Home LiteratureArticle Details
PMID: 11016950 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Genome sequence of Halobacterium species NRC-1.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 97 ·No. 22 ·2000-10-24 ·Pages 12176-81

Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S

Abstract

We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea.

MeSH Terms
Biological Evolution Cell Membrane/metabolism DNA Repair DNA Replication Energy Metabolism Genome, Bacterial Halobacterium/genetics,metabolism Lipid Bilayers Molecular Sequence Data Protein Biosynthesis Recombination, Genetic Signal Transduction Transcription, Genetic
Chemicals
Lipid Bilayers
Authors & Affiliations
43 authors, click to expand affiliations / ORCID
Ng W V
Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195, USA. tment of Microbiology, University of Massachusetts, Amherst, MA 01003; Centre for Extremophile Research, Department of Biology and Biochemistry, Univer.
Kennedy S P
Mahairas G G
Berquist B
Pan M
Shukla H D
Lasky S R
Baliga N S
Thorsson V
Sbrogna J
Swartzell S
Weir D
Hall J
Dahl T A
Welti R
Goo Y A
Leithauser B
Keller K
Cruz R
Danson M J
Hough D W
Maddocks D G
Jablonski P E
Krebs M P
Angevine C M
Dale H
Isenbarger T A
Peck R F
Pohlschroder M
Spudich J L
Jung K W
Alam M
Freitas T
Hou S
Daniels C J
Dennis P P
Omer A D
Ebhardt H
Lowe T M
Liang P
Riley M
Hood L
DasSarma S
References (68)
68 references, click to expand
  1. Bacteriorhodopsin and the purple membrane of halobacteria.
    Biochim Biophys Acta. 1979 Mar 14;505(3-4):215-78 PMID: 35226
  2. Cooperative regulation of the Na+/H(+)-antiporter in Halobacterium halobium by delta pH and delta phi.
    Arch Biochem Biophys. 1990 Aug 15;281(1):13-20 PMID: 2166477
  3. Operation of glyoxylate cycle in halophilic archaea: presence of malate synthase and isocitrate lyase in Haloferax volcanii.
    FEBS Lett. 1998 Aug 28;434(1-2):13-6 PMID: 9738442
  4. Consed: a graphical tool for sequence finishing.
    Genome Res. 1998 Mar;8(3):195-202 PMID: 9521923
  5. Protein translocation in the three domains of life: variations on a theme.
    Cell. 1997 Nov 28;91(5):563-6 PMID: 9393849
  6. Solute concentrations within cells of halophilic and non-halophilic bacteria.
    Biochim Biophys Acta. 1962 Dec 17;65:506-8 PMID: 14021131
  7. Microbial gene identification using interpolated Markov models.
    Nucleic Acids Res. 1998 Jan 15;26(2):544-8 PMID: 9421513
  8. Metabolic Pathways in Methanococcus jannaschii and Other Methanogenic Bacteria.
    Appl Environ Microbiol. 1993 Apr;59(4):1092-8 PMID: 16348909
  9. The metabolism of carbohydrates by extremely halophilic bacteria: glucose metabolism via a modified Entner-Doudoroff pathway.
    Can J Microbiol. 1974 Aug;20(8):1085-91 PMID: 4153875
  10. Circadian programs in cyanobacteria: adaptiveness and mechanism.
    Annu Rev Microbiol. 1999;53:389-409 PMID: 10547696
  11. Isoprenoid synthesis in Halobacterium halobium. Modulation of 3-hydroxy-3-methylglutaryl coenzyme a concentration in response to mevalonate availability.
    J Biol Chem. 1986 Mar 15;261(8):3578-83 PMID: 3633268
  12. Improved purification, crystallization and primary structure of pyruvate:ferredoxin oxidoreductase from Halobacterium halobium.
    Eur J Biochem. 1992 Apr 1;205(1):391-7 PMID: 1555599
  13. Exhaustive matching of the entire protein sequence database.
    Science. 1992 Jun 5;256(5062):1443-5 PMID: 1604319
  14. Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?
