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. Cohen Kupiec R, Marx C, Leigh J. Function and regulation of glnA in the methanogenic archaeon Methanococcus maripaludis. J Bacteriol. 1999;181:256-61 pubmed
    ..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...
  2. Herrmann U, Soppa J. Cell cycle-dependent expression of an essential SMC-like protein and dynamic chromosome localization in the archaeon Halobacterium salinarum. Mol Microbiol. 2002;46:395-409 pubmed
    ..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...
  3. Bell S. Archaeal transcriptional regulation--variation on a bacterial theme?. Trends Microbiol. 2005;13:262-5 pubmed
    ..It is anticipated that the application of post-genomic technologies will begin to shed light on this fascinating area. ..
  4. Geiduschek E, Ouhammouch M. Archaeal transcription and its regulators. Mol Microbiol. 2005;56:1397-407 pubmed
    ..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. ..
  5. Pfeifer F, Zotzel J, Kurenbach B, Roder R, Zimmermann P. 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. Microbiology. 2001;147:63-73 pubmed
    ..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...
  6. Peeters E, Thia Toong T, Gigot D, Maes D, Charlier D. Ss-LrpB, a novel Lrp-like regulator of Sulfolobus solfataricus P2, binds cooperatively to three conserved targets in its own control region. Mol Microbiol. 2004;54:321-36 pubmed
    ..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. ..
  7. Leonard P, Smits S, Sedelnikova S, Brinkman A, de Vos W, van der Oost J, et al. Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. EMBO J. 2001;20:990-7 pubmed publisher
    ..A possible location for an effector binding site is proposed by using sequence comparisons with other members of the family coupled to mutational analysis...
  8. Zaigler A, Schuster S, Soppa J. Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii. Mol Microbiol. 2003;48:1089-105 pubmed
    ..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...
  9. Vierke G, Engelmann A, Hebbeln C, Thomm M. A novel archaeal transcriptional regulator of heat shock response. J Biol Chem. 2003;278:18-26 pubmed
    ..Our findings suggest that heat shock response in Archaea is negatively regulated by a mechanism involving binding of Phr to conserved sequences. ..

More Information

Publications62

  1. Thompson D, Daniels C. Heat shock inducibility of an archaeal TATA-like promoter is controlled by adjacent sequence elements. Mol Microbiol. 1998;27:541-51 pubmed
    ..volcanii differs from the bacterial and eukaryal strategies. ..
  2. Lie T, Leigh J. A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis. Mol Microbiol. 2003;47:235-46 pubmed
    ..NrpR represents a new family of regulators unique to the Euryarchaeota...
  3. Brinkman A, Ettema T, de Vos W, van der Oost J. The Lrp family of transcriptional regulators. Mol Microbiol. 2003;48:287-94 pubmed
  4. Reeve J. Archaeal chromatin and transcription. Mol Microbiol. 2003;48:587-98 pubmed
    ..However, this seems unlikely as it might limit repressor competition at this site to only the first round of transcription initiation. ..
  5. Lee S, Moulakakis C, Koning S, Hausner W, Thomm M, Boos W. TrmB, a sugar sensing regulator of ABC transporter genes in Pyrococcus furiosus exhibits dual promoter specificity and is controlled by different inducers. Mol Microbiol. 2005;57:1797-807 pubmed
    ..We believe this to represent a novel strategy of prokaryotic transcription regulation...
  6. Reindel S, Schmidt C, Anem ller S, Matzanke B. Expression and regulation pattern of ferritin-like DpsA in the archaeon Halobacterium salinarum. Biometals. 2006;19:19-29 pubmed publisher
    ..This protein exhibits features of a non-heme type bacterial ferritin although it shares only little sequence similarity with Ftn from E. coli...
  7. Veit K, Ehlers C, Ehrenreich A, Salmon K, Hovey R, Gunsalus R, et al. Global transcriptional analysis of Methanosarcina mazei strain Gö1 under different nitrogen availabilities. Mol Genet Genomics. 2006;276:41-55 pubmed
    ..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. ..
  8. Williams E, Lowe T, Savas J, DiRuggiero J. Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation. Extremophiles. 2007;11:19-29 pubmed
    ..Finally, we identified several transcriptional regulators and protein kinases highly regulated in response to gamma irradiation. ..
  9. Lie T, Leigh J. Regulatory response of Methanococcus maripaludis to alanine, an intermediate nitrogen source. J Bacteriol. 2002;184:5301-6 pubmed
    ..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. ..
  10. Bell S, Botting C, Wardleworth B, Jackson S, White M. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science. 2002;296:148-51 pubmed
    ..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. ..
  11. Adams M, Holden J, Menon A, Schut G, Grunden A, Hou C, et al. Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 2001;183:716-24 pubmed publisher
    ..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...
