RESUMEN
Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria.
Asunto(s)
Bifidobacterium/genética , Bifidobacterium/fisiología , Fimbrias Bacterianas/genética , Fimbrias Bacterianas/fisiología , Genoma Bacteriano , Secuencia de Aminoácidos , Animales , Proteínas Bacterianas/genética , Proteínas Bacterianas/fisiología , Secuencia de Bases , Bifidobacterium/crecimiento & desarrollo , Bifidobacterium/ultraestructura , Hibridación Genómica Comparativa , ADN Bacteriano/genética , Femenino , Fimbrias Bacterianas/ultraestructura , Tracto Gastrointestinal/microbiología , Regulación Bacteriana de la Expresión Génica , Vida Libre de Gérmenes , Humanos , Masculino , Metagenoma , Ratones , Ratones Endogámicos BALB C , Microscopía Electrónica de Transmisión , Microscopía Inmunoelectrónica , Datos de Secuencia Molecular , Familia de Multigenes , Mutación , Homología de Secuencia de AminoácidoRESUMEN
Modern omics technologies allow us to obtain global information on different types of biological networks. However, integrating these different types of analyses into a coherent framework for a comprehensive biological interpretation remains challenging. Here, we present a conceptual framework that integrates protein interaction, phosphoproteomics, and transcriptomics data. Applying this method to analyze HRAS signaling from different subcellular compartments shows that spatially defined networks contribute specific functions to HRAS signaling. Changes in HRAS protein interactions at different sites lead to different kinase activation patterns that differentially regulate gene transcription. HRAS-mediated signaling is the strongest from the cell membrane, but it regulates the largest number of genes from the endoplasmic reticulum. The integrated networks provide a topologically and functionally resolved view of HRAS signaling. They reveal distinct HRAS functions including the control of cell migration from the endoplasmic reticulum and TP53-dependent cell survival when signaling from the Golgi apparatus.
Asunto(s)
Compartimento Celular , Proteínas Proto-Oncogénicas p21(ras)/metabolismo , Transducción de Señal , Apoptosis , Membrana Celular/metabolismo , Retículo Endoplásmico/metabolismo , Células HeLa , Humanos , Mapas de Interacción de Proteínas , Procesamiento Proteico-Postraduccional , Proteínas Proto-Oncogénicas p21(ras)/genética , Transcriptoma , Proteína p53 Supresora de TumorRESUMEN
Lactobacillus salivarius subsp. salivarius strain UCC118 is a bacteriocin-producing strain with probiotic characteristics. The 2.13-Mb genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously have not been characterized in lactic acid bacteria or intestinal lactobacilli. Annotation of the genome sequence indicated an intermediate level of auxotrophy compared with other sequenced lactobacilli. No single-copy essential genes were located on the megaplasmid. However, contingency amino acid metabolism genes and carbohydrate utilization genes, including two genes for completion of the pentose phosphate pathway, were megaplasmid encoded. The megaplasmid also harbored genes for the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation locus, and other genes potentially relevant for probiotic properties. Two subspecies of L. salivarius are recognized, salivarius and salicinius, and we detected megaplasmids in both subspecies by pulsed-field gel electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of megaplasmids of widely varying size in L. salivarius suggests a possible mechanism for genome expansion or contraction to adapt to different environments.
Asunto(s)
Genoma Bacteriano , Lactobacillus/genética , Replicón/genética , Aminoácidos/metabolismo , Metabolismo de los Hidratos de Carbono , Elementos Transponibles de ADN/genética , Electroforesis en Gel de Campo Pulsado , Lactobacillus/clasificación , Lactobacillus/metabolismo , Datos de Secuencia Molecular , Vía de Pentosa Fosfato/genética , Peptidoglicano/biosíntesis , Plásmidos/genética , Plásmidos/aislamiento & purificación , Polisacáridos Bacterianos/biosíntesis , SeudogenesRESUMEN
The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or amino acid sequences. The most familiar version is ClustalW, which uses a simple text menu system that is portable to more or less all computer systems. ClustalX features a graphical user interface and some powerful graphical utilities for aiding the interpretation of alignments and is the preferred version for interactive usage. Users may run Clustal remotely from several sites using the Web or the programs may be downloaded and run locally on PCs, Macintosh, or Unix computers. The protocols in this unit discuss how to use ClustalX and ClustalW to construct an alignment, and create profile alignments by merging existing alignments.
Asunto(s)
Algoritmos , Alineación de Secuencia/métodos , Análisis de Secuencia/métodos , Programas Informáticos , Interfaz Usuario-ComputadorRESUMEN
MOTIVATION: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods. RESULTS: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages.