RESUMEN
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.
Asunto(s)
Bases de Datos de Ácidos Nucleicos , Genómica , Animales , Secuencia de Bases , Variación Genética , Genoma Humano , Humanos , Internet , Ratones , Proteínas/genética , ARN/genética , Ratas , Secuencias Reguladoras de Ácidos Nucleicos , Alineación de Secuencia , Interfaz Usuario-ComputadorRESUMEN
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.
Asunto(s)
Bases de Datos de Ácidos Nucleicos , Genómica , Animales , Secuencia de Bases , Bovinos , Perros , Humanos , Internet , Ratones , Ratas , Alineación de Secuencia , Programas Informáticos , Interfaz Usuario-ComputadorRESUMEN
The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes. Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata. In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish. Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser. Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions.
Asunto(s)
Bases de Datos Genéticas , Genómica , Vertebrados/genética , Animales , Cromosomas Humanos/química , Sistemas de Administración de Bases de Datos , Bases de Datos Genéticas/normas , Genoma , Humanos , Ratones , Interfaz Usuario-Computador , Pez Cebra/genéticaRESUMEN
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.
Asunto(s)
Biología Computacional , Bases de Datos Genéticas , Genoma , Genómica , Animales , Humanos , Almacenamiento y Recuperación de la Información , Internet , Programas InformáticosRESUMEN
In the filamentous fungus Acremonium chrysogenum, biosynthesis of the beta-lactam antibiotic cephalosporin C is repressed by glucose. A wild-type strain grown in the presence of glucose shows a reduction of transcripts derived from the pcbC and cefEF biosynthesis genes. Interestingly, the amount of the pcbC transcript is not affected in another strain with enhanced cephalosporin C production, suggesting a correlation between strain improvement and deregulation of glucose repression. The function of the glucose repressor CRE1 in this regulation was further analyzed by transforming both A. chrysogenum strains with multiple copies of the cre1 gene. The molecular analysis of transformants revealed that additional copies of the cre1 gene restore wild-type-like regulation of pcbC gene expression in the semi-producer strain, while repression of the cefEF gene expression is increased. Overall, our data indicate a regulation of the pcbC and the cefEF gene expression by CRE1.
Asunto(s)
Acremonium/metabolismo , Antibacterianos/biosíntesis , Proteínas de Unión al ADN/genética , Proteínas Fúngicas , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Glucosa/farmacología , Proteínas de Unión a las Penicilinas , Proteínas Represoras/genética , Acremonium/genética , Transferasas Intramoleculares/genética , Oxidorreductasas/genética , beta-LactamasRESUMEN
The complete DNA sequence of the mitochondrial genome of the chlorophyceen alga Scenedesmus obliquus was determined. The circular genome of 42781bp contains a basic set of 13 mitochondrial genes, which are conserved among plant or algal chondriomes. In addition, two scrambled rRNA and 27 tRNA genes are present, together with four intronic sequences (group I and II) and five open reading frames (ORFs), which show no significant homology to other ORFs from organellar genomes. The comparison with deduced amino acid sequences from 13 conserved mitochondrial genes gives rise to the conclusion that two deviations from the standard genetic code must be present in S. obliquus mitochondria: (i) UAG codes for leucine as was already found in some other algal mitochondria; (ii) UCA is a stop codon, which seems unique for mitochondrial genomes. This was supported by our finding that a tRNA-Leu gene possesses a UCA anticodon and by a missing tRNA-serine, able to decode the UCA codon. Consistent with these data is the absence of any UCA codon from conserved mitochondrial ORFs. This codon occurs only close to the end of all ORFs, while UAA or UGA codons are found at some distance from any conserved ORF. Codon changes by RNA editing can be excluded, since RT-PCR analysis does not reveal any evidence for post-transcriptional RNA modifications of the primary transcript.
Asunto(s)
Chlorophyta/genética , ADN Mitocondrial/genética , Proteínas Algáceas/genética , Secuencia de Aminoácidos , Secuencia de Bases , Codón/genética , ADN Mitocondrial/química , Variación Genética , Leucina/genética , Datos de Secuencia Molecular , NADH Deshidrogenasa/genética , Edición de ARN , ARN de Transferencia/genética , Análisis de Secuencia de ADN , Homología de Secuencia de AminoácidoRESUMEN
The cre1 gene from the beta-lactam producer Acremonium chrysogenum has been isolated and characterized in order to study glucose-dependent gene expression in this biotechnically important fungus. The deduced protein sequence is highly similar to amino-acid sequences of other known glucose repressors from filamentous fungi, and carries conserved zinc-finger and regulatory motifs. Contrary to cre gene expression in Trichoderma reesei and Aspergillus nidulans, the transcript level of the cre1 gene from an A. chrysogenum wild-type strain is increased in the presence of glucose. Remarkably, the glucose-dependent transcriptional upregulation does not take place in another A. chysogenum strain, which displays enhanced production of the beta-lactam antibiotic cephalosporin C. We surmise that the de-regulation of cre1 is connected with the increased production rate in this strain.
