RESUMEN
Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion-reducing capabilities.
Asunto(s)
Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Análisis de Secuencia de ADN , Análisis de Secuencia de Proteína , Shewanella/genética , Shewanella/metabolismo , Secuencia de Aminoácidos , Biodegradación Ambiental , Respiración de la Célula , Transporte de Electrón , Expresión Génica , Metales/metabolismo , Datos de Secuencia Molecular , Sistemas de Lectura Abierta/genética , Compuestos Orgánicos/metabolismo , Oxidación-Reducción , Plásmidos , Proteómica/métodos , Alineación de Secuencia/métodos , Shewanella/clasificación , Shewanella/patogenicidad , Especificidad de la Especie , Contaminantes Químicos del Agua/metabolismo , Purificación del Agua/métodosRESUMEN
Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.
Asunto(s)
Desulfovibrio vulgaris/genética , Genoma Bacteriano , Desulfovibrio vulgaris/metabolismo , Metabolismo Energético , Datos de Secuencia MolecularRESUMEN
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
Asunto(s)
Genoma de Protozoos , Análisis de Secuencia de ADN , Trichomonas vaginalis/genética , Animales , Transporte Biológico/genética , Elementos Transponibles de ADN , ADN Protozoario/genética , Transferencia de Gen Horizontal , Genes Protozoarios , Humanos , Hidrógeno/metabolismo , Redes y Vías Metabólicas/genética , Datos de Secuencia Molecular , Familia de Multigenes , Orgánulos/metabolismo , Estrés Oxidativo/genética , Péptido Hidrolasas/genética , Péptido Hidrolasas/metabolismo , Proteínas Protozoarias/genética , Proteínas Protozoarias/fisiología , Procesamiento Postranscripcional del ARN , Secuencias Repetitivas de Ácidos Nucleicos , Enfermedades de Transmisión Sexual/parasitología , Tricomoniasis/parasitología , Tricomoniasis/transmisión , Trichomonas vaginalis/citología , Trichomonas vaginalis/metabolismo , Trichomonas vaginalis/patogenicidadRESUMEN
The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.
Asunto(s)
Clima Frío , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Genoma Bacteriano , Aminoácidos/análisis , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Carbono/metabolismo , ADN Bacteriano/química , ADN Bacteriano/genética , Metabolismo Energético , Genómica , Biología Marina , Fluidez de la Membrana , Modelos Biológicos , Datos de Secuencia Molecular , Nitrógeno/metabolismo , Proteómica , Especificidad de la EspecieRESUMEN
Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.