  12. Gregor D, Pfeifer F. Use of a halobacterial bgaH reporter gene to analyse the regulation of gene expression in halophilic archaea. Microbiology. 2001;147:1745-54 pubmed
    ..Among the three GvpE proteins tested, cGvpE appeared to be the strongest transcriptional activator...
  13. Bell S, Jackson S. Mechanism and regulation of transcription in archaea. Curr Opin Microbiol. 2001;4:208-13 pubmed
    ..The presence of these shared bacterial-archaeal regulators has given insight into the evolution of gene regulatory processes in all three domains of life. ..
  14. Napoli A, van der Oost J, Sensen C, Charlebois R, Rossi M, Ciaramella M. An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. J Bacteriol. 1999;181:1474-80 pubmed
    ..coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus. ..
  15. Kuo Y, Thompson D, St Jean A, Charlebois R, Daniels C. Characterization of two heat shock genes from Haloferax volcanii: a model system for transcription regulation in the Archaea. J Bacteriol. 1997;179:6318-24 pubmed
    ..Comparison of the cct promoter regions also revealed a striking degree of sequence conservation immediately 5' and 3' of the TATA element...
  16. Marsh V, Peak Chew S, Bell S. Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba. J Biol Chem. 2005;280:21122-8 pubmed
    ..Therefore, our data suggest that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation. ..
  17. Rohlin L, Trent J, Salmon K, Kim U, Gunsalus R, Liao J. Heat shock response of Archaeoglobus fulgidus. J Bacteriol. 2005;187:6046-57 pubmed
  18. Brinkman A, Dahlke I, Tuininga J, Lammers T, Dumay V, de Heus E, et al. An Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus is negatively autoregulated. J Biol Chem. 2000;275:38160-9 pubmed publisher
    ..The molecular basis of the transcription inhibition by LrpA is discussed...
  19. Bonneau R, Reiss D, Shannon P, Facciotti M, Hood L, Baliga N, et al. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 2006;7:R36 pubmed
    ..Several specific regulatory predictions were experimentally tested and verified...
  20. Brioukhanov A, Netrusov A, Eggen R. The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri. Microbiology. 2006;152:1671-7 pubmed publisher
    ..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...
  21. Whitehead K, Kish A, Pan M, Kaur A, Reiss D, King N, et al. An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol. 2006;2:47 pubmed
  22. Santangelo T, Cubonová L, James C, Reeve J. TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro. J Mol Biol. 2007;367:344-57 pubmed
  23. Lie T, Dodsworth J, Nickle D, Leigh J. Diverse homologues of the archaeal repressor NrpR function similarly in nitrogen regulation. FEMS Microbiol Lett. 2007;271:281-8 pubmed publisher
    ..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...
  24. van Ooyen J, Soppa J. Three 2-oxoacid dehydrogenase operons in Haloferax volcanii: expression, deletion mutants and evolution. Microbiology. 2007;153:3303-13 pubmed
    ..This view is underscored by a phylogenetic tree of 33 archaeal and bacterial OADHCs...
  25. Lange C, Zaigler A, Hammelmann M, Twellmeyer J, Raddatz G, Schuster S, et al. Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genomics. 2007;8:415 pubmed
    ..Additional species have not been investigated yet. Particularly, until now no global study of translational control with any prokaryotic species was available...
  26. Hendrickson E, Liu Y, Rosas Sandoval G, Porat I, Soll D, Whitman W, et al. Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J Bacteriol. 2008;190:2198-205 pubmed publisher
    ..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...
  27. Reich C, McNeil L, Brace J, Brucker J, Olsen G. Archaeal RecA homologues: different response to DNA-damaging agents in mesophilic and thermophilic Archaea. Extremophiles. 2001;5:265-75 pubmed
    ..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. ..
  28. Gregor D, Pfeifer F. In vivo analyses of constitutive and regulated promoters in halophilic archaea. Microbiology. 2005;151:25-33 pubmed
    ..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)...
  29. Zimmermann P, Pfeifer F. Regulation of the expression of gas vesicle genes in Haloferax mediterranei: interaction of the two regulatory proteins GvpD and GvpE. Mol Microbiol. 2003;49:783-94 pubmed
    ..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...
  30. Salerno V, Napoli A, White M, Rossi M, Ciaramella M. Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus. Nucleic Acids Res. 2003;31:6127-38 pubmed
    ..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. ..
  31. Richard D, Bell S, White M. Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase. Nucleic Acids Res. 2004;32:1065-74 pubmed
    ..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. ..
  32. Xie Y, Reeve J. Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome. J Bacteriol. 2004;186:3492-8 pubmed
    ..This inhibited transcription presumably by preventing archaeal TATA-box binding protein, general transcription factor TFB, and RNAP access and thus inhibiting transcription initiation...
