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  • 1
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    Complete genome sequence of Neisseria meningitidis serogroup B strain MC58 (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-10
    Description: The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tettelin, H -- Saunders, N J -- Heidelberg, J -- Jeffries, A C -- Nelson, K E -- Eisen, J A -- Ketchum, K A -- Hood, D W -- Peden, J F -- Dodson, R J -- Nelson, W C -- Gwinn, M L -- DeBoy, R -- Peterson, J D -- Hickey, E K -- Haft, D H -- Salzberg, S L -- White, O -- Fleischmann, R D -- Dougherty, B A -- Mason, T -- Ciecko, A -- Parksey, D S -- Blair, E -- Cittone, H -- Clark, E B -- Cotton, M D -- Utterback, T R -- Khouri, H -- Qin, H -- Vamathevan, J -- Gill, J -- Scarlato, V -- Masignani, V -- Pizza, M -- Grandi, G -- Sun, L -- Smith, H O -- Fraser, C M -- Moxon, E R -- Rappuoli, R -- Venter, J C -- New York, N.Y. -- Science. 2000 Mar 10;287(5459):1809-15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10710307" target="_blank"〉PubMed〈/a〉
    Keywords: Antigenic Variation ; Antigens, Bacterial/immunology ; Bacteremia/microbiology ; Bacterial Capsules/genetics ; Bacterial Proteins/genetics/physiology ; DNA Transposable Elements ; Evolution, Molecular ; Fimbriae, Bacterial/genetics ; *Genome, Bacterial ; Humans ; Meningitis, Meningococcal/microbiology ; Meningococcal Infections/microbiology ; Molecular Sequence Data ; Mutation ; Neisseria meningitidis/classification/*genetics/*pathogenicity/physiology ; Open Reading Frames ; Operon ; Phylogeny ; Recombination, Genetic ; *Sequence Analysis, DNA ; Serotyping ; Transformation, Bacterial ; Virulence/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Complete genome sequence of a virulent isolate of Streptococcus pneumoniae (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-21
    Description: The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tettelin, H -- Nelson, K E -- Paulsen, I T -- Eisen, J A -- Read, T D -- Peterson, S -- Heidelberg, J -- DeBoy, R T -- Haft, D H -- Dodson, R J -- Durkin, A S -- Gwinn, M -- Kolonay, J F -- Nelson, W C -- Peterson, J D -- Umayam, L A -- White, O -- Salzberg, S L -- Lewis, M R -- Radune, D -- Holtzapple, E -- Khouri, H -- Wolf, A M -- Utterback, T R -- Hansen, C L -- McDonald, L A -- Feldblyum, T V -- Angiuoli, S -- Dickinson, T -- Hickey, E K -- Holt, I E -- Loftus, B J -- Yang, F -- Smith, H O -- Venter, J C -- Dougherty, B A -- Morrison, D A -- Hollingshead, S K -- Fraser, C M -- R01 AI40645-01A1/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Jul 20;293(5529):498-506.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11463916" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Bacterial ; Bacterial Proteins/chemistry/genetics/immunology/metabolism ; Bacterial Vaccines ; Base Composition ; Carbohydrate Metabolism ; Carrier Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Computational Biology ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Gene Duplication ; Genes, Bacterial ; *Genome, Bacterial ; Hexosamines/metabolism ; Oligonucleotide Array Sequence Analysis ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Species Specificity ; Streptococcus pneumoniae/*genetics/immunology/metabolism/*pathogenicity ; Virulence ; rRNA Operon
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Genome transplantation in bacteria: changing one species to another (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-30
