RESUMO
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.
Assuntos
Genoma Bacteriano , Análise de Sequência de DNA , Treponema pallidum/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sequência de Bases , Grupo Borrelia Burgdorferi/genética , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Reparo do DNA/genética , Replicação do DNA/genética , Enzimas de Restrição do DNA/genética , Metabolismo Energético/genética , Genes Bacterianos , Genes Reguladores , Resposta ao Choque Térmico/genética , Lipoproteínas/genética , Proteínas de Membrana/genética , Dados de Sequência Molecular , Movimento , Fases de Leitura Aberta , Consumo de Oxigênio/genética , Biossíntese de Proteínas , Recombinação Genética , Origem de Replicação , Transcrição Gênica , Treponema pallidum/metabolismo , Treponema pallidum/patogenicidadeRESUMO
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.
Assuntos
Genoma Bacteriano , Análise de Sequência de DNA , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/patogenicidade , Antígenos de Bactérias , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/imunologia , Proteínas de Bactérias/metabolismo , Vacinas Bacterianas , Composição de Bases , Metabolismo dos Carboidratos , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Cromossomos Bacterianos/genética , Biologia Computacional , Elementos de DNA Transponíveis , DNA Bacteriano/química , DNA Bacteriano/genética , Duplicação Gênica , Genes Bacterianos , Hexosaminas/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos , Recombinação Genética , Sequências Repetitivas de Ácido Nucleico , Especificidade da Espécie , Streptococcus pneumoniae/imunologia , Streptococcus pneumoniae/metabolismo , Virulência , Óperon de RNArRESUMO
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.
Assuntos
Genoma Bacteriano , Neisseria meningitidis/genética , Neisseria meningitidis/patogenicidade , Análise de Sequência de DNA , Variação Antigênica , Antígenos de Bactérias/imunologia , Bacteriemia/microbiologia , Cápsulas Bacterianas/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/fisiologia , Elementos de DNA Transponíveis , Evolução Molecular , Fímbrias Bacterianas/genética , Humanos , Meningite Meningocócica/microbiologia , Infecções Meningocócicas/microbiologia , Dados de Sequência Molecular , Mutação , Neisseria meningitidis/classificação , Neisseria meningitidis/fisiologia , Fases de Leitura Aberta , Óperon , Filogenia , Recombinação Genética , Sorotipagem , Transformação Bacteriana , Virulência/genéticaRESUMO
The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.
Assuntos
Genoma Bacteriano , Cocos Gram-Positivos/genética , Mapeamento Físico do Cromossomo , Análise de Sequência de DNA , Proteínas de Bactérias/biossíntese , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Catalase/genética , Cromossomos Bacterianos/genética , Dano ao DNA , Reparo do DNA/genética , DNA Bacteriano/genética , Metabolismo Energético , Genes Bacterianos , Cocos Gram-Positivos/química , Cocos Gram-Positivos/classificação , Cocos Gram-Positivos/efeitos da radiação , Dados de Sequência Molecular , Fases de Leitura Aberta , Estresse Oxidativo , Plasmídeos , Tolerância a Radiação , Sequências Repetitivas de Ácido Nucleico , Superóxido Dismutase/genética , Thermus/química , Thermus/genética , Raios UltravioletaRESUMO
One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.
Assuntos
Bactérias/genética , Bases de Dados Factuais , Genes Bacterianos/genética , Genoma Bacteriano , Serviços de Informação , InternetRESUMO
The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun strategy. The MoPn genome exhibited a general conservation of gene order and content with the previously sequenced C.trachomatis serovar D. Differences between C.trachomatis strains were focused on an approximately 50 kb 'plasticity zone' near the termination origins. In this region MoPn contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a predicted toxin from Escherichia coli O157:H7 but had apparently lost the tryptophan biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was >99.9% identical to the previously sequenced C.pneumoniae CWL029 genome, however, comparative analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in different orientations in the two genomes. AR39 also contained a novel 4524 nt circular single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C. pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing differences in key nucleotide salvage pathways: C.pneumoniae has a uridine kinase gene for dUTP production, MoPn has a uracil phosphororibosyl transferase, while C.trachomatis serovar D contains neither gene. Chromosomal comparison revealed that there had been multiple large inversion events since the species divergence of C.trachomatis and C.pneumoniae, apparently oriented around the axis of the origin of replication and the termination region. The striking synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological isolation of the obligate intracellular parasites. In the absence of genetic analysis, comparative genomics will continue to provide insight into the virulence mechanisms of these important human pathogens.
