Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii

American Association for the Advancement of Science (AAAS) - Tập 273 Số 5278 - Trang 1058-1073 - 1996
Carol J. Bult1, Owen White1, Gary J. Olsen1, Lixin Zhou1, Robert Fleischmann1, Granger G. Sutton1, Judith A. Blake1, Lisa M. Fitzgerald1, Rebecca A. Clayton1, Jeannine D. Gocayne1, Anthony R. Kerlavage1, Brian Dougherty1, Jean-François Tomb1, Mark D. Adams1, Claudia I. Reich1, Ross Overbeek2, Ewen F. Kirkness1, Keith G. Weinstock1, Joseph M. Merrick3, Anna Glodek1, John Scott1, Neil S. Geoghagen1, Janice Weidman1, Joyce L. Fuhrmann1, D.-T. Nguyen1, Teresa R. Utterback1, Jenny M. Kelley1, Jeremy Peterson1, Paul W. Sadow1, Michael C. Hanna1, Matthew Cotton1, Kevin Roberts1, Margaret A. Hurst1, Brian P. Kaine1, Mark Borodovsky4, Hans‐Peter Klenk1, Claire M. Fraser1, Hamilton O. Smith5, Carl R. Woese1, J. Craig Venter1
1G. J. Olsen, C. I. Reich, B. P. Kaine, and C. R. Woese are in the Microbiology Department, University of Illinois, Champaign-Urbana, IL 61801, USA.
2R. Overbeek is with the Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL 60439, USA.
3J. M. Merrick is in the Department of Microbiology, State University of New York, Buffalo, NY 14214, USA.
4M. Borodovsky is with the School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
5H. O. Smith is in the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. All other authors are with The Institute for Genomic Research (TIGR), Rockville, MD 20850, USA.

Tóm tắt

The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii , and its 58- and 16-kilobase pair extrachromosomal elements have been determined by whole-genome random sequencing. A total of 1738 predicted protein-coding genes were identified; however, only a minority of these (38 percent) could be assigned a putative cellular role with high confidence. Although the majority of genes related to energy production, cell division, and metabolism in M. jannaschii are most similar to those found in Bacteria, most of the genes involved in transcription, translation, and replication in M. jannaschii are more similar to those found in Eukaryotes. The Methanococcus jannaschii Genome Database

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Tài liệu tham khảo

ADAMS M.D., INITIAL ASSESSMENT OF HUMAN GENE DIVERSITY AND EXPRESSION PATTERNS BASED UPON 83-MILLION NUCLEOTIDES OF CDNA SEQUENCE, NATURE 377, 3 (1995).

BELAY N, DINITROGEN FIXATION BY A THERMOPHILIC METHANOGENIC BACTERIUM, NATURE 312, 286 (1984).

BERNAD A, STRUCTURAL AND FUNCTIONAL-RELATIONSHIPS BETWEEN PROKARYOTIC AND EUKARYOTIC DNA-POLYMERASES, EMBO JOURNAL 6, 4219 (1987).

BLAAT M, A LEEWENHOEK 66, 187 (1994).

BORODOVSKY M, GENMARK - PARALLEL GENE RECOGNITION FOR BOTH DNA STRANDS, COMPUTERS & CHEMISTRY 17, 123 (1993).

BROWN J.R., ROOT OF THE UNIVERSAL TREE OF LIFE BASED ON ANCIENT AMINOACYL-TRANSFER-RNA SYNTHETASE GENE DUPLICATIONS, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 92, 2441 (1995).

COOPER A.A., PROTEIN SPLICING OF THE YEAST TFP1 INTERVENING PROTEIN-SEQUENCE - A MODEL FOR SELF-EXCISION, EMBO JOURNAL 12, 2575 (1993).

COOPER A.A., PROTEIN SPLICING - SELF-SPLICING OF GENETICALLY MOBILE ELEMENTS AT THE PROTEIN LEVEL, TRENDS IN BIOCHEMICAL SCIENCES 20, 351 (1995).

