Schnittspahnstr 10, D 64287 Darmstadt, Germany
    Microbiology 151:25-33. 2005
    ..None of these alterations influenced the basal promoter activity, but the sequence TGAAACGG-n4-TGAACCAA was important for the GvpE-mediated activation of P(mcA)...
  21. ncbi Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes
    Eveline Peeters
    Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, B 1050 Brussel, Belgium
    Mol Microbiol 71:972-88. 2009
    ..Based on these results, it appears that not all regulators belonging to the archaeal Lrp family perform a function related to the amino acid metabolism, unlike the bacterial Lrp-like regulators...
  22. pmc Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus
    M W Adams
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 7229, USA
    J Bacteriol 183:716-24. 2001
    ..This study provides the first evidence for a highly regulated fermentation-based metabolism in P. furiosus and a significant regulatory role for elemental sulfur or its metabolites...
  23. pmc Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus
    Keith R Shockley
    Department of Chemical Engineering, North Carolina State University, Raleigh 27695 7905, USA
    Appl Environ Microbiol 69:2365-71. 2003
    ....
  24. pmc Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate
    Erik L Hendrickson
    University of Washington, Department of Microbiology, Box 357242, Seattle, WA 98195 7242, USA
    J Bacteriol 190:2198-205. 2008
    ..Increased growth rate resulted in increased mRNA levels for ribosomal protein genes, increased rRNA abundance, and increased mRNA for a gene encoding an S-layer protein...
  25. ncbi Global transcriptional analysis of Methanosarcina mazei strain Gö1 under different nitrogen availabilities
    Katharina Veit
    Institut fur Allgemeine Mikrobiologie, Christian Albrechts Universitat Kiel, Am Botanischen Garten 1 9, 24118, Kiel, Germany
    Mol Genet Genomics 276:41-55. 2006
    ..We therefore hypothesize that this DNA element is involved in nitrogen control in M. mazei where it may act as a binding site for a regulatory protein...
  26. ncbi GvpD-induced breakdown of the transcriptional activator GvpE of halophilic archaea requires a functional p-loop and an arginine-rich region of GvpD
    Sandra Scheuch
    Institut fur Mikrobiologie und Genetik, Technische Universitat Darmstadt, D 64287 Darmstadt, Germany
    Microbiology 153:947-58. 2007
    ..These results underlined that a functional p-loop and the arginine-rich region bR1 of GvpD were required for the GvpD-mediated reduction in the amount of GvpE...
  27. pmc Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea
    Erik L Hendrickson
    Department of Microbiology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 104:8930-4. 2007
    ..Rapid growth increased mRNA levels of the gene for an unusual hydrogenase, the hydrogen-dependent methylenetetrahydromethanopterin dehydrogenase...
  28. ncbi Three 2-oxoacid dehydrogenase operons in Haloferax volcanii: expression, deletion mutants and evolution
    Jan van Ooyen
    Goethe University, Biocentre, Institute for Molecular Biosciences, Max von Laue Str 9, D 60438 Frankfurt, Germany
    Microbiology 153:3303-13. 2007
    ..This view is underscored by a phylogenetic tree of 33 archaeal and bacterial OADHCs...
  29. ncbi Identification and characterization of 1-Cys peroxiredoxin from Sulfolobus solfataricus and its involvement in the response to oxidative stress
    Danila Limauro
    Dipartimento Biologia Strutturale e Funzionale, University of Naples Federico II, Complesso Universitario Monte S Angelo, Naples, Italy
    FEBS J 273:721-31. 2006
    ..Lastly, the presence of this Cys in the sequence confirms that Bcp2 is the first archaeal 1-Cysteine peroxiredoxin (1-Cys Prx) so far identified...
  30. ncbi Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba
    Victoria L Marsh
    Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
    J Biol Chem 280:21122-8. 2005
    ..Therefore, our data suggest that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation...
  31. ncbi Archaeal transcription and its regulators
    E Peter Geiduschek
    Division of Biological Sciences and Center for Molecular Genetics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0634, USA
    Mol Microbiol 56:1397-407. 2005
    ..It is this combination of elements commonly regarded as separate and mutually exclusive that promises unifying insights into basic transcription mechanisms across all three domains of life...