    Mol Microbiol. 2000 Jun;36(5):1184-5 PMID: 10844702
  15. Phylogenetic classification and the universal tree.
    Science. 1999 Jun 25;284(5423):2124-9 PMID: 10381871
  16. A family of halobacterial transducer proteins.
    FEMS Microbiol Lett. 1996 Jun 1;139(2-3):161-8 PMID: 8674984
  17. Light-activated amino acid transport systems in Halobacterium halobium envelope vesicles: role of chemical and electrical gradients.
    Biochemistry. 1977 Jul 12;16(14):3227-35 PMID: 889797
  18. Identification and analysis of the gas vesicle gene cluster on an unstable plasmid of Halobacterium halobium.
    Experientia. 1993 Jul 5;49(6-7):482-6 PMID: 8335077
  19. Primary structure of an archaebacterial transducer, a methyl-accepting protein associated with sensory rhodopsin I.
    Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):11915-9 PMID: 1465418
  20. Base-calling of automated sequencer traces using phred. II. Error probabilities.
    Genome Res. 1998 Mar;8(3):186-94 PMID: 9521922
  21. Characterization of the L11, L1, L10 and L12 equivalent ribosomal protein gene cluster of the halophilic archaebacterium Halobacterium cutirubrum.
    EMBO J. 1989 Apr;8(4):1225-35 PMID: 2743981
  22. Ancient ciphers: translation in Archaea.
    Cell. 1997 Jun 27;89(7):1007-10 PMID: 9215623
  23. A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea.
    Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):8873-8 PMID: 10430863
  24. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module.
    J Mol Biol. 1997 May 23;268(5):857-68 PMID: 9180377
  25. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
    Nucleic Acids Res. 1997 Mar 1;25(5):955-64 PMID: 9023104
  26. Transcription factor S, a cleavage induction factor of the archaeal RNA polymerase.
    J Biol Chem. 2000 Apr 28;275(17):12393-9 PMID: 10777522
  27. Signal transduction in the archaeon Halobacterium salinarium is processed through three subfamilies of 13 soluble and membrane-bound transducer proteins.
    Proc Natl Acad Sci U S A. 1996 May 14;93(10):4649-54 PMID: 8643458
  28. Archaeal DNA replication: identifying the pieces to solve a puzzle.
    Genetics. 1999 Aug;152(4):1249-67 PMID: 10430556
  29. Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium.
    J Bacteriol. 1994 Dec;176(24):7711-8 PMID: 8002597
  30. Bacterial evolution.
    Microbiol Rev. 1987 Jun;51(2):221-71 PMID: 2439888
  31. Characterization of the ribosomal RNA gene clusters in Halobacterium cutirubrum.
    J Biol Chem. 1985 Jan 25;260(2):899-906 PMID: 2981849
  32. Saturation mutagenesis of the haloarchaeal bop gene promoter: identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity.
    Mol Microbiol. 2000 Jun;36(5):1175-83 PMID: 10844701
  33. Characterization of the deoxyribonucleic acid of various strains of halophilic bacteria.
    J Bacteriol. 1969 Jul;99(1):248-54 PMID: 4979441
  34. Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a counterselectable marker.
    Mol Microbiol. 2000 Feb;35(3):667-76 PMID: 10672188
  35. Archaeal aminoacyl-tRNA synthesis: diversity replaces dogma.
    Genetics. 1999 Aug;152(4):1269-76 PMID: 10430557
  36. Light energy conversion in Halobacterium halobium.
    Microbiol Rev. 1978 Dec;42(4):682-706 PMID: 368557
  37. Structure of the gas vesicle plasmid in Halobacterium halobium: inversion isomers, inverted repeats, and insertion sequences.
    J Bacteriol. 1991 Mar;173(6):1958-64 PMID: 1848217
  38. Saturation mutagenesis of the TATA box and upstream activator sequence in the haloarchaeal bop gene promoter.
    J Bacteriol. 1999 Apr;181(8):2513-8 PMID: 10198017
  39. An unusual class I (Schiff base) fructose-1,6-bisphosphate aldolase from the halophilic archaebacterium Haloarcula vallismortis.
    Eur J Biochem. 1991 Jan 30;195(2):343-50 PMID: 1900049
  40. Improved microbial gene identification with GLIMMER.
    Nucleic Acids Res. 1999 Dec 1;27(23):4636-41 PMID: 10556321
  41. Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit.
