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      • Record: found
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      Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1 T)

      research-article
      Author(s): 1 , 2 , 2 , 2 , 2 , 2 , 2 , 2 , 2 , 2 , 3 , 2 , 3 , 2 , 3 , 2 , 3 , 2 , 3 , 2 , 3 , 2 , 3 , 2 , 2 , 2 , 2 , 2 , 4 , 4 , 1 , 5 , 2 , 6 , 2 , 6 , 1 , 2 ,   2 , 7 , 4 , 2 , 1 , 2 , *
      Publication date (Electronic):
      Journal: Standards in Genomic Sciences
      Publisher: Michigan State University
      Keywords: Gram-positive coccus, anaerobic, asaccharolytic, pyrrolizidine alkaloids, Coriobacteriaceae

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          Abstract

          Slackia heliotrinireducens (Lanigan 1983) Wade et al. 1999 is of phylogenetic interest because of its location in a genomically yet uncharted section of the family Coriobacteriaceae, within the deep branching Actinobacteria. Strain RHS 1 T was originally isolated from the ruminal flora of a sheep. It is a proteolytic anaerobic coccus, able to reductively cleave pyrrolizidine alkaloids. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Slackia, and the 3,165,038 bp long single replicon genome with its 2798 protein-coding and 60 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

            C R Woese, O Kandler, M L Wheelis (1990)
            Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.
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              GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

              J Besemer (2001)
              Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene start prediction can be improved by combining models of protein-coding and non-coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method, called GeneMarkS, utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely 83.2% of the translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts in an experimentally validated set of Escherichia coli genes. We have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames containing real genes, with an accuracy matching the level of the best currently used gene detection methods. Accurate translation start prediction, in addition to the refinement of protein sequence N-terminal data, provides the benefit of precise positioning of the sequence region situated upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites can be revealed and analyzed with higher precision. These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed.
              Article 0 comments Cited 1012 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Stand Genomic Sci
                Journal ID (publisher-id): SIGS
                Title: Standards in Genomic Sciences
                Publisher: Michigan State University
                ISSN (Electronic): 1944-3277
                Publication date (Electronic): 22 November 2009
                Publication date Collection: 31 December 2009
                Volume: 1
                Issue: 3
                Pages: 234-241
                Affiliations
                [1 ]DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
                [2 ]DOE Joint Genome Institute, Walnut Creek, California, USA
                [3 ]Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
                [4 ]Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
                [5 ]HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
                [6 ]Lawrence Livermore National Laboratory, Livermore, California, USA
                [7 ]University of California Davis Genome Center, Davis, California, USA
                Author notes
                [* ] Corresponding author: Philip Hugenholtz
                Article
                Publisher ID: sigs.37633
                DOI: 10.4056/sigs.37633
                PMC ID: 3035243
                PubMed ID: 21304663
                SO-VID: 2c794c34-8dd1-4cc0-bc00-5e28206c43d0
                Copyright statement: Copyright @ 2009
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Funding
                Funded by: US Department of Energy's Office of Science
                Award ID: DE-AC02-05CH11231
                Award ID: DE-AC52-07NA27344
                Award ID: DE-AC02-06NA25396
                Funded by: German Research Foundation (DFG)
                Award ID: INST 599/1-1
                Categories
                Subject: Short Genome Reports

                ScienceOpen disciplines: Genetics
                Keywords: coriobacteriaceae,anaerobic,asaccharolytic,pyrrolizidine alkaloids,gram-positive coccus
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: coriobacteriaceae, anaerobic, asaccharolytic, pyrrolizidine alkaloids, gram-positive coccus

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