메뉴 건너뛰기




Volumn 14, Issue 11, 2004, Pages 2221-2234

Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; BACTERIAL PROTEIN; CYTOSINE; GUANINE; OPSIN;

EID: 8744235102     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2700304     Document Type: Article
Times cited : (255)

References (64)
  • 2
    • 0030712081 scopus 로고    scopus 로고
    • The GAF domain: An evolutionary link between diverse phototransducing proteins
    • Aravind, L. and Ponting, C.P. 1997. The GAF domain: An evolutionary link between diverse phototransducing proteins. Trends Biochem. Sci. 22: 458-459.
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 458-459
    • Aravind, L.1    Ponting, C.P.2
  • 3
    • 0034077514 scopus 로고    scopus 로고
    • Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?
    • Baliga, N.S., Goo, Y.A., Ng, W.V., Hood, L., Daniels, C.J., and DasSarma, S. 2000. Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol. Microbiol. 36: 1184-1185.
    • (2000) Mol. Microbiol. , vol.36 , pp. 1184-1185
    • Baliga, N.S.1    Goo, Y.A.2    Ng, W.V.3    Hood, L.4    Daniels, C.J.5    DasSarma, S.6
  • 5
    • 3042615963 scopus 로고    scopus 로고
    • Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1
    • Baliga, N.S., Bjork, S.J., Bonneau, R., Pan, M., Iloanusi, C., Kottemann, M.C.H., Hood, L., and DiRuggiero, J. 2004. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14: 1025-1035.
    • (2004) Genome Res. , vol.14 , pp. 1025-1035
    • Baliga, N.S.1    Bjork, S.J.2    Bonneau, R.3    Pan, M.4    Iloanusi, C.5    Kottemann, M.C.H.6    Hood, L.7    DiRuggiero, J.8
  • 8
    • 0031844818 scopus 로고    scopus 로고
    • Archaea and the cell cycle
    • Bernander, R. 1998. Archaea and the cell cycle. Mol. Microbiol. 29: 955-961.
    • (1998) Mol. Microbiol. , vol.29 , pp. 955-961
    • Bernander, R.1
  • 9
    • 0034212268 scopus 로고    scopus 로고
    • Chromosome replication, nucleoid segregation and cell division in archaea
    • Bernander, R. 2000. Chromosome replication, nucleoid segregation and cell division in archaea. Trends Microbiol. 8: 278-283.
    • (2000) Trends Microbiol. , vol.8 , pp. 278-283
    • Bernander, R.1
  • 10
    • 0141960376 scopus 로고    scopus 로고
    • An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1
    • Berquist, B.R. and DasSarma, S. 2003. An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J. Bacteriol. 185: 5959-5966.
    • (2003) J. Bacteriol. , vol.185 , pp. 5959-5966
    • Berquist, B.R.1    DasSarma, S.2
  • 11
    • 0033753844 scopus 로고    scopus 로고
    • Homologous recombination as a mechanism for genome rearrangements: Environmental and genetic effects
    • Bishop, A.J.R. and Schiestl, R.H. 2000. Homologous recombination as a mechanism for genome rearrangements: Environmental and genetic effects. Hum. Mol. Genet. 9: 2427-2434.
    • (2000) Hum. Mol. Genet. , vol.9 , pp. 2427-2434
    • Bishop, A.J.R.1    Schiestl, R.H.2
  • 12
    • 0036482709 scopus 로고    scopus 로고
    • Archaeal DNA replication: Spotlight on a rapidly moving field
    • Bohlke, K., Pisani, F.M., Rossi, M., and Antranikian, G. 2002. Archaeal DNA replication: Spotlight on a rapidly moving field. Extremophiles 6: 1-14.
    • (2002) Extremophiles , vol.6 , pp. 1-14
    • Bohlke, K.1    Pisani, F.M.2    Rossi, M.3    Antranikian, G.4
  • 14
    • 10044281116 scopus 로고    scopus 로고
    • Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
    • Bonneau, R., Baliga, N.S., Deutsch, E.W., Shannon, P., and Hood, L. 2004. Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol. 5: R52.
    • (2004) Genome Biol. , vol.5
    • Bonneau, R.1    Baliga, N.S.2    Deutsch, E.W.3    Shannon, P.4    Hood, L.5
  • 15
    • 0033617475 scopus 로고    scopus 로고
    • Cryptochromes: Blue light receptors for plants and animals
    • Cashmore, A.R., Jarillo, J.A., Wu, Y.J., and Liu, D. 1999. Cryptochromes: Blue light receptors for plants and animals. Science 284: 760-765.
