Home LiteratureArticle Details
PMID: 17350933 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C.

Archaea (Vancouver, B.C.) ·Vol. 2 ·No. 2 ·2007-05-00 ·Pages 127-35

Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP

Abstract

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific to H. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Two cdc6 genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H(2)S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-type cas gene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.

MeSH Terms
Carbon/metabolism DNA Repair DNA Replication Fermentation Genes, Archaeal Genome, Archaeal Hot Temperature Molecular Sequence Data Oxidation-Reduction Peptides/metabolism Phylogeny Protein Biosynthesis Pyrodictiaceae/classification,genetics,growth & development,metabolism Sequence Analysis, DNA Sulfur/metabolism Transcription, Genetic
Chemicals
Peptides Sulfur Carbon
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Brügger Kim
Danish Archaea Centre, Institute of Molecular Biology, Copenhagen University, Sølvgade 83H, 1307 Copenhagen K, Denmark.
Chen Lanming
Stark Markus
Zibat Arne
Redder Peter
Ruepp Andreas
Awayez Mariana
She Qunxin
Garrett Roger A
Klenk Hans-Peter
References (61)
61 references, click to expand
  1. Identification of genes that are associated with DNA repeats in prokaryotes.
    Mol Microbiol. 2002 Mar;43(6):1565-75 PMID: 11952905
  2. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
    J Mol Biol. 2001 Jan 19;305(3):567-80 PMID: 11152613
  3. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus.
    Mol Microbiol. 2005 Jan;55(2):469-81 PMID: 15659164
  4. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
    Nucleic Acids Res. 2002 Jan 15;30(2):482-96 PMID: 11788711
  5. Consed: a graphical tool for sequence finishing.
    Genome Res. 1998 Mar;8(3):195-202 PMID: 9521923
  6. The Sulfolobus database.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D413-5 PMID: 17088281
  7. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.
    Genome Res. 2004 Nov;14(11):2221-34 PMID: 15520287
  8. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes.
    J Bacteriol. 2003 Apr;185(8):2410-7 PMID: 12670964
  9. Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease.
    Biochem Biophys Res Commun. 2006 Aug 4;346(3):1024-32 PMID: 16781672
  10. Divergent transcriptional and translational signals in Archaea.
    Environ Microbiol. 2005 Jan;7(1):47-54 PMID: 15643935
  11. Identification of replication origins in archaeal genomes based on the Z-curve method.
    Archaea. 2005 May;1(5):335-46 PMID: 15876567
  12. History of discovery of the first hyperthermophiles.
    Extremophiles. 2006 Oct;10(5):357-62 PMID: 16941067
  13. Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination.
    Proc Natl Acad Sci U S A. 2004 May 4;101(18):7046-51 PMID: 15107501
  14. EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance.
    BMC Bioinformatics. 2003 Jun 3;4:21 PMID: 12783628
  15. Viruses of hyperthermophilic Crenarchaea.
    Trends Microbiol. 2005 Nov;13(11):535-42 PMID: 16154357
  16. A putative viral defence mechanism in archaeal cells.
    Archaea. 2006 Aug;2(1):59-72 PMID: 16877322
  17. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications.
    RNA. 2003 Dec;9(12):1516-31 PMID: 14624007
  18. The ald gene, encoding a coenzyme A-acylating aldehyde dehydrogenase, distinguishes Clostridium beijerinckii and two other solvent-producing clostridia from Clostridium acetobutylicum.
    Appl Environ Microbiol. 1999 Nov;65(11):4973-80 PMID: 10543811
  19. Purification and properties of an extremely thermostable membrane-bound sulfur-reducing complex from the hyperthermophilic Pyrodictium abyssi.
    Eur J Biochem. 1998 Mar 15;252(3):486-91 PMID: 9546664
  20. Base-calling of automated sequencer traces using phred. II. Error probabilities.
    Genome Res. 1998 Mar;8(3):186-94 PMID: 9521922
  21. GenBank.
    Nucleic Acids Res. 2003 Jan 1;31(1):23-7 PMID: 12519940
  22. Improved prediction of signal peptides: SignalP 3.0.
    J Mol Biol. 2004 Jul 16;340(4):783-95 PMID: 15223320
  23. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action.
    Biol Direct. 2006 Mar 16;1:7 PMID: 16545108
  24. 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
  25. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus.
    Cell. 2004 Jan 9;116(1):25-38 PMID: 14718164
  26. Membrane-bound hydrogenase and sulfur reductase of the hyperthermophilic and acidophilic archaeon Acidianus ambivalens.
    Microbiology. 2003 Sep;149(Pt 9):2357-71 PMID: 12949162
  27. An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum.
    Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2547-50 PMID: 8460170
  28. Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications.