Assuntos
Chlamydia trachomatis/genética , Chlamydophila pneumoniae/genética , Genoma Bacteriano , Animais , Proteínas de Bactérias/genética , Bacteriófagos/genética , Sequência de Bases , Infecções por Chlamydia/microbiologia , Chlamydia trachomatis/enzimologia , Chlamydia trachomatis/metabolismo , Chlamydia trachomatis/patogenicidade , Chlamydophila pneumoniae/enzimologia , Chlamydophila pneumoniae/patogenicidade , Chlamydophila pneumoniae/virologia , Inversão Cromossômica , Sequência Conservada/genética , Evolução Molecular , Genes Bacterianos/genética , Genes Duplicados/genética , Humanos , Camundongos/microbiologia , Dados de Sequência Molecular , Nucleotídeos/metabolismo , Mapeamento Físico do Cromossomo , Recombinação Genética/genética , Origem de Replicação/genéticaRESUMO
Iron is required for the intracellular and extracellular growth of Legionella pneumophila (Lp). In addition, variations in iron levels may serve as a signal for changes in gene expression. In a number of bacterial pathogens, the regulation of gene expression by iron is usually mediated by the Fur (ferric uptake regulation) repressor protein. Through complementation of an Escherichia coli fur mutation and nucleotide sequence analysis, we have cloned and characterized the Lp fur gene. Lp fur encoded a 15.0-kDa protein whose repressive activity was, as expected, highest in bacteria grown in iron-rich media. Computer analysis determined that Lp Fur had an amino-acid identity of over 54% and a similarity of over 72% to the Fur of E. coli, Yersinia pestis, Vibrio species and Pseudomonas aeruginosa. The promoter region of Lp fur contained sequences homologous to the Fur-binding site, suggesting that fur is autoregulated in Lp. Finally, Southern blot hybridizations demonstrated that fur is conserved among Lp strains and Legionella species.
Assuntos
Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Legionella pneumophila/genética , Proteínas Repressoras/genética , Adaptação Fisiológica , Sequência de Aminoácidos , Sequência de Bases , Clonagem Molecular , Sequência Conservada , DNA Bacteriano/genética , Escherichia coli/genética , Ferro/metabolismo , Legionella pneumophila/metabolismo , Dados de Sequência Molecular , Fases de Leitura Aberta , Pseudomonas aeruginosa/genética , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido NucleicoRESUMO
Legionella pneumophila, a parasite of alveolar macrophages, requires iron for intra- and extracellular growth. Although its mechanisms for iron assimilation are poorly understood, this bacterium produces Fur, a protein that can repress gene transcription in response to iron concentration. Because iron- and Fur-regulated genes are important for infection in other bacteria, the identification of similar genes in L. pneumophila was undertaken. A wild-type strain of L. pneumophila was randomly mutated with a mini-Tn10' lacZ transposon, and the resulting gene fusions were tested for iron regulation by assessing beta-galactosidase production in the presence and absence of iron chelators. Of the initial six mutants with iron-repressed lacZ fusions, two strains, NU229 and NU232, possessed fusions that were stably iron regulated. To assay for Fur regulation, the levels of beta-galactosidase were measured in strains no longer producing Fur. As in a number of pathogenic bacteria, L. pneumophila fur could not be insertionally inactivated, but spontaneous Fur- derivatives were generated by selecting for manganese resistance. Strain NU229 contained a Fur-repressed fusion based on derepression of lacZ expression in its manganese-resistant derivative. Extracellular growth of NU229 in bacteriological media was similar to that of wild-type strain 130b. To assess the role of an iron- and Fur-regulated (frgA) gene in intracellular infection, the ability of NU229 to grow within U937 cell monolayers was tested. Quantitative infection assays demonstrated that intracellular growth of NU229 was impaired as much as 80-fold. Reconstruction of the mutant by allelic exchange proved that the infectivity defect in NU229 was due to the inactivation of frgA and not to a second-site mutation. Subsequently, complementation of the interrupted gene by an intact plasmid-encoded gene demonstrated that the infectivity defect was due to the loss of frgA and not to a polar effect. Nucleotide sequence analysis revealed that the 63-kDa FrgA protein has homology with the aerobactin synthetases IucA and IucC of Escherichia coli, raising the possibility that L. pneumophila encodes a siderophore which is required for optimal intracellular replication. Southern hybridization analysis determined that frgA is specific to L. pneumophila.
Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos , Ferro/farmacologia , Legionella pneumophila/genética , Proteínas Repressoras/metabolismo , Sequência de Aminoácidos , Sequência de Bases , Células Cultivadas , Relação Dose-Resposta a Droga , Escherichia coli/enzimologia , Escherichia coli/genética , Teste de Complementação Genética , Humanos , Legionella pneumophila/patogenicidade , Dados de Sequência Molecular , Mutagênese , Oxo-Ácido-Liases/genética , Mapeamento por Restrição , Análise de Sequência de DNA , Homologia de Sequência de AminoácidosRESUMO
The ability to bind and utilize hemin is a trait common to many human pathogens. Nevertheless, the relationship between Legionella pneumophila, the agent of Legionnaires' disease, and hemin has received little attention. Thus, we explored the capacity of a virulent, serogroup 1 strain of L. pneumophila to bind hemin and use it as an iron source. Hemin, but not protoporphyrin IX, restored bacterial growth in iron-limiting media, indicating that it can serve as an iron source for L. pneumophila. In support of this idea, we observed that wildtype legionellae were able to bind 50 to 60% of added hemin, a binding capacity that was comparable to those of other pathogens. To begin to identify proteins involved in hemin acquisition, we identified a Legionella locus that conferred hemin binding upon Escherichia coli. Subcloning and nucleotide sequence analysis determined that a single open reading frame, which was designated hbp for hemin-binding promotion, was responsible for this binding activity. The hbp gene was predicted to encode a secreted, 15.5-kDa protein. To ascertain the importance of this gene in L. pneumophila biology, we used allelic exchange to construct an hbp mutant. Importantly, the mutant displayed a 42% reduction in hemin binding, confirming that hbp potentiates hemin acquisition by L. pneumophila. However, the strain was unaltered in its ability to grow within macrophage-like cells and freshwater amoebae, indicating that hbp is not required for intracellular infection. Despite this, Southern hybridization analysis and database searches demonstrated that hbp is nearly exclusive to the L. pneumophila species.
Assuntos
Genes Bacterianos , Hemina/metabolismo , Legionella pneumophila/genética , Sequência de Aminoácidos , Sequência de Bases , Legionella pneumophila/metabolismo , Dados de Sequência Molecular , Mutação , Fases de Leitura AbertaRESUMO
Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading frames. The vast majority of recognizable genes for essential cell functions (such as DNA replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for example, toxins, surface antigens and adhesins) are located on the large chromosome. In contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared with the large chromosome (42%), and also contains many more genes that appear to have origins other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system (the integron island) and host 'addiction' genes that are typically found on plasmids; thus, the small chromosome may have originally been a megaplasmid that was captured by an ancestral Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding how a free-living, environmental organism emerged to become a significant human bacterial pathogen.
Assuntos
Cromossomos Bacterianos , DNA Bacteriano , Vibrio cholerae/genética , Sequência de Bases , Transporte Biológico , Cólera/microbiologia , Reparo do DNA , Metabolismo Energético , Evolução Molecular , Regulação Bacteriana da Expressão Gênica , Genoma Bacteriano , Humanos , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Vibrio cholerae/classificação , Vibrio cholerae/patogenicidadeRESUMO
The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions. Because B. burgdorferi and M. genitalium are distantly related eubacteria, we suggest that their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors. Of 430 genes on 11 plasmids, most have no known biological function; 39% of plasmid genes are paralogues that form 47 gene families. The biological significance of the multiple plasmid-encoded genes is not clear, although they may be involved in antigenic variation or immune evasion.
Assuntos
Grupo Borrelia Burgdorferi/genética , Genoma Bacteriano , Transporte Biológico , Quimiotaxia , Cromossomos Bacterianos , Reparo do DNA , DNA Bacteriano/biossíntese , DNA Bacteriano/genética , Metabolismo Energético , Regulação Bacteriana da Expressão Gênica , Doença de Lyme/microbiologia , Proteínas de Membrana/genética , Dados de Sequência Molecular , Plasmídeos , Biossíntese de Proteínas , Recombinação Genética , Origem de Replicação , Telômero , Transcrição GênicaRESUMO
The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.
Assuntos
Archaea/genética , Genoma Bacteriano , Recombinação Genética , Thermotoga maritima/genética , Proteínas de Bactérias/metabolismo , DNA Bacteriano , Genes Arqueais , Dados de Sequência Molecular , Família Multigênica , Fases de Leitura Aberta , Filogenia , Biossíntese de Proteínas , Análise de Sequência de DNA , Thermotoga maritima/classificação , Thermotoga maritima/fisiologia , Transcrição Gênica , Transformação BacterianaRESUMO
Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.
Assuntos
Genoma Bacteriano , Helicobacter pylori/genética , Variação Antigênica , Aderência Bacteriana , Proteínas de Bactérias/metabolismo , Sequência de Bases , Evolução Biológica , Divisão Celular , Reparo do DNA , DNA Bacteriano/genética , Regulação Bacteriana da Expressão Gênica , Helicobacter pylori/metabolismo , Helicobacter pylori/patogenicidade , Concentração de Íons de Hidrogênio , Dados de Sequência Molecular , Biossíntese de Proteínas , Recombinação Genética , Transcrição Gênica , VirulênciaRESUMO
Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.