    • (1999) Science , vol.284 , pp. 760-765
    • Cashmore, A.R.1    Jarillo, J.A.2    Wu, Y.J.3    Liu, D.4
  • 16
    • 0026351181 scopus 로고
    • Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2
    • Charlebois, R.L., Schalkwyk, L.C., Hofman, J.D., and Doolittle, W.F. 1991. Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2. J. Mol. Biol. 222: 509-524.
    • (1991) J. Mol. Biol. , vol.222 , pp. 509-524
    • Charlebois, R.L.1    Schalkwyk, L.C.2    Hofman, J.D.3    Doolittle, W.F.4
  • 18
    • 0041358614 scopus 로고    scopus 로고
    • Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
    • Date, S.V. and Marcotte, E.M. 2003. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol. 21: 1055-1062.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 1055-1062
    • Date, S.V.1    Marcotte, E.M.2
  • 20
    • 0031659282 scopus 로고    scopus 로고
    • Transcription analysis of two disparate rRNA operons in the halophilic archaeon Haloarcula marismortui
    • Dennis, P.P., Ziesche, S., and Mylvaganam, S. 1998. Transcription analysis of two disparate rRNA operons in the halophilic archaeon Haloarcula marismortui. J. Bacteriol. 180: 4804-4813.
    • (1998) J. Bacteriol. , vol.180 , pp. 4804-4813
    • Dennis, P.P.1    Ziesche, S.2    Mylvaganam, S.3
  • 21
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred, II: Error probabilities
    • Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred, II: Error probabilities. Genome Res. 8: 186-194.
    • (1998) Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 22
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred, I: Accuracy assessment
    • Ewing, B,, Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred, I: Accuracy assessment. Genome Res. 8: 175-185.
    • (1998) Genome Res. , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 23
    • 0037974251 scopus 로고    scopus 로고
    • Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: Principles of ion pumping
    • Facciotti, M.T., Cheung, V.S., Nguyen, D., Rouhani, S., and Glaeser, R.M. 2003. Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: Principles of ion pumping. Biophys. J. 85: 451-458.
    • (2003) Biophys. J. , vol.85 , pp. 451-458
    • Facciotti, M.T.1    Cheung, V.S.2    Nguyen, D.3    Rouhani, S.4    Glaeser, R.M.5
  • 24
    • 0024961673 scopus 로고
    • Light guides: Directional energy transfer in a photosynthetic antenna
    • Glazer, A. 1989. Light guides: Directional energy transfer in a photosynthetic antenna. J. Biol. Chem. 264: 1-4.
    • (1989) J. Biol. Chem. , vol.264 , pp. 1-4
    • Glazer, A.1
  • 26
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon, D., Abajian, C., and Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
    • (1998) Genome Res. , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 27
    • 0032524384 scopus 로고    scopus 로고
    • Analyzing genomes with cumulative skew diagrams
    • Grigoriev, A. 1998. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26: 2286-2290.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2286-2290
    • Grigoriev, A.1
  • 28
    • 0034660609 scopus 로고    scopus 로고
    • Bacterial cryptochrome and photolyase: Characterization of two photolyase-like genes of Synechocystis sp. PCC6803
    • Hitomi, K., Okamoto, K., Daiyasu, H., Miyashita, H., Iwai, S., Toh, H., Ishiura, M., and Todo, T. 2000. Bacterial cryptochrome and photolyase: Characterization of two photolyase-like genes of Synechocystis sp. PCC6803. Nucleic Acids Res. 28: 2353-2362.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2353-2362
    • Hitomi, K.1    Okamoto, K.2    Daiyasu, H.3    Miyashita, H.4    Iwai, S.5    Toh, H.6    Ishiura, M.7    Todo, T.8
  • 29
    • 0034967182 scopus 로고    scopus 로고
    • Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui
    • Ichiki, H., Tanaka, Y., Mochizuki, K., Yoshimatsu, K., Sakurai, T., and Fujiwara, T. 2001. Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui. J. Bacteriol. 183: 4149-4156.
    • (2001) J. Bacteriol. , vol.183 , pp. 4149-4156
    • Ichiki, H.1    Tanaka, Y.2    Mochizuki, K.3    Yoshimatsu, K.4    Sakurai, T.5    Fujiwara, T.6
  • 30
    • 0037805576 scopus 로고    scopus 로고
    • The KEGG database
    • discussion 101-103, 119-128, 244-252
    • Kanehisa, M. 2002. The KEGG database. Novartis Found. Symp. 247: 91-101; discussion 101-103, 119-128, 244-252.
