Pathogenicity in Francisella tularensis subspecies .Sequencing of the non-pathogenic
BackgroundMethylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared.Methodology/Principal FindingsThe 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid).Conclusion/SignificanceThese two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass spectrometric identification of unique peptides. Genes for most known functions and pathways were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was identified, including eight selenocysteine-containing proteins, with each being paralogous to a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox functions. The methanogenic Archaea (methanogens) occupy a unique metabolic niche, as they produce methane, which is a useful energy source and a powerful greenhouse gas. These organisms are found in diverse anaerobic habitats, ranging from aquatic and marine sediments to sewage digesters and the rumens and large intestines of herbivores and other mammals (127). In these habitats, the degradation of organic matter results in the production of H 2 and other intermediates by fermentative organisms. By maintaining an extremely low partial pressure of H 2 , the methanogens keep fermentative pathways energetically favorable. In addition, some methanogens may occupy niches where hydrogen is produced predominately by geothermal reactions.Metabolically, methanogens are divided into those that specialize in CO 2 reduction and those that also use acetate and/or methyl compounds. The former group, the hydrogenotrophs, use H 2 as an electron donor to reduce CO 2 to methane. Many hydrogenotrophic species can substitute formate or certain low-molecular-weight alcohols and ketones for H 2 . Complete genome sequences have been published for three hydrogenotrophic methanogens, Methanocaldococcus jannaschii (13), Methanothermobacter thermautotrophicus (105), and Methanopyrus kandleri (104), all of which are thermophiles or hyperthermophiles. Of the methanogens that utilize acetate and methyl compounds, complete genome sequences have been published for two species, Methanosarcina acetivorans (26) and Methanosarcina mazei (19), both of which are mesophiles. In addition, partial sequences have been published for two psychrophiles, the hydrogenotroph Methanogenium frigidum and the methylotroph Methanolobus burtonii (97).Genome sequences of methanogens have answered many questions, but they have inspired many others. More than half of the genes in Methanocaldococcus jannaschii lack a predicted function (13), and this proportion has not declined significantly as other methanogen sequences have been determined. The proportions of genes of unknown functions, which are either homologous to other genes of unknown function...
Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.
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