CULLMANN G, CHARACTERIZATION OF THE 5 REPLICATION FACTOR-C GENES OF SACCHAROMYCES-CEREVISIAE, MOLECULAR AND CELLULAR BIOLOGY 15, 4661 (1995).

DELARUE M, AN ATTEMPT TO UNIFY THE STRUCTURE OF POLYMERASES, PROTEIN ENGINEERING 3, 461 (1990).

DEPOUPLANA R, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 93, 166 (1996).

DIMARCO A.A., UNUSUAL COENZYMES OF METHANOGENESIS, ANNUAL REVIEW OF BIOCHEMISTRY 59, 355 (1990).

EBERHART C.G., THE PELOTA LOCUS ENCODES A PROTEIN REQUIRED FOR MEIOTIC CELL-DIVISION - AN ANALYSIS OF G(2)/M ARREST IN DROSOPHILA SPERMATOGENESIS, DEVELOPMENT 121, 3477 (1995).

FAGUY D.M., MOLECULAR ANALYSIS OF ARCHAEAL FLAGELLINS - SIMILARITY TO THE TYPE-IV PILIN - TRANSPORT SUPERFAMILY WIDESPREAD IN BACTERIA, CANADIAN JOURNAL OF MICROBIOLOGY 40, 67 (1994).

FELSENFELD G, FORMATION OF A 3-STRANDED POLYNUCLEOTIDE MOLECULE, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 79, 2023 (1957).

10.1126/science.7542800

FOX G.E., CLASSIFICATION OF METHANOGENIC BACTERIA BY 16S RIBOSOMAL-RNA CHARACTERIZATION, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 74, 4537 (1977).

10.1126/science.270.5235.397

10.1126/science.270.5242.1667

GOGARTEN J.P., EVOLUTION OF THE VACUOLAR H+-ATPASE - IMPLICATIONS FOR THE ORIGIN OF EUKARYOTES, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 86, 6661 (1989).

HAMILTON P.T., STRUCTURE OF GENES AND AN INSERTION ELEMENT IN THE METHANE PRODUCING ARCHAEBACTERIUM METHANOBREVIBACTER-SMITHII, MOLECULAR & GENERAL GENETICS 200, 47 (1985).

HARTMANN E, URIDINE AND DOLICHYL DIPHOSPHATE ACTIVATED OLIGOSACCHARIDES ARE INTERMEDIATES IN THE BIOSYNTHESIS OF THE S-LAYER GLYCOPROTEIN OF METHANOTHERMUS-FERVIDUS, ARCHIVES OF MICROBIOLOGY 151, 274 (1989).

HENIKOFF S, PROTEIN FAMILY CLASSIFICATION BASED ON SEARCHING A DATABASE OF BLOCKS, GENOMICS 19, 97 (1994).

HIRATA R, MOLECULAR-STRUCTURE OF A GENE, VMA1, ENCODING THE CATALYTIC SUBUNIT OF H+-TRANSLOCATING ADENOSINE-TRIPHOSPHATASE FROM VACUOLAR MEMBRANES OF SACCHAROMYCES-CEREVISIAE, JOURNAL OF BIOLOGICAL CHEMISTRY 265, 6726 (1990).

IWABE N, EVOLUTIONARY RELATIONSHIP OF ARCHAEBACTERIA, EUBACTERIA, AND EUKARYOTES INFERRED FROM PHYLOGENETIC TREES OF DUPLICATED GENES, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 86, 9355 (1989).

JIANG X.M., STRUCTURE AND SEQUENCE OF THE RFB (O-ANTIGEN) GENE-CLUSTER OF SALMONELLA SEROVAR TYPHIMURIUM (STRAIN-LT2), MOLECULAR MICROBIOLOGY 5, 695 (1991).

JONES W.J., METHANOCOCCUS-JANNASCHII SP-NOV, AN EXTREMELY THERMOPHILIC METHANOGEN FROM A SUBMARINE HYDROTHERMAL VENT, ARCHIVES OF MICROBIOLOGY 136, 254 (1983).

KAINE B.P., ISOLATION AND CHARACTERIZATION OF THE 7S RNA GENE FROM METHANOCOCCUS-VOLTAE, JOURNAL OF BACTERIOLOGY 171, 4261 (1989).