    • (2002) Novartis Found. Symp. , vol.247 , pp. 91-101
    • Kanehisa, M.1
  • 31
    • 0034767491 scopus 로고    scopus 로고
    • Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence
    • Kennedy, S.P., Ng, W.V., Salzberg, S.L., Hood, L., and DasSarma, S. 2001. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res. 11: 1641-1650.
    • (2001) Genome Res. , vol.11 , pp. 1641-1650
    • Kennedy, S.P.1    Ng, W.V.2    Salzberg, S.L.3    Hood, L.4    DasSarma, S.5
  • 32
    • 0027963488 scopus 로고
    • Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA
    • Koop, B.F. and Hood, L. 1994. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nat. Genet. 7: 48-53.
    • (1994) Nat. Genet. , vol.7 , pp. 48-53
    • Koop, B.F.1    Hood, L.2
  • 33
    • 0032793852 scopus 로고    scopus 로고
    • Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes
    • Lawrence, J. 1999. Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9: 642-648.
    • (1999) Curr. Opin. Genet. Dev. , vol.9 , pp. 642-648
    • Lawrence, J.1
  • 34
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 35
    • 0035943457 scopus 로고    scopus 로고
    • Crystal structure of sensory rhodopsin II at 2.4 angstroms: Insights into color tuning and transducer interaction
    • Luecke, H., Schobert, B., Lanyi, J.K., Spudich, E.N., and Spudich, J.L. 2001. Crystal structure of sensory rhodopsin II at 2.4 angstroms: Insights into color tuning and transducer interaction. Science 293: 1499-1503.
    • (2001) Science , vol.293 , pp. 1499-1503
    • Luecke, H.1    Schobert, B.2    Lanyi, J.K.3    Spudich, E.N.4    Spudich, J.L.5
  • 36
    • 0037162464 scopus 로고    scopus 로고
    • Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds
    • Mallick, P., Boutz, D.R., Eisenberg, D., and Yeates, T.O. 2002. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl. Acad. Sci. 99: 9679-9684.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 9679-9684
    • Mallick, P.1    Boutz, D.R.2    Eisenberg, D.3    Yeates, T.O.4
  • 37
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 38
    • 0028246909 scopus 로고
    • The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation
    • Mattar, S., Scharf, B., Kent, S., Rodewald, K., Oesterhelt, D., and Engelhard, M. 1994. The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation. J. Biol. Chem. 269: 14939-14945.
    • (1994) J. Biol. Chem. , vol.269 , pp. 14939-14945
    • Mattar, S.1    Scharf, B.2    Kent, S.3    Rodewald, K.4    Oesterhelt, D.5    Engelhard, M.6
  • 39
    • 0037864281 scopus 로고    scopus 로고
    • Repair of UV damage in Halobacterium salinarum
    • McCready, S. and Marcello, L. 2003. Repair of UV damage in Halobacterium salinarum. Biochem. Soc. Trans. 31: 694-698.
    • (2003) Biochem. Soc. Trans. , vol.31 , pp. 694-698
    • McCready, S.1    Marcello, L.2
  • 41
    • 0001291140 scopus 로고    scopus 로고
    • A powerful non-homology method for the prediction of operons in prokaryotes
    • Moreno-Hagelsieb, G. and Collado-Vides, J. 2002. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18(Suppl 1): S329-S336.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Moreno-Hagelsieb, G.1    Collado-Vides, J.2
  • 42
    • 0026602645 scopus 로고
    • Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui
    • Mylvaganam, S. and Dennis, P.P. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130: 399-410.
    • (1992) Genetics , vol.130 , pp. 399-410
    • Mylvaganam, S.1    Dennis, P.P.2
  • 45
  • 46
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz, A.R., Strauss, C.E., and Olmea, O. 2002. MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison. Protein Sci. 11: 2606-2621.
    • (2002) Protein Sci. , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 50
    • 0029761908 scopus 로고    scopus 로고
    • Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): Genes, gene products, and transcripts of the arcRACB gene cluster
    • Ruepp, A. and Soppa, J. 1996. Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): Genes, gene products, and transcripts of the arcRACB gene cluster. J. Bacteriol. 178: 4942-4947.
    • (1996) J. Bacteriol. , vol.178 , pp. 4942-4947
    • Ruepp, A.1    Soppa, J.2
  • 54
    • 0025863275 scopus 로고
    • Metabolic regulation including anaerobic metabolism in Paracoccus denitrificans
    • Stouthamer, A.H. 1991. Metabolic regulation including anaerobic metabolism in Paracoccus denitrificans. J. Bioenerg. Biomembr. 23: 163-185.