    Description: As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Intact genomic DNA from Mycoplasma mycoides large colony (LC), virtually free of protein, was transplanted into Mycoplasma capricolum cells by polyethylene glycol-mediated transformation. Cells selected for tetracycline resistance, carried by the M. mycoides LC chromosome, contain the complete donor genome and are free of detectable recipient genomic sequences. These cells that result from genome transplantation are phenotypically identical to the M. mycoides LC donor strain as judged by several criteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lartigue, Carole -- Glass, John I -- Alperovich, Nina -- Pieper, Rembert -- Parmar, Prashanth P -- Hutchison, Clyde A 3rd -- Smith, Hamilton O -- Venter, J Craig -- New York, N.Y. -- Science. 2007 Aug 3;317(5838):632-8. Epub 2007 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Craig Venter Institute, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600181" target="_blank"〉PubMed〈/a〉
    Keywords: Acetate Kinase/chemistry/genetics ; Amino Acid Sequence ; DNA, Bacterial/*genetics/isolation & purification ; *Genome, Bacterial ; Genotype ; Molecular Sequence Data ; Mycoplasma/chemistry/*genetics ; Mycoplasma mycoides/chemistry/*genetics ; Phenotype ; Polyethylene Glycols ; Proteome/analysis ; Recombination, Genetic ; Sequence Analysis, DNA ; *Transformation, Bacterial
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-26
    Description: We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibson, Daniel G -- Benders, Gwynedd A -- Andrews-Pfannkoch, Cynthia -- Denisova, Evgeniya A -- Baden-Tillson, Holly -- Zaveri, Jayshree -- Stockwell, Timothy B -- Brownley, Anushka -- Thomas, David W -- Algire, Mikkel A -- Merryman, Chuck -- Young, Lei -- Noskov, Vladimir N -- Glass, John I -- Venter, J Craig -- Hutchison, Clyde A 3rd -- Smith, Hamilton O -- New York, N.Y. -- Science. 2008 Feb 29;319(5867):1215-20. doi: 10.1126/science.1151721. Epub 2008 Jan 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Craig Venter Institute, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218864" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chromosomes, Artificial, Bacterial ; Chromosomes, Artificial, Yeast ; *Cloning, Molecular ; DNA, Bacterial/*chemical synthesis ; DNA, Recombinant ; Escherichia coli/genetics ; Genetic Vectors ; *Genome, Bacterial ; Genomics/*methods ; Mycoplasma genitalium/*genetics ; Oligodeoxyribonucleotides/chemical synthesis ; Plasmids ; Recombination, Genetic ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; Transformation, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Complete genome sequence of Treponema pallidum, the syphilis spirochete (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-17
    Description: The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fraser, C M -- Norris, S J -- Weinstock, G M -- White, O -- Sutton, G G -- Dodson, R -- Gwinn, M -- Hickey, E K -- Clayton, R -- Ketchum, K A -- Sodergren, E -- Hardham, J M -- McLeod, M P -- Salzberg, S -- Peterson, J -- Khalak, H -- Richardson, D -- Howell, J K -- Chidambaram, M -- Utterback, T -- McDonald, L -- Artiach, P -- Bowman, C -- Cotton, M D -- Fujii, C -- Garland, S -- Hatch, B -- Horst, K -- Roberts, K -- Sandusky, M -- Weidman, J -- Smith, H O -- Venter, J C -- AI31068/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 17;281(5375):375-88.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, Rockville, MD 20850, USA. tpdb@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9665876" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; Base Sequence ; Borrelia burgdorferi Group/genetics ; Carrier Proteins/genetics/metabolism ; DNA Repair/genetics ; DNA Replication/genetics ; DNA Restriction Enzymes/genetics ; Energy Metabolism/genetics ; Genes, Bacterial ; Genes, Regulator ; *Genome, Bacterial ; Heat-Shock Response/genetics ; Lipoproteins/genetics ; Membrane Proteins/genetics ; Molecular Sequence Data ; Movement ; Open Reading Frames ; Oxygen Consumption/genetics ; Protein Biosynthesis ; Recombination, Genetic ; Replication Origin ; *Sequence Analysis, DNA ; Transcription, Genetic ; Treponema pallidum/*genetics/metabolism/pathogenicity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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