What is synteny of genes

Decoding of the genomes of Ralstonia eutropha H16 and Methanosphaera stadtmanae and comparative studies on adaptations of the genome organization - eDiss

dc.contributor.advisorGottschalk, Gerhard Prof. Dr.dedc.contributor.authorFricke, Wolfgang Floriandedc.date.accessioned2012-04-16T14: 56: 42Zdedc.date.available2013-01-30T23: 50: 32Zdedc.date.issued2006-04-04dedc.identifier.urihttp://hdl.handle.net/11858/00-1735-0000-0006-ABB8-Ddedc.description.abstractThe genomes of two microorganisms - Ralstonia eutropha H16 and Methanosphaera stadtmanae - were sequenced using the whole-genome shotgun method and examined with a focus on comparative analysis of the genomes and related strains and species: the Gram-negative β-proteobacterium R. eutropha H16 has been characterized in terms of its facultative chemolithoautotrophic and anaerobic way of life and serves as a model organism for a number of different metabolic pathways, including the production of biodegradable polymers or the investigation of H2-dependent processes. The pronounced metabolic versatility of R. eutropha H16 is reflected in the three-part genome structure, which consists of two chromosomes (Chr.1: 4.053 MBp and Chr.2: 2.912 MBp) and the already sequenced megaplasmid pHG1 (452.156 bp; Schwartz et al ., 2003). Both chromosomes are characterized by similar G + C contents (66.5% and 66.3%) and comparable proportions of coding sequences (87.8% and 88.8%) and foreign DNA (5% and 13%). These values ​​differ significantly from those of the Megaplasmids (G + C: 61.3%; coding sequences: 80.5%; foreign DNA: 34%). The genome shows an uneven distribution of coding properties in that essential household genes are coded predominantly on Chr.1 and additional functions with selective advantage under special growth conditions on Chr.2 and pHG1. In contrast to Chr.1, the replication origins of Chr.2 and pHG1 show typical features of a plasmid origin. Bidirectional BLAST comparisons identify only low conservation of the gene composition and order between Chr.1, Chr.2 and pHG1 and indicate different evolutionary origins of these replicons. A significant degree of gene synteny between the largest chromosomes of the genomes of different Burkholderiaceae, on the other hand, indicates a common ancestor of these replicons and thus of the associated genomes as a whole. Methanosphaera stadtmanae lives as a methanogenic commensal in the human colon. With the reduction of methanol, which comes from the pectins of plant cell walls, to methane, Msp. Stadtmanae is pursuing a restricted form of methanogenesis. The genome of Msp. Stadtmanae consists of a single circular replicon 1,767,405 bp in length and is characterized by the lowest number of coding sequences (CDS) found in methanogens sequenced to date and the lowest G + C content found in archaea sequenced to date . Metabolic limitations of Msp. Stadtmanae compared to other methanogens are due to the absence of coding sequences for elementary components of the methanogenic and autotrophic metabolism. Those CDSs that are not homologous in other archaea include genes that are associated with the biosynthesis of cell wall components in bacteria and a group of very homologous and unusually long CDSs that code for potential transmembrane proteins with repetitive structure. In analogy to mechanisms as observed in pathogenic bacteria, an adaptation of Msp. Stadtmanae to the intestinal habitat could be the expression of long, repetitive CDSs in order to generate phenotypic variability and thereby hide the organism from the human immune system.dedc.format.mimetypeapplication / pdfdedc.language.isogerdedc.rights.urihttp://webdoc.sub.gwdg.de/diss/copyr_diss.htmldedc.titleDecoding of the genomes of Ralstonia eutropha H16 and Methanosphaera stadtmanae and comparative studies on adaptations of the genome organizationdedc.typedoctoralThesisdedc.title.translatedDecipherment of the genomes of Ralstonia eutropha H16 and Methanosphaera stadtmanae and comparative analysis of adaptations of the genome organizationdedc.contributor.refereeBowien, Botho Prof. Dr.dedc.date.examination2005-06-30dedc.subject.dnb570 