RESUMEN
Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in freshwater ponds, sewage ditches, activated sludge, and food processing wastewater. There have not been many studies on photosynthetic betaproteobacteria. Here we announce the complete genome sequence of the best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC 100245).
Asunto(s)
Betaproteobacteria/clasificación , Betaproteobacteria/genética , Genoma Bacteriano , Procesos Fototróficos , Análisis de Secuencia de ADN , Betaproteobacteria/aislamiento & purificación , Betaproteobacteria/fisiología , ADN Bacteriano/genética , Agua Dulce/microbiología , Gelatina/metabolismo , Datos de Secuencia Molecular , Eliminación de Residuos Líquidos/métodosRESUMEN
Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls and monoaryls, and the catabolic genes for these compounds are useful for the production of industrially valuable metabolites from lignin. Here we report the complete nucleotide sequence of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and the 148,801-bp-long plasmid.
Asunto(s)
Genoma Bacteriano , Lignina/química , Sphingomonadaceae/genética , Sphingomonadaceae/metabolismo , Datos de Secuencia MolecularRESUMEN
Magnetotactic bacteria are ubiquitous microorganisms that synthesize intracellular magnetite particles (magnetosomes) by accumulating Fe ions from aquatic environments. Recent molecular studies, including comprehensive proteomic, transcriptomic, and genomic analyses, have considerably improved our hypotheses of the magnetosome-formation mechanism. However, most of these studies have been conducted using pure-cultured bacterial strains of alpha-proteobacteria. Here, we report the whole-genome sequence of Desulfovibrio magneticus strain RS-1, the only isolate of magnetotactic microorganisms classified under delta-proteobacteria. Comparative genomics of the RS-1 and four alpha-proteobacterial strains revealed the presence of three separate gene regions (nuo and mamAB-like gene clusters, and gene region of a cryptic plasmid) conserved in all magnetotactic bacteria. The nuo gene cluster, encoding NADH dehydrogenase (complex I), was also common to the genomes of three iron-reducing bacteria exhibiting uncontrolled extracellular and/or intracellular magnetite synthesis. A cryptic plasmid, pDMC1, encodes three homologous genes that exhibit high similarities with those of other magnetotactic bacterial strains. In addition, the mamAB-like gene cluster, encoding the key components for magnetosome formation such as iron transport and magnetosome alignment, was conserved only in the genomes of magnetotactic bacteria as a similar genomic island-like structure. Our findings suggest the presence of core genetic components for magnetosome biosynthesis; these genes may have been acquired into the magnetotactic bacterial genomes by multiple gene-transfer events during proteobacterial evolution.
Asunto(s)
Desulfovibrio/genética , Genes Bacterianos , Genoma Bacteriano , Magnetospirillum/genética , Familia de Multigenes , Desulfovibrio/metabolismo , Metabolismo Energético/genética , Genes Bacterianos/fisiología , Genómica/métodos , Magnetosomas/genética , Magnetospirillum/metabolismo , Familia de Multigenes/fisiologíaRESUMEN
Gluconacetobacter xylinus is involved in the industrial production of cellulose. We have determined the genome sequence of G. xylinus NBRC 3288, a cellulose-nonproducing strain. Comparative analysis of genomes of G. xylinus NBRC 3288 with those of the cellulose-producing strains clarified the genes important for cellulose production in Gluconacetobacter.
Asunto(s)
Ácido Acético/análisis , Celulosa/biosíntesis , Condimentos/microbiología , Genoma Bacteriano , Gluconacetobacter xylinus/genética , Secuencia de Bases , Gluconacetobacter xylinus/aislamiento & purificación , Gluconacetobacter xylinus/metabolismo , Datos de Secuencia MolecularRESUMEN
Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein-magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.
Asunto(s)
Biotecnología/métodos , Desulfovibrio/metabolismo , Óxido Ferrosoférrico/metabolismo , Magnetospirillum/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Desulfovibrio/genética , Óxido Ferrosoférrico/química , Magnetospirillum/genética , Datos de Secuencia Molecular , Propiedades de SuperficieRESUMEN
Selenomonas ruminantium subsp. lactilytica, a strictly anaerobic ruminal bacterium, possesses typical Gram-negative cell surface structure comprising cytoplasmic membrane, peptidoglycan layer and outer membrane, whereas its 16S rRNA-based taxonomy shows that the bacteria belongs to Gram-positive Firmicutes. Complete genome analysis showed that genes or gene clusters involved in Gram-negative cell structure were scattered in the S. ruminantium genome, and might provide the new insight of phylogenetic relationship between the bacterium and other bacterial species.
Asunto(s)
Firmicutes/genética , Genoma Bacteriano , Filogenia , Selenomonas/genética , Secuencia de Bases , Membrana Celular/metabolismo , ADN Bacteriano/genética , Peptidoglicano/metabolismo , ARN Ribosómico 16S/genética , Selenomonas/clasificaciónRESUMEN
Ilumatobacter coccineum YM16-304(T) (=NBRC 103263(T)) is a novel marine actinobacterium isolated from a sand sample collected at a beach in Shimane Prefecture, Japan. Strain YM16-304(T) is the type strain of the species. Phylogenetically, strain YM16-304(T) is close to Ilumatobacter nonamiense YM16-303(T) (=NBRC 109120(T)), Ilumatobacter fluminis YM22-133(T) and some uncultured bacteria including putative marine sponge symbionts. Whole genome sequence of these species has not been reported. Here we report the complete genome sequence of strain YM16-304(T). The 4,830,181 bp chromosome was predicted to encode a total of 4,291 protein-coding genes.
RESUMEN
Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actinobacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phosphovorus NM-1(T) (NBRC 101784(T)), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H(+) symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs. Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.
Asunto(s)
Genoma Bacteriano/genética , Polifosfatos/metabolismo , Propionibacteriaceae/genética , Ácido Anhídrido Hidrolasas/genética , Secuencia de Bases , Datos de Secuencia Molecular , Proteínas de Transporte de Fosfato/genética , Fosfotransferasas/genética , Filogenia , Mapeo Físico de Cromosoma , Polihidroxialcanoatos/genética , Propionibacteriaceae/enzimología , Propionibacteriaceae/metabolismo , Análisis de Secuencia de ADNRESUMEN
Oscillibacter valericigenes is a mesophilic, strictly anaerobic bacterium belonging to the clostridial cluster IV. Strain Sjm18-20(T) (=NBRC 101213(T) =DSM 18026(T)) is the type strain of the species and represents the genus Oscillibacter Iino et al. 2007. It was isolated from the alimentary canal of a Japanese corbicula clam (Corbicula japonica) collected on a seacoast in Shimane Prefecture in Japan. Phylogenetically, strain Sjm18-20(T) is closest to uncultured bacteria in digestive tracts, including the enriched cells thought to represent Oscillospira guilliermondii Chatton and Perard 1913. The isolated phylogenetic position and some distinct characteristics prompted us to determine the complete genome sequence. The 4,410,036 bp chromosome and the 60,586 bp plasmid were predicted to encode a total of 4,723 protein-coding genes.