  32. ncbi GvpE- and GvpD-mediated transcription regulation of the p-gvp genes encoding gas vesicles in Halobacterium salinarum
    Annette Hofacker
    Institut fur Mikrobiologie und Genetik, Technische Universitat Darmstadt, Schnittspahnstr 10, D 64287 Darmstadt, Germany
    Microbiology 150:1829-38. 2004
    ..These results suggested that the transcription activation by GvpE is in close contact with the core transcription machinery...
  33. pmc An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter
    A Napoli
    Institute of Protein Biochemistry and Enzymology, Consiglio Nazionale delle Ricerche, 80125 Naples, Italy
    J Bacteriol 181:1474-80. 1999
    ..coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus...
  34. pmc Heat shock response of Archaeoglobus fulgidus
    Lars Rohlin
    Department of Chemical Engineering, 5531 Boelter Hall, University of California, Los Angeles, Los Angeles, CA 90095, USA
    J Bacteriol 187:6046-57. 2005
    ....
  35. ncbi Crystal structure of the archaeal heat shock regulator from Pyrococcus furiosus: a molecular chimera representing eukaryal and bacterial features
    Wei Liu
    Karolinska Institutet NOVUM, Center for Structural Biochemistry, 141 57 Huddinge, Sweden
    J Mol Biol 369:474-88. 2007
    ..Molecular docking and mutational analyses suggested a novel binding mode in which the major specific contacts occur at the minor groove interacting with the strongly basic wing containing a cluster of three arginine residues...
  36. ncbi Diverse homologues of the archaeal repressor NrpR function similarly in nitrogen regulation
    Thomas J Lie
    Department of Microbiology, University of Washington, Seattle, WA 98195 7242, USA
    FEMS Microbiol Lett 271:281-8. 2007
    ..The results show that distantly related NrpR homologues that are present in widely dispersed phyla regulate the expression of nitrogen assimilation genes in a similar fashion...
  37. pmc An integrated systems approach for understanding cellular responses to gamma radiation
    Kenia Whitehead
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 2:47. 2006
    ....
  38. pmc The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    Richard Bonneau
    New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
    Genome Biol 7:R36. 2006
    ..Several specific regulatory predictions were experimentally tested and verified...
  39. pmc Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA
    James A Coker
    University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 East Pratt Street, Baltimore, MD 21202, USA
    BMC Genet 8:61. 2007
    ..NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters...
  40. ncbi TrmB, a sugar sensing regulator of ABC transporter genes in Pyrococcus furiosus exhibits dual promoter specificity and is controlled by different inducers
    Sung Jae Lee
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    Mol Microbiol 57:1797-807. 2005
    ..We believe this to represent a novel strategy of prokaryotic transcription regulation...
  41. pmc Regulatory response of Methanococcus maripaludis to alanine, an intermediate nitrogen source
    Thomas J Lie
    Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
    J Bacteriol 184:5301-6. 2002
    ..In contrast, in the case of glnA the single operator was sufficient for repression by ammonia or alanine. These results suggest a uniform cellular response to nitrogen that is mediated by a different mechanism in each case...
  42. ncbi Biology, biochemistry and the molecular machinery of Archaea
    John N Reeve
    Curr Opin Microbiol 8:627-9. 2005
  43. pmc Function and regulation of glnA in the methanogenic archaeon Methanococcus maripaludis
    R Cohen-Kupiec
    Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
    J Bacteriol 181:256-61. 1999
    ..maripaludis, suggesting a common mechanism of nitrogen regulation. Efforts to produce a glnA null mutant failed, suggesting that glnA is an essential gene in M. maripaludis...
  44. pmc TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha
    B L Hanzelka
    Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
    J Bacteriol 183:1813-8. 2001
    ....
  45. pmc Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea
    Christian Lange
    Institute for Molecular Biosciences, Johann Wolfgang Goethe University, Max von Laue Strasse 9, 60438 Frankfurt a, M, Germany
    BMC Genomics 8:415. 2007
    ..Additional species have not been investigated yet. Particularly, until now no global study of translational control with any prokaryotic species was available...
  46. ncbi Regulation of nif expression in Methanococcus maripaludis: roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators
    Thomas J Lie
    Department of Microbiology, University of Washington, Seattle, WA 98195, USA
    J Biol Chem 280:5236-41. 2005
    ..This model is upheld by the recent finding (J. A. Dodsworth and J. A. Leigh, submitted for publication) in our laboratory that 2OG levels in M. maripaludis vary with growth on different nitrogen sources...