    J Mol Microbiol Biotechnol. 2006;11(3-5):167-91 PMID: 16983194
  29. Prokaryotes that grow optimally in acid have purine-poor codons in long open reading frames.
    Extremophiles. 2007 Jan;11(1):9-18 PMID: 16957882
  30. The RNA Modification Database: 1999 update.
    Nucleic Acids Res. 1999 Jan 1;27(1):196-7 PMID: 9847178
  31. Characterization of an 8-oxoguanine DNA glycosylase from Methanococcus jannaschii.
    J Biol Chem. 1999 Oct 22;274(43):30447-50 PMID: 10521423
  32. The COG database: new developments in phylogenetic classification of proteins from complete genomes.
    Nucleic Acids Res. 2001 Jan 1;29(1):22-8 PMID: 11125040
  33. Identification of an archaeal alpha-L-fucosidase encoded by an interrupted gene. Production of a functional enzyme by mutations mimicking programmed -1 frameshifting.
    J Biol Chem. 2003 Apr 25;278(17):14622-31 PMID: 12569098
  34. The complete genome of the crenarchaeon Sulfolobus solfataricus P2.
    Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7835-40 PMID: 11427726
  35. Archaeal integrases and mechanisms of gene capture.
    Biochem Soc Trans. 2004 Apr;32(Pt 2):222-6 PMID: 15046576
  36. Initiator tRNAs from archaebacteria show common unique sequence characteristics.
    Nature. 1982 Aug 12;298(5875):684-5 PMID: 6178978
  37. Introns in protein-coding genes in Archaea.
    FEBS Lett. 2002 Jan 2;510(1-2):27-30 PMID: 11755525
  38. MUTAGEN: multi-user tool for annotating genomes.
    Bioinformatics. 2003 Dec 12;19(18):2480-1 PMID: 14668237
  39. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.
    DNA Res. 1999 Apr 30;6(2):83-101, 145-52 PMID: 10382966
  40. Genomic comparison of archaeal conjugative plasmids from Sulfolobus.
    Archaea. 2004 Oct;1(4):231-9 PMID: 15810432
  41. Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron- cells of Sulfolobus acidocaldarius.
    Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12285-9 PMID: 8618886
  42. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.
    Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):984-9 PMID: 11792869
  43. Mobile elements in archaeal genomes.
    FEMS Microbiol Lett. 2002 Jan 10;206(2):131-41 PMID: 11814653
  44. Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization.
    Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):8933-8 PMID: 15937113
  45. Portraits of a Y-family DNA polymerase.
    FEBS Lett. 2005 Feb 7;579(4):868-72 PMID: 15680965
  46. In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin.
    Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11152-7 PMID: 11562464
  47. InBase: the Intein Database.
    Nucleic Acids Res. 2002 Jan 1;30(1):383-4 PMID: 11752343
  48. Non-autonomous mobile elements in the crenarchaeon Sulfolobus solfataricus.
    J Mol Biol. 2001 Feb 9;306(1):1-6 PMID: 11178888
  49. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.
    Brief Bioinform. 2004 Jun;5(2):150-63 PMID: 15260895
  50. Structural and genomic correlates of hyperthermostability.
    J Biol Chem. 2000 Oct 20;275(42):32383-6 PMID: 10940293
  51. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements.
    J Mol Evol. 2005 Feb;60(2):174-82 PMID: 15791728
  52. Functional reconstitution of a crenarchaeal splicing endonuclease in vitro.
    Biochem Biophys Res Commun. 2005 Sep 9;334(4):1254-9 PMID: 16039609
  53. Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus.
    Proc Natl Acad Sci U S A. 2002 May 28;99(11):7536-41 PMID: 12032318
  54. The Pfam protein families database.
    Nucleic Acids Res. 2002 Jan 1;30(1):276-80 PMID: 11752314
  55. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.
    PLoS Comput Biol. 2005 Nov;1(6):e60 PMID: 16292354
  56. Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides.
    J Bacteriol. 1990 Jul;172(7):3959-65 PMID: 2113915
  57. Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
    Genome Res. 1998 Mar;8(3):175-85 PMID: 9521921
  58. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota.
    J Bacteriol. 2005 Jul;187(14):4992-9 PMID: 15995215
  59. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
    Nucleic Acids Res. 2003 Jan 1;31(1):365-70 PMID: 12520024
  60. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves.
    Nature. 2005 Feb 3;433(7025):537-41 PMID: 15690044
  61. Genetic elements in the extremely thermophilic archaeon Sulfolobus.
    Extremophiles. 1998 Aug;2(3):131-40 PMID: 9783157
Article Info
Journal
Archaea (Vancouver, B.C.)
Abbr.
Archaea
ISSN
1472-3646
DOI
10.1155/2007/745987
Published
2007-05-00
Pages
127-35
Language
English
Region
United States
NLM ID
101142614
PMCID
PMC2686385
Subset
IM
Databases
GENBANK
CP000493
External Links
PubMed source DOI: 10.1155/2007/745987 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