KALMOKOFF M.L., RELATEDNESS OF THE FLAGELLINS FROM METHANOGENS, ARCHIVES OF MICROBIOLOGY 157, 481 (1992).

10.1126/science.2146742

KEELING P, IN PRESS SYST APPL M .

KLENK H.P., EVOLUTION - ARCHAEA AND EUKARYOTES VERSUS BACTERIA, CURRENT BIOLOGY 4, 920 (1994).

KOPKE AKE, COMPARATIVE STUDIES OF RIBOSOMAL-PROTEINS AND THEIR GENES FROM METHANOCOCCUS-VANNIELII AND OTHER ORGANISMS, CANADIAN JOURNAL OF MICROBIOLOGY 35, 11 (1989).

KYTE J, A SIMPLE METHOD FOR DISPLAYING THE HYDROPATHIC CHARACTER OF A PROTEIN, JOURNAL OF MOLECULAR BIOLOGY 157, 105 (1982).

LANGER D, TRANSCRIPTION IN ARCHAEA - SIMILARITY TO THAT IN EUCARYA, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 92, 5768 (1995).

LANZENDORFER M, STRUCTURE AND FUNCTION OF THE DNA-DEPENDENT RNA-POLYMERASE OF SULFOLOBUS, SYSTEMATIC AND APPLIED MICROBIOLOGY 16, 656 (1994).

LECHNER K, ORGANIZATION AND NUCLEOTIDE-SEQUENCE OF A TRANSCRIPTIONAL UNIT OF METHANOCOCCUS-VANNIELII COMPRISING GENES FOR PROTEIN-SYNTHESIS ELONGATION-FACTORS AND RIBOSOMAL-PROTEINS, JOURNAL OF MOLECULAR EVOLUTION 29, 20 (1989).

LETAI A.G., SPECIFICITY IN FORMATION OF TRIPLE-STRANDED NUCLEIC-ACID HELICAL COMPLEXES - STUDIES WITH AGAROSE-LINKED POLYRIBONUCLEOTIDE AFFINITY COLUMNS, BIOCHEMISTRY 27, 9108 (1988).

LOGAN D.T., CRYSTAL-STRUCTURE OF GLYCYL-TRANSFER-RNA SYNTHETASE FROM THERMUS-THERMOPHILUS, EMBO JOURNAL 14, 4156 (1995).

LUTKENHAUS J, CURR OPIN GENE DEV 3, 783 (1993).

MARTIN N, ISOACCEPTING MITOCHONDRIAL GLUTAMYL-TRNA SPECIES TRANSCRIBED FROM DIFFERENT REGIONS OF MITOCHONDRIAL GENOME OF SACCHAROMYCES-CEREVISIAE, JOURNAL OF MOLECULAR BIOLOGY 101, 285 (1976).

MARTIN N.C., YEAST MITOCHONDRIAL-DNA SPECIFIES TRANSFER-RNA FOR 19 AMINO-ACIDS - DELETION MAPPING OF TRANSFER-RNA GENES, BIOCHEMISTRY 16, 4672 (1977).

MICHEL F, COMPARISON OF FUNGAL MITOCHONDRIAL INTRONS REVEALS EXTENSIVE HOMOLOGIES IN RNA SECONDARY STRUCTURE, BIOCHIMIE 64, 867 (1982).

MOJICA FJM, LONG STRETCHES OF SHORT TANDEM REPEATS ARE PRESENT IN THE LARGEST REPLICONS OF THE ARCHAEA HALOFERAX-MEDITERRANEI AND HALOFERAX-VOLCANII AND COULD BE INVOLVED IN REPLICON PARTITIONING, MOLECULAR MICROBIOLOGY 17, 85 (1995).

PERLER F.B., INTERVENING SEQUENCES IN AN ARCHAEA DNA-POLYMERASE GENE, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 89, 5577 (1992).