  47. pmc TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro
    Thomas J Santangelo
    Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 367:344-57. 2007
    ....
  48. ncbi Expression and regulation pattern of ferritin-like DpsA in the archaeon Halobacterium salinarum
    Sabine Reindel
    Isotopenlabor TNF, Universitaet zu Luebeck, Ratzeburger Allee 160, D 23538, Luebeck, Germany
    Biometals 19:19-29. 2006
    ..This protein exhibits features of a non-heme type bacterial ferritin although it shares only little sequence similarity with Ftn from E. coli...
  49. ncbi Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation
    Ernest Williams
    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
    Extremophiles 11:19-29. 2007
    ..Finally, we identified several transcriptional regulators and protein kinases highly regulated in response to gamma irradiation...
  50. pmc Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR
    Qiangwei Xia
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
    Mol Cell Proteomics 5:868-81. 2006
    ..15 ORFs were shown to be overexpressed by both methods, and two ORFs were shown to be overexpressed by proteomics and underexpressed by microarray...
  51. pmc Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1
    Nitin S Baliga
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 14:1025-35. 2004
    ....
  52. pmc Transcriptional regulation of the gene encoding an alcohol dehydrogenase in the archaeon Sulfolobus solfataricus involves multiple factors and control elements
    Gabriella Fiorentino
    Dipartimento di Chimica Biologica, Universita degli Studi di Napoli Federico II, Naples, Italy
    J Bacteriol 185:3926-34. 2003
    ....
  53. ncbi Regulation of the expression of gas vesicle genes in Haloferax mediterranei: interaction of the two regulatory proteins GvpD and GvpE
    Peter Zimmermann
    Institut fur Mikrobiologie und Genetik, Technische Universitat Darmstadt, Darmstadt, Germany
    Mol Microbiol 49:783-94. 2003
    ..Vice versa, GvpD was purified using the GvpE-his-Ni-NTA matrix. These results strongly suggested that GvpD and GvpE were able to interact and might constitute a regulatory system...
  54. pmc A thermostable platform for transcriptional regulation: the DNA-binding properties of two Lrp homologs from the hyperthermophilic archaeon Methanococcus jannaschii
    M Ouhammouch
    Division of Biology and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0634, USA
    EMBO J 20:146-56. 2001
    ....
  55. pmc Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus
    P M Leonard
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    EMBO J 20:990-7. 2001
    ..A possible location for an effector binding site is proposed by using sequence comparisons with other members of the family coupled to mutational analysis...
  56. ncbi Use of a halobacterial bgaH reporter gene to analyse the regulation of gene expression in halophilic archaea
    D Gregor
    Institut fur Mikrobiologie und Genetik, Technische Universitat Darmstadt, Schnittspahnstr 10, D 64287 Darmstadt, Germany
    Microbiology 147:1745-54. 2001
    ..Among the three GvpE proteins tested, cGvpE appeared to be the strongest transcriptional activator...
  57. ncbi Basal and regulated transcription in Archaea
    S D Bell
    Wellcome Trust and Cancer Research Campaign Institute of Cancer and Developmental Biology, Tennis Court Road, Cambridge, CB2 1QR, UK
    Biochem Soc Trans 29:392-5. 2001
    ..The mode of action of two such regulators has been characterized to determine how these 'bacterial-like' regulators impinge on the 'eucaryal-like' basal machinery...
  58. pmc Characterization of two heat shock genes from Haloferax volcanii: a model system for transcription regulation in the Archaea
    Y P Kuo
    Department of Microbiology, The Ohio State University, Columbus 43210, USA
    J Bacteriol 179:6318-24. 1997
    ..Comparison of the cct promoter regions also revealed a striking degree of sequence conservation immediately 5' and 3' of the TATA element...
  59. ncbi A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis
    Thomas J Lie
    Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
    Mol Microbiol 47:235-46. 2003
    ..NrpR represents a new family of regulators unique to the Euryarchaeota...
  60. ncbi A novel archaeal transcriptional regulator of heat shock response
    Gudrun Vierke
    Institut fur Allgemeine Mikrobiologie, Am Botanischen Garten 1 9, 24118 Kiel, Germany
    J Biol Chem 278:18-26. 2003
    ..Our findings suggest that heat shock response in Archaea is negatively regulated by a mechanism involving binding of Phr to conserved sequences...