    • (1991) J. Bioenerg. Biomembr. , vol.23 , pp. 163-185
    • Stouthamer, A.H.1
  • 55
    • 0032990441 scopus 로고    scopus 로고
    • PAS domains: Internal sensors of oxygen, redox potential, and light
    • Taylor, B.L. and Zhulin, I.B. 1999. PAS domains: Internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63: 479-506.
    • (1999) Microbiol. Mol. Biol. Rev. , vol.63 , pp. 479-506
    • Taylor, B.L.1    Zhulin, I.B.2
  • 56
    • 0036211065 scopus 로고    scopus 로고
    • GRIMM: Genome rearrangements web server
    • Tesler, G. 2002. GRIMM: Genome rearrangements web server. Bioinformatics 18: 492-493.
    • (2002) Bioinformatics , vol.18 , pp. 492-493
    • Tesler, G.1
  • 57
    • 0032880054 scopus 로고    scopus 로고
    • Expression and heat-responsive regulation of a TFIIB homologue from the archaeon Haloferax volcanii
    • Thompson, D.K., Palmer, J.R., and Daniels, C.J. 1999. Expression and heat-responsive regulation of a TFIIB homologue from the archaeon Haloferax volcanii. Mol. Microbiol. 33: 1081-1092.
    • (1999) Mol. Microbiol. , vol.33 , pp. 1081-1092
    • Thompson, D.K.1    Palmer, J.R.2    Daniels, C.J.3
  • 58
    • 0036852286 scopus 로고    scopus 로고
    • The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice
    • Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., and Van De Peer, Y. 2002. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 12: 1792-1801.
    • (2002) Genome Res. , vol.12 , pp. 1792-1801
    • Vandepoele, K.1    Saeys, Y.2    Simillion, C.3    Raes, J.4    Van De Peer, Y.5
  • 59
    • 10044244323 scopus 로고    scopus 로고
    • Predicting functional linkages from gene fusions with confidence
    • Verjovsky Maycotte, C.J. and Marcotte, E.M. 2002. Predicting functional linkages from gene fusions with confidence. Appl. Bioinformatics 1: 37-44.
    • (2002) Appl. Bioinformatics , vol.1 , pp. 37-44
    • Verjovsky Maycotte, C.J.1    Marcotte, E.M.2
  • 60
    • 3042663808 scopus 로고    scopus 로고
    • Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Weston, A.D., Baliga, N.S., Bonneau, R., and Hood, L. 2004. Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (2004)
    • Weston, A.D.1    Baliga, N.S.2    Bonneau, R.3    Hood, L.4
  • 61
    • 0038219594 scopus 로고    scopus 로고
    • Cyanobacterial circadian clockwork: Roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC
    • Xu, Y., Mori, T., and Johnson, C.H. 2003. Cyanobacterial circadian clockwork: Roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC. EMBO J. 22: 2117-2126.
    • (2003) EMBO J. , vol.22 , pp. 2117-2126
    • Xu, Y.1    Mori, T.2    Johnson, C.H.3
  • 62
    • 0034708409 scopus 로고    scopus 로고
    • Purification and characterization of dissimilatory nitrate reductase from a denitrifying halophilic archaeon, Haloarcula marismortui
    • Yoshimatsu, K., Sakurai, T., and Fujiwara, T. 2000. Purification and characterization of dissimilatory nitrate reductase from a denitrifying halophilic archaeon, Haloarcula marismortui. FEBS Lett. 470: 216-220.
    • (2000) FEBS Lett. , vol.470 , pp. 216-220
    • Yoshimatsu, K.1    Sakurai, T.2    Fujiwara, T.3
  • 63
    • 0037051993 scopus 로고    scopus 로고
    • Sequence and electron paramagnetic resonance analyses of nitrate reductase NarGH from a denitrifying halophilic euryarchaeote Haloarcula marismortui
    • Yoshimatsu, K., Iwasaki, T., and Fujiwara, T. 2002. Sequence and electron paramagnetic resonance analyses of nitrate reductase NarGH from a denitrifying halophilic euryarchaeote Haloarcula marismortui. FEBS Lett. 516: 145-150.
    • (2002) FEBS Lett. , vol.516 , pp. 145-150
    • Yoshimatsu, K.1    Iwasaki, T.2    Fujiwara, T.3
  • 64
    • 0037459196 scopus 로고    scopus 로고
    • Multiple replication origins of the archaeon Halobacterium species NRC-1
    • Zhang, R. and Zhang, C.T. 2003. Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem. Biophys. Res. Commun. 302: 728-734.
    • (2003) Biochem. Biophys. Res. Commun. , vol.302 , pp. 728-734
    • Zhang, R.1    Zhang, C.T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.