Life Sciences, Biologydedc.description.abstractengThe genomes of two micoorganisms - Ralstonia eutropha H16 and Methanosphaera stadtmanae - have been sequenced with the whole-genome shotgun approach and analyzed with special emphasis on genomic comparisons within the genomes and with related strains and species. The Gram-negative β-proteobacterium R. Eutropha H16 has been characterized for its facultative chemolithoautotrophic and anaerobic lifestyles and serves as a model organism for various metabolisms such as the production of biodegradable polymers and H2-dependent processes. High metabolic versatility of R. eutropha H16 is reflected by the tripartite genome structure comprising two chromosomes (Chr.1: 4.053 Mbp and Chr.2: 2.912 Mbp) and the previously sequenced megaplasmid pHG1 (452.156 bp; Schwartz et al., 2003) . Both chromosomes share similar G + C contents (66.5% and 66.3%), coding densities (87.8% and 88.8%) and comparable fractions of alien DNA (15% and 13%), which differ significantly from the megaplasmid (G + C: 61.3%; coding density: 80.5%; alien DNA: 34%). The genome shows a biased distribution of coding properties with basic housekeeping genes primarily encoded on Chr.1 and additional functions with selective advantage only under special growth conditions encoded on Chr.2 and pHG1. In contrast to Chr.1 the origins of replication of Chr.2 and pHG1 show typical characteristics of a plasmid origin. Bidirectional BLAST comparisons identify only marginal conservations of gene content and order between Chr.1, Chr.2 and pHG1 suggesting different evolutionary origins of these replicons. Instead, a significant degree of gene synteny found between the largest chromosomes of several Burkholderiaceae genomes indicates a common ancestor of these replicons and thus of the genomes. Methanosphaera stadtmanae thrives as a methanogenic commensal in the human large intestine. Reducing methanol from pectines of plant cell walls to methane Msp. Stadtmanae pursues a restricted form of methanogenesis. The genome of Msp. Stadtmanae consists of a single circular replicon of 1,767,405 bp length and is characterized by the lowest number of coding sequences (CDS) found in any methanogen and the lowest G + C content found in any archaeon sequenced so far. Metabolic constraints of Msp. Stadtmanae are reflected by the absence of genes for basic components of the methanogenic and autotrophic metabolism as compared to other methanogens. CDS without homology to other archaea include genes associated with the biosynthesis of cell wall components in bacteria and a group of highly homologous and unsually large CDS coding for predicted trans-membrane proteins with a repetitive structure. In analogy to mechanisms observed in pathogenic bacteria an adaptation of Msp. Stadtmanae to the intestinal habitat could consist in the expression of the group of large CDS thereby generating a phenotypic variation to evade the human immune system.dedc.subject.topicMathematics and Computer Sciencededc.subject.ger<i>Ralstonia eutropha</i>dedc.subject.ger<i>Methanosphaera stadtmanae</i>dedc.subject.gerGenome sequencededc.subject.gercomparative genomicsdedc.subject.gerGenome evolutiondedc.subject.gerGene syntenydedc.subject.gerMethanoldedc.subject.gerMethanogenesisdedc.subject.gerCommensaldedc.subject.gerintestinal habitatdedc.subject.gerlong repetitive CDSdedc.subject.gerphenotypic variation.dedc.subject.eng<i>Ralstonia eutropha</i>dedc.subject.eng<i>Methanosphaera stadtmanae</i>dedc.subject.enggenome sequencededc.subject.engcomparative genomicsdedc.subject.enggenome evolutiondedc.subject.enggene syntenydedc.subject.engmethanoldedc.subject.engmethanogenesisdedc.subject.engcommensaldedc.subject.englarge repetitive CDSdedc.subject.engintestinal habitatdedc.subject.engphenotypic variation.dedc.subject.bk42.3dedc.identifier.urnurn: nbn: de: gbv: 7-webdoc-698-7dedc.identifier.purlwebdoc-698dedc.affiliation.instituteBiological faculty including psychologydedc.subject.gokfullWUK 000: Genetics of Microorganisms, Molecular Biology of Microorganisms {Microbiology}dedc.identifier.ppn57921172Xde