  61. ncbi High resolution contact probing of the Lrp-like DNA-binding protein Ss-Lrp from the hyperthermoacidophilic crenarchaeote Sulfolobus solfataricus P2
    Julius Enoru-Eta
    Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussels, Belgium
    Mol Microbiol 45:1541-55. 2002
    ..Moreover, the results demonstrate profound Ss-Lrp induced structural alterations of sequence stretches flanking the core contact site, and reveal that the deformability of these regions significantly contributes to binding selectivity...
  62. ncbi A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei
    F Pfeifer
    Institut fur Mikrobiologie und Genetik, TU Darmstadt, Schnittspahnstr 10, D 64287 Darmstadt, Germany
    Microbiology 147:63-73. 2001
    ..All these results imply that the GvpD protein is able to prevent the GvpE-mediated gvpA promoter activation, and that the p-loop motif as well as the two basic regions are important for this function...
  63. ncbi Heat shock inducibility of an archaeal TATA-like promoter is controlled by adjacent sequence elements
    D K Thompson
    Department of Microbiology, The Ohio State University, Columbus 43210, USA
    Mol Microbiol 27:541-51. 1998
    ..volcanii differs from the bacterial and eukaryal strategies...
  64. ncbi The gene for a halophilic beta-galactosidase (bgaH) of Haloferax alicantei as a reporter gene for promoter analyses in Halobacterium salinarum
    N Patenge
    Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18a, 82152 Martinsried, Germany
    Mol Microbiol 36:105-13. 2000
    ..Therefore, the bgaH gene of Haloferax alicantei appears to be a useful tool for in vivo studies of gene expression in Halobacterium salinarum and possibly other halophilic Archaea...
  65. ncbi An Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus is negatively autoregulated
    A B Brinkman
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    J Biol Chem 275:38160-9. 2000
    ..The molecular basis of the transcription inhibition by LrpA is discussed...
  66. ncbi Archaeal RecA homologues: different response to DNA-damaging agents in mesophilic and thermophilic Archaea
    C I Reich
    Department of Microbiology, University of Illinois, Urbana 61801, USA
    Extremophiles 5:265-75. 2001
    ..On the other hand, RadB is not coregulated with RadA, and its role remains unclear. Neither RadA nor RadB from a mesophile or from a thermophile rescued the UV-sensitive phenotype of an Escherichia coli recA- host...
  67. ncbi Insights into the NrpR regulon in Methanosarcina mazei Gö1
    Katrin Weidenbach
    Institut fur Allgemeine Mikrobiologie, Christian Albrechts Universitat zu Kiel, Am Botanischen Garten 1 9, 24118 Kiel, Germany
    Arch Microbiol 190:319-32. 2008
    ..Deletion of various bases in the promoter region of nifH confirmed that the regulatory element ACC-N(7)-GGT is required for specific binding of NrpRI to the promoter...
  68. ncbi Analysis of the AAA+ chaperone clpB gene and stress-response expression in the halophilic methanogenic archaeon Methanohalophilus portucalensis
    Chao Jen Shih
    Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
    Microbiology 153:2572-83. 2007
    ..In conclusion, a novel AAA+ chaperone clpB gene from a halophilic methanogen that responded to the fluctuations in temperature, salt concentration and betaine has been identified and analysed for the first time...
  69. pmc The genome of M. acetivorans reveals extensive metabolic and physiological diversity
    James E Galagan
    Whitehead Institute Center for Genome Research, Cambridge, Massachusetts 02141, USA
    Genome Res 12:532-42. 2002
    ..acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]..
  70. ncbi Structural evolution of multisubunit RNA polymerases
    Finn Werner
    Research Department of Structural and Molecular Biology, University College London, Gower Street, London, UK
    Trends Microbiol 16:247-50. 2008
    ..Two reports from the Murakami and Cramer laboratories have now filled this gap in our knowledge and enable us to hypothesize about the evolution of the structure and function of RNAPs...
  71. ncbi Differential regulation of Ota and Otb, two primary glycine betaine transporters in the methanogenic archaeon methanosarcina mazei Gö1
    R Spanheimer
    Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Frankfurt am Main, Germany
    J Mol Microbiol Biotechnol 15:255-63. 2008
    ..In addition to osmolarity Ota expression was regulated by the growth phase. Expression of Ota as well as transport of betaine was downregulated in the presence of glycine betaine...
