RESUMO
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
Objectives: To highlight and provide insights into key developments in translational bioinformatics between 2014 and 2016. Methods: This review describes some of the most influential bioinformatics papers and resources that have been published between 2014 and 2016 as well as the national genome sequencing initiatives that utilize these resources to routinely embed genomic medicine into healthcare. Also discussed are some applications of the secondary use of patient data followed by a comprehensive view of the open challenges and emergent technologies. Results: Although data generation can be performed routinely, analyses and data integration methods still require active research and standardization to improve streamlining of clinical interpretation. The secondary use of patient data has resulted in the development of novel algorithms and has enabled a refined understanding of cellular and phenotypic mechanisms. New data storage and data sharing approaches are required to enable diverse biomedical communities to contribute to genomic discovery. Conclusion: The translation of genomics data into actionable knowledge for use in healthcare is transforming the clinical landscape in an unprecedented way. Exciting and innovative models that bridge the gap between clinical and academic research are set to open up the field of translational bioinformatics for rapid growth in a digital era.
Assuntos
Biologia Computacional , Genômica , Pesquisa Translacional Biomédica , Mineração de Dados , Registros Eletrônicos de Saúde , Humanos , Medicina de PrecisãoRESUMO
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 complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
Assuntos
Evolução Biológica , Enterococcus faecalis/genética , Genoma Bacteriano , Sequências Repetitivas Dispersas , Análise de Sequência de DNA , Resistência a Vancomicina/genética , Adesinas Bacterianas/genética , Aderência Bacteriana , Proteínas de Bactérias/genética , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Cromossomos Bacterianos/genética , Conjugação Genética , Sequência Conservada , Elementos de DNA Transponíveis , Sistema Digestório/microbiologia , Farmacorresistência Bacteriana Múltipla , Enterococcus faecalis/efeitos dos fármacos , Enterococcus faecalis/patogenicidade , Enterococcus faecalis/fisiologia , Transferência Genética Horizontal , Infecções por Bactérias Gram-Positivas/microbiologia , Humanos , Lisogenia , Fases de Leitura Aberta , Estresse Oxidativo , Plasmídeos , Sintenia , Virulência/genética , Fatores de Virulência/genéticaRESUMO
The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.