PIETROKOVSKI S, CONSERVED SEQUENCE FEATURES OF INTEINS (PROTEIN INTRONS) AND THEIR USE IN IDENTIFYING NEW INTEINS AND RELATED PROTEINS, PROTEIN SCIENCE 3, 2340 (1994).

PORITZ M.A., HUMAN SRP RNA AND ESCHERICHIA-COLI 4.5S RNA CONTAIN A HIGHLY HOMOLOGOUS STRUCTURAL DOMAIN, CELL 55, 4 (1988).

RILEY M, FUNCTIONS OF THE GENE-PRODUCTS OF ESCHERICHIA-COLI, MICROBIOLOGICAL REVIEWS 57, 862 (1993).

ROTHFIELD L.I., How do bacteria decide where to divide?CELL 84, 183 (1996).

SANDMAN K, HMF, A DNA-BINDING PROTEIN ISOLATED FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS-FERVIDUS, IS MOST CLOSELY RELATED TO HISTONES, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 87, 5788 (1990).

SCHON A, MISAMINOACYLATION AND TRANSAMIDATION ARE REQUIRED FOR PROTEIN-BIOSYNTHESIS IN LACTOBACILLUS-BULGARICUS, BIOCHIMIE 70, 391 (1988).

SOLL D, TRNA STRUCTURE BIOSY (1995).

10.1089/gst.1995.1.9

UEMORI T, THE HYPERTHERMOPHILIC ARCHAEON PYRODICTIUM-OCCULTUM HAS 2 ALPHA-LIKE DNA-POLYMERASES, JOURNAL OF BACTERIOLOGY 177, 2164 (1995).

WAGNER E.A., J BACTERIOL 177, 5179 (1995).

WALLACE J.C., PATMAT - A SEARCHING AND EXTRACTION PROGRAM FOR SEQUENCE, PATTERN AND BLOCK QUERIES AND DATABASES, COMPUTER APPLICATIONS IN THE BIOSCIENCES 8, 249 (1992).

WHITBREAD L.A., CDC54 BELONGS TO THE CDC46/MCM3 FAMILY OF PROTEINS WHICH ARE ESSENTIAL FOR INITIATION OF EUKARYOTIC DNA-REPLICATION, GENE 155, 113 (1995).

WILCOX M, GAMMA-GLUTAMYL PHOSPHATE ATTACHED TO GLUTAMINE-SPECIFIC TRNA - A PRECURSOR OF GLUTAMINYL-TRNA IN BACILLUS-SUBTILIS, EUROPEAN JOURNAL OF BIOCHEMISTRY 11, 405 (1969).

10.1126/science.272.5261.481

WILSON R, 2.2 MB OF CONTIGUOUS NUCLEOTIDE-SEQUENCE FROM CHROMOSOME-III OF C-ELEGANS, NATURE 368, 32 (1994).

WOESE C.R., BACTERIA 8, (1985).

WOESE C.R., PHYLOGENETIC STRUCTURE OF PROKARYOTIC DOMAIN - PRIMARY KINGDOMS, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 74, 5088 (1977).

WOESE C.R., TOWARDS A NATURAL SYSTEM OF ORGANISMS - PROPOSAL FOR THE DOMAINS ARCHAEA, BACTERIA, AND EUCARYA, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 87, 4576 (1990).

WOOD H.G., THE ACETYL-COA PATHWAY - A NEWLY DISCOVERED PATHWAY OF AUTOTROPHIC GROWTH, TRENDS IN BIOCHEMICAL SCIENCES 11, 14 (1986).

XU M.Q., IN-VITRO PROTEIN SPLICING OF PURIFIED PRECURSOR AND THE IDENTIFICATION OF A BRANCHED INTERMEDIATE, CELL 75, 1371 (1993).

ZHAO H, AN EXTREMELY THERMOPHILIC METHANOCOCCUS FROM A DEEP-SEA HYDROTHERMAL VENT AND ITS PLASMID, ARCHIVES OF MICROBIOLOGY 150, 178 (1988).

ZILLIG W, DID EUKARYOTES ORIGINATE BY A FUSION EVENT, ENDOCYTOBIOSIS AND CELL RESEARCH 6, 1 (1989).