  72. ncbi The in vitro activity of a Rad55 homologue from Sulfolobus tokodaii, a candidate mediator in RadA-catalyzed homologous recombination
    Duohong Sheng
    State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd, 250100 Jinan, People s Republic of China
    Extremophiles 12:147-57. 2008
    ..tokodaii) on the strand exchange catalyzed by stRadA (RadA homologue from S. tokodaii), by interacting directly with both stRadA and stSSB. StRad55A may function as a mediator to accelerate the displacement of stSSB by stRadA...
  73. ncbi Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors
    Katsushi Yokoyama
    National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Center, Tsukuba, Japan
    FEMS Microbiol Rev 30:89-108. 2006
    ....
  74. ncbi Regulation of expression of the arabinose and glucose transporter genes in the thermophilic archaeon Sulfolobus solfataricus
    Joanna M Lubelska
    Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
    Extremophiles 10:383-91. 2006
    ..Expression of the glucose transporter genes appeared constitutive. These data confirm the earlier observation of a catabolite repression-like system in S. solfataricus...
  75. pmc Polarity in archaeal operon transcription in Thermococcus kodakaraensis
    Thomas J Santangelo
    Department of Microbiology, Ohio State University, Columbus, OH 43210 1292, USA
    J Bacteriol 190:2244-8. 2008
    ..Following the introduction of nonsense codons into promoter-proximal genes, polarity in operon expression in this archaeon has been established by both microarray hybridization assays and a reporter gene expression system...
  76. pmc A small protein from the bop-brp intergenic region of Halobacterium salinarum contains a zinc finger motif and regulates bop and crtB1 transcription
    Valery Y Tarasov
    Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Microbiol 67:772-80. 2008
    ..In silico analysis of the genomes from H. salinarum and other archaea revealed a large family of similar small zinc finger motif proteins, some of which may also be involved in transcription regulation of their adjacent genes...
  77. ncbi Interrupted genes in extremophilic archaea: mechanisms of gene expression in early organisms
    Beatrice Cobucci-Ponzano
    Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P Castellino 111, 80131 Naples, Italy
    Orig Life Evol Biosph 36:487-92. 2006
    ..We review here the expression of interrupted genes in a recently discovered nanoarchaeon and the mechanisms of reprogrammed genetic decoding in Archaea...
  78. pmc TrpY regulation of trpB2 transcription in Methanothermobacter thermautotrophicus
    Elizabeth A Karr
    Department of Microbiology, Ohio State University, Columbus, OH 43210 1292, USA
    J Bacteriol 190:2637-41. 2008
    ..Inhibitory complex formation is prevented by insertions within the regulatory region and by a G149R substitution in TrpY, even though TrpY(G149R) retains both TRP box DNA- and tryptophan-binding abilities...
  79. pmc A polymerase III-like reinitiation mechanism is operating in regulation of histone expression in archaea
    Patrizia Spitalny
    Department of Microbiology, University of Regensburg, Universitatsstrasse 31, 93053 Regensburg, Germany
    Mol Microbiol 67:958-70. 2008
    ....
  80. ncbi Regulation of gvp genes encoding gas vesicle proteins in halophilic Archaea
    Sandra Scheuch
    Institut fur Mikrobiologie und Genetik, Technische Universitat Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
    Arch Microbiol 190:333-9. 2008
    ..Mutations here negatively affect the GvpE-induced activities of both gvp promoters, whereas alterations in the proximal UAS portions only affect the activity of the promoter located close by...
  81. ncbi The archaeal P-type ATPases
    Benoît De Hertogh
    Unité de Génétique GENA, Universite Catholique de Louvain, Louvain la Neuve, Belgique
    J Bioenerg Biomembr 36:135-42. 2004
    ..Moreover recent biochemical data are reviewed that report functional expression of putative archaea metal- or proton-ATPases in bacteria or yeast...
  82. pmc Spontaneous trpY mutants and mutational analysis of the TrpY archaeal transcription regulator
    Kathleen Sandman
    Department of Microbiology, Ohio State University, Columbus, OH 43210 1292, USA
    J Bacteriol 189:4338-42. 2007
    ..In vivo and in vitro studies revealed that DNA binding was sufficient for TrpY repression of trpY transcription but that TrpY must bind DNA and tryptophan to assemble a complex that represses trpEGCFBAD...