    Nature. 1999 Aug 26;400(6747):841-7 PMID: 10476961
  42. Retinylidene proteins: structures and functions from archaea to humans.
    Annu Rev Cell Dev Biol. 2000;16:365-92 PMID: 11031241
  43. An archaeal genomic signature.
    Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3304-8 PMID: 10716711
  44. Homologs of small nucleolar RNAs in Archaea.
    Science. 2000 Apr 21;288(5465):517-22 PMID: 10775111
  45. Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster.
    J Bacteriol. 1996 Aug;178(16):4942-7 PMID: 8759859
  46. Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene.
    Nucleic Acids Res. 1992 Oct 11;20(19):5047-52 PMID: 1408820
  47. Recent developments in the molecular biology of extremely halophilic bacteria.
    CRC Crit Rev Microbiol. 1978;6(2):151-205 PMID: 365457
  48. An improved synthetic growth medium for Halobacterium cutirubrum.
    Can J Microbiol. 1976 Mar;22(3):440-2 PMID: 3277
  49. Alternative routes of carbohydrate metabolism in halophilic archaebacteria.
    Indian J Biochem Biophys. 1988 Dec;25(6):674-86 PMID: 3255682
  50. Protective roles of bacterioruberin and intracellular KCl in the resistance of Halobacterium salinarium against DNA-damaging agents.
    J Radiat Res. 1998 Dec;39(4):251-62 PMID: 10196780
  51. Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae.
    J Mol Biol. 1989 Mar 5;206(1):1-17 PMID: 2495365
  52. Electron crystallography of bacteriorhodopsin with millisecond time resolution.
    J Struct Biol. 1999 Dec 1;128(1):19-25 PMID: 10600554
  53. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification.
    Nature. 1988 Nov 10;336(6195):179-81 PMID: 3054566
  54. The presence of two species of DNA in some halobacteria.
    J Mol Biol. 1963 Jan;6:34-8 PMID: 13964964
  55. Biology of halophilic bacteria, Part II. Membrane lipids of extreme halophiles: biosynthesis, function and evolutionary significance.
    Experientia. 1993 Dec 15;49(12):1027-36 PMID: 8270029
  56. Cartography of ribosomal proteins of the 30S subunit from the halophilic Haloarcula marismortui and complete sequence analysis of protein HS26.
    Eur J Biochem. 1995 Nov 15;234(1):24-31 PMID: 8529646
  57. Metabolism of methanogens.
    Antonie Van Leeuwenhoek. 1994;66(1-3):187-208 PMID: 7747931
  58. Nus A is involved in transcriptional termination on lambda tI.
    Biochimie. 1999 Jul;81(7):757-64 PMID: 10492023
  59. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?
    Genome Res. 1998 Nov;8(11):1131-41 PMID: 9847077
  60. Cryptochromes: blue light receptors for plants and animals.
    Science. 1999 Apr 30;284(5415):760-5 PMID: 10221900
  61. Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.
    Science. 1999 Oct 8;286(5438):255-61 PMID: 10514362
  62. The Pfam protein families database.
    Nucleic Acids Res. 2000 Jan 1;28(1):263-6 PMID: 10592242
  63. The Tat protein export pathway.
    Mol Microbiol. 2000 Jan;35(2):260-74 PMID: 10652088
  64. Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
    Genome Res. 1998 Mar;8(3):175-85 PMID: 9521921
  65. 2-Oxoacid dehydrogenase multienzyme complexes in the halophilic Archaea? Gene sequences and protein structural predictions.
    Microbiology. 2000 May;146 ( Pt 5):1061-9 PMID: 10832633
  66. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  67. Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic Archaea.
    Adv Protein Chem. 1996;48:101-80 PMID: 8791625
  68. recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae.
    Nucleic Acids Res. 1996 Jun 1;24(11):2125-32 PMID: 8668545
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.190337797
Published
2000-10-24
Pages
12176-81
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC17314
Subset
IM
Databases
GENBANK
AE004437, AE004438, AE016485
External Links
PubMed source DOI: 10.1073/pnas.190337797 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2