  33. Ouhammouch M, Geiduschek E. A thermostable platform for transcriptional regulation: the DNA-binding properties of two Lrp homologs from the hyperthermophilic archaeon Methanococcus jannaschii. EMBO J. 2001;20:146-56 pubmed publisher
  34. Peeters E, Albers S, Vassart A, Driessen A, Charlier D. Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes. Mol Microbiol. 2009;71:972-88 pubmed publisher
    ..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. ..
  35. Ouhammouch M, Langham G, Hausner W, Simpson A, El Sayed N, Geiduschek E. Promoter architecture and response to a positive regulator of archaeal transcription. Mol Microbiol. 2005;56:625-37 pubmed publisher
  36. Bell S, Magill C, Jackson S. Basal and regulated transcription in Archaea. Biochem Soc Trans. 2001;29:392-5 pubmed
    ..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. ..
  37. Hendrickson E, Haydock A, Moore B, Whitman W, Leigh J. Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea. Proc Natl Acad Sci U S A. 2007;104:8930-4 pubmed
    ..Rapid growth increased mRNA levels of the gene for an unusual hydrogenase, the hydrogen-dependent methylenetetrahydromethanopterin dehydrogenase...
  38. Lundgren M, Bernander R. Genome-wide transcription map of an archaeal cell cycle. Proc Natl Acad Sci U S A. 2007;104:2939-44 pubmed
  39. Peeters E, Willaert R, Maes D, Charlier D. Ss-LrpB from Sulfolobus solfataricus condenses about 100 base pairs of its own operator DNA into globular nucleoprotein complexes. J Biol Chem. 2006;281:11721-8 pubmed
    ..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. ..
  40. Limauro D, Pedone E, Pirone L, Bartolucci S. Identification and characterization of 1-Cys peroxiredoxin from Sulfolobus solfataricus and its involvement in the response to oxidative stress. FEBS J. 2006;273:721-31 pubmed publisher
    ..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...
  41. Santangelo T, Reeve J. Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences. J Mol Biol. 2006;355:196-210 pubmed
  42. Lie T, Wood G, Leigh J. Regulation of nif expression in Methanococcus maripaludis: roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators. J Biol Chem. 2005;280:5236-41 pubmed publisher
    ..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...
  43. Enoru Eta J, Gigot D, Glansdorff N, Charlier D. High resolution contact probing of the Lrp-like DNA-binding protein Ss-Lrp from the hyperthermoacidophilic crenarchaeote Sulfolobus solfataricus P2. Mol Microbiol. 2002;45:1541-55 pubmed
    ..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. ..
  44. Hanzelka B, Darcy T, Reeve J. TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha. J Bacteriol. 2001;183:1813-8 pubmed publisher
  45. Aravind L, Anantharaman V, Balaji S, Babu M, Iyer L. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev. 2005;29:231-62 pubmed
    ..This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus. ..
  46. Hofacker A, Schmitz K, Cichonczyk A, Sartorius Neef S, Pfeifer F. GvpE- and GvpD-mediated transcription regulation of the p-gvp genes encoding gas vesicles in Halobacterium salinarum. Microbiology. 2004;150:1829-38 pubmed
    ..These results suggested that the transcription activation by GvpE is in close contact with the core transcription machinery...
  47. Patenge N, Haase A, Bolhuis H, Oesterhelt D. The gene for a halophilic beta-galactosidase (bgaH) of Haloferax alicantei as a reporter gene for promoter analyses in Halobacterium salinarum. Mol Microbiol. 2000;36:105-13 pubmed
    ..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...
  48. Reeve J, Schmitz R. Biology, biochemistry and the molecular machinery of Archaea. Curr Opin Microbiol. 2005;8:627-9 pubmed
  49. Scheuch S, Pfeifer F. GvpD-induced breakdown of the transcriptional activator GvpE of halophilic archaea requires a functional p-loop and an arginine-rich region of GvpD. Microbiology. 2007;153:947-58 pubmed
    ..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...
  50. Liu W, Vierke G, Wenke A, Thomm M, Ladenstein R. Crystal structure of the archaeal heat shock regulator from Pyrococcus furiosus: a molecular chimera representing eukaryal and bacterial features. J Mol Biol. 2007;369:474-88 pubmed publisher
    ..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...
  51. Fiorentino G, Cannio R, Rossi M, Bartolucci S. Transcriptional regulation of the gene encoding an alcohol dehydrogenase in the archaeon Sulfolobus solfataricus involves multiple factors and control elements. J Bacteriol. 2003;185:3926-34 pubmed
  52. Shockley K, Ward D, Chhabra S, Conners S, Montero C, Kelly R. Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus. Appl Environ Microbiol. 2003;69:2365-71 pubmed
  53. Large A, Stamme C, Lange C, Duan Z, Allers T, Soppa J, et al. Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene. Mol Microbiol. 2007;66:1092-106 pubmed
    ..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. ..