  83. ncbi Low temperature regulated DEAD-box RNA helicase from the Antarctic archaeon, Methanococcoides burtonii
    J Lim
    School of Microbiology and Immunology, The University of New South Wales, Sydney, UNSW, 2052, Australia
    J Mol Biol 297:553-67. 2000
    ..In addition, it provides the foundation for further studies into the function and regulation of DEAD-box RNA helicases in archaea, and in particular, their roles in low temperature adaptation...
  84. ncbi The role of TrmB and TrmB-like transcriptional regulators for sugar transport and metabolism in the hyperthermophilic archaeon Pyrococcus furiosus
    Sung Jae Lee
    Department of Biology, Research Institute for Basic Science, Kyung Hee University, Seoul, 130 701, South Korea
    Arch Microbiol 190:247-56. 2008
    ..It recognizes the MD promoter, but not all TGM harboring promoters. It is evolutionary the most conserved among the Thermococcales. The regulatory range of TrmBL2 remains unclear...
  85. ncbi Archaeal proteasomes and other regulatory proteases
    Julie A Maupin-Furlow
    Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 0700, USA
    Curr Opin Microbiol 8:720-8. 2005
    ....
  86. ncbi RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA
    Susanne K Christensen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Mol Microbiol 48:1389-400. 2003
    ..RelE proteins from Gram-positive Bacteria and Archaea cleaved tmRNA with a pattern similar to that of E. coli RelE, suggesting that the function and target of RelE may be conserved across the prokaryotic domains...
  87. pmc The role of cis-acting sequences governing catabolite repression control of lacS expression in the archaeon Sulfolobus solfataricus
    Viet Hoang
    George Beadle Center for Genetics, University of Nebraska, Lincoln, Nebraska 68588 0666, USA
    Genetics 167:1563-72. 2004
    ..These results indicate that car acts at the lacS promoter and that the response to medium composition involves locus-specific sequences exclusive of those present 5' to lacS or within the lacS transcription unit...
  88. pmc Genetic screen for regulatory mutations in Methanococcus maripaludis and its use in identification of induction-deficient mutants of the euryarchaeal repressor NrpR
    Thomas J Lie
    Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195 7242, USA
    Appl Environ Microbiol 73:6595-600. 2007
    ..The results indicate that in M. maripaludis, both NrpR domains participate in the 2-oxoglutarate response. The approach used here has wide adaptability to other regulatory systems in methanogenic Archaea and other strict anaerobes...
  89. ncbi A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii
    Amber Goodchild
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia
    Mol Microbiol 53:309-21. 2004
    ..Thermal regulation in M. burtonii is achieved through complex gene expression events involving gene clusters and operons, through to protein modifications...
  90. ncbi Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition
    Peter T Chivers
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
    J Mol Biol 348:597-607. 2005
    ..Analysis of the PhNikR structures and structure-based mutational studies with EcNikR reveals a plausible mechanism of nickel-dependent promoter recognition by the NikR family of proteins...
  91. ncbi Insights into ABC transport in archaea
    Sonja Verena Albers
    Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    J Bioenerg Biomembr 36:5-15. 2004
    ..Furthermore, a profiling and comparison of ABC transporters in the three sequenced pyrococcal strains was performed...
  92. ncbi [Comprehensive expression of thermo-stable proteins in acidothermophilic archaea]
    Masanari Tsujimura
    Precision System Science Co, Ltd PSS Co, Ltd, 88, Kamihongou, Matsudo, Chiba 271 0064, Japan
    Seikagaku 76:149-54. 2004
  93. ncbi A lysR-type regulator is involved in the negative regulation of genes encoding selenium-free hydrogenases in the archaeon Methanococcus voltae
    Junsong Sun
    Genetics, Department of Biology, Philipps University of Marburg, D 35032 Marburg, Germany
    Mol Microbiol 52:563-71. 2004
    ..A putative HrsM binding site was also detected in the intergenic region in front of the hrsM gene. Northern blot analysis indicated that the hrsM gene might be autoregulated...
  94. ncbi Divergent transcriptional and translational signals in Archaea
    Elfar Torarinsson
    Danish Archaea Centre, Institute of Molecular Biology, Copenhagen University, Sølvgade 83H, DK 1307 Copenhagen K, Denmark
    Environ Microbiol 7:47-54. 2005
    ..High levels of leaderless transcripts are found in the longer branched Archaea...
  95. ncbi Oligonucleotide cleavage and rejoining by topoisomerase III from the hyperthermophilic archaeon Sulfolobus solfataricus: temperature dependence and strand annealing-promoted DNA religation
    Liang Chen
    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
    Mol Microbiol 60:783-94. 2006
    ..These results suggest that Sso topo III is well suited for a role in DNA rewinding, whether it leads to homoduplex or heteroduplex formation...
  96. ncbi Determinants of transcription initiation by archaeal RNA polymerase
    Michael S Bartlett
    Department of Biology, Portland State University, SB2 Room 246, 1719 SW 10th Avenue, Portland, OR 97201, USA
    Curr Opin Microbiol 8:677-84. 2005
    ....
  97. ncbi Expression profiles and physiological roles of two types of prefoldins from the hyperthermophilic archaeon Thermococcus kodakaraensis
    Atsushi Danno
    Department of Bioscience, Nanobiotechnology Research Center, School of Science and Technology, Kwansei Gakuin University, 2 1 Gakuen, Sanda, Hyogo 669 1337, Japan
    J Mol Biol 382:298-311. 2008
    ..The results suggest that the PfdA/PfdB complex plays a crucial role at all growth temperatures and the PfdC/PfdD complex contributes to survival in a high-temperature environment...
  98. ncbi Variations in the multiple tbp genes in different Halobacterium salinarum strains and their expression during growth
    Katharina Teufel
    Institute for Microbiology and Genetics, Technische Universitat Darmstadt, Schnittspahnstr 10, 64287 Darmstadt, Germany
    Arch Microbiol 190:309-18. 2008
    ..The plasmid deletion variant Hbt. salinarum PHH4 lacked all of the tbp genes except for tbpE and showed an altered growth behaviour compared to PHH1 wild-type in the stationary growth phase under anaerobic growth conditions...
  99. ncbi Purification, regulation, and molecular and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain deltaH
    B Mukhopadhyay
    Department of Microbiology, University of Illinois, Urbana, Illinois 61801, USA
    J Biol Chem 273:5155-66. 1998
    ..thermoautotrophicum strain DeltaH (Kenealy, W. R., and Zeikus, J. G. (1982) FEMS Microbiol. Lett. 14, 7-10) raise several questions for future investigations...
  100. ncbi MvaL1 autoregulates the synthesis of the three ribosomal proteins encoded on the MvaL1 operon of the archaeon Methanococcus vannielii by inhibiting its own translation before or at the formation of the first peptide bond
    C Mayer
    Institut für Medizinische Chemie und Biochemie, Universitat Innsbruck, Austria
    Mol Microbiol 27:455-68. 1998
    ..coil. However, we show that MvaL10 does not have a regulatory function...
  101. pmc Microarray analysis of juvenile hormone response in Drosophila melanogaster S2 cells
    David K Willis
    USDA ARS Vegetable Crops Research Unit, University of Wisconsin Madison, Madison, WI 53706, USA
    J Insect Sci 10:66. 2010
    ..05). Among the confirmed JH III up-regulated genes were two loci of unknown function (FBgn0040887 and FBgn0037057) and Epac, an exchange protein directly activated by cyclic AMP, a guanine nucleotide exchange factor for Rap1 small GTPase...

Research Grants5

  1. Interrogation of systems level mechanisms controlling DNA repair processes
    Nitin S Baliga; Fiscal Year: 2010
    ..e. a predictive model for regulatory mechanisms for repair. This basic model will serve as a template for designing systems approaches to model higher complexities of eukaryotic repair processes. ..
  2. GENOME SEQUENCE AND REGULATION IN M MARIPALUDIS
    JOHN LEIGH; Fiscal Year: 2002
    ..Genes will be identified that either vary in expression with changing conditions, or change in expression after mutagenesis of regulatory genes. ..
  3. Transcriptional Nitrogen Regulation in Methanococcus
    JOHN LEIGH; Fiscal Year: 2007
    ..These studies in Archaea have wide importance, as regulatory mechanisms are central to human development and disease. ..
  4. Novel Responses to Oxygen by Anaerobic Microorganisms
    Michael Adams; Fiscal Year: 2008
    ..abstract_text> ..
  5. Histones and Nucleosomes in Archaea
    JOHN REEVE; Fiscal Year: 2007
    ..abstract_text> ..