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  • 1
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 191, No. 6 ( 2009-03-15), p. 1974-1978
    Abstract: Lateral gene transfers (LGT) (also called horizontal gene transfers) have been a major force shaping the Thermosipho africanus TCF52B genome, whose sequence we describe here. Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea .
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2009
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Annual Reviews ; 2002
    In:  Annual Review of Microbiology Vol. 56, No. 1 ( 2002-10), p. 263-287
    In: Annual Review of Microbiology, Annual Reviews, Vol. 56, No. 1 ( 2002-10), p. 263-287
    Abstract: ▪ Abstract  Inteins are genetic elements that disrupt the coding sequence of genes. However, in contrast to introns, inteins are transcribed and translated together with their host protein. Inteins appear most frequently in Archaea, but they are found in organisms belonging to all three domains of life and in viral and phage proteins. Most inteins consist of two domains: One is involved in autocatalytic splicing, and the other is an endonuclease that is important in the spread of inteins. This review focuses on the evolution and technical application of inteins and only briefly summarizes recent advances in the study of the catalytic activities and structures of inteins. In particular, this review considers inteins as selfish or parasitic genetic elements, a point of view that explains many otherwise puzzling aspects of inteins.
    Type of Medium: Online Resource
    ISSN: 0066-4227 , 1545-3251
    URL: Issue
    RVK:
    Language: English
    Publisher: Annual Reviews
    Publication Date: 2002
    detail.hit.zdb_id: 1470471-7
    SSG: 12
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  • 3
    In: Environmental Microbiology, Wiley, Vol. 23, No. 11 ( 2021-11), p. 7105-7120
    Abstract: Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga , Kosmotoga , Marinitoga , Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga . Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Elsevier BV ; 2004
    In:  Trends in Genetics Vol. 20, No. 4 ( 2004-4), p. 182-187
    In: Trends in Genetics, Elsevier BV, Vol. 20, No. 4 ( 2004-4), p. 182-187
    Type of Medium: Online Resource
    ISSN: 0168-9525
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2004
    detail.hit.zdb_id: 2010993-3
    SSG: 12
    SSG: 15,3
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  • 5
    Online Resource
    Online Resource
    Elsevier BV ; 2004
    In:  Trends in Genetics Vol. 20, No. 5 ( 2004-05), p. 254-260
    In: Trends in Genetics, Elsevier BV, Vol. 20, No. 5 ( 2004-05), p. 254-260
    Type of Medium: Online Resource
    ISSN: 0168-9525
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2004
    detail.hit.zdb_id: 2010993-3
    SSG: 12
    SSG: 15,3
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  • 6
    In: mBio, American Society for Microbiology, Vol. 11, No. 4 ( 2020-08-25)
    Abstract: Gene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria . The GTAs can be induced under conditions of nutritional stress, incorporate random fragments of bacterial DNA into miniphage particles, lyse the host cells, and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that GTA genes evolve under conditions of pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with those of both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases in which viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein production is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs represent bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTAs facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increases in nutrient availability resulting from the altruistic suicide of GTA-producing cells. IMPORTANCE Kin selection and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial gene transfer agents (GTAs), but not related viruses, evolve under conditions of positive selection for the reduction of the energy cost of GTA particle production. We hypothesize that GTAs are dedicated devices mediating the survival of bacteria under conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress conditions appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and increases of nutrient availability occurring through the lysis of GTA-producing bacteria.
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 2557172-2
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  • 7
    Online Resource
    Online Resource
    Canadian Science Publishing ; 2015
    In:  Canadian Journal of Microbiology Vol. 61, No. 9 ( 2015-09), p. 655-670
    In: Canadian Journal of Microbiology, Canadian Science Publishing, Vol. 61, No. 9 ( 2015-09), p. 655-670
    Abstract: Thermophiles are extremophiles that grow optimally at temperatures 〉 45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.
    Type of Medium: Online Resource
    ISSN: 0008-4166 , 1480-3275
    RVK:
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2015
    detail.hit.zdb_id: 280534-0
    detail.hit.zdb_id: 1481972-7
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Wiley ; 2008
    In:  Environmental Microbiology Vol. 10, No. 4 ( 2008-04), p. 1039-1056
    In: Environmental Microbiology, Wiley, Vol. 10, No. 4 ( 2008-04), p. 1039-1056
    Abstract: Proteorhodopsins are light‐energy‐harvesting transmembrane proteins encoded by genes recently discovered in the surface waters of the world's oceans. Metagenomic data from the Global Ocean Sampling expedition (GOS) recovered 2674 proteorhodopsin‐related sequences from 51 aquatic samples. Four of these samples were from non‐marine environments, specifically, Lake Gatun within the Panama Canal, Delaware Bay and Chesapeake Bay and the Punta Cormorant Lagoon in Ecuador. Rhodopsins related to but phylogenetically distinct from most sequences designated proteorhodopsins were present at all four of these non‐marine sites and comprised three different clades that were almost completely absent from marine samples. Phylogenomic analyses of genes adjacent to those encoding these novel rhodopsins suggest affiliation to the Actinobacteria , and hence we propose to name these divergent, non‐marine rhodopsins ‘actinorhodopsins’. Actinorhodopsins conserve the acidic amino acid residues critical for proton pumping and their genes lack genomic association with those encoding photo‐sensory transducer proteins, thus supporting a putative ion pumping function. The ratio of rec A and rad A to rhodopsin genes in the different environment types sampled within the GOS indicates that rhodopsins of one type or another are abundant in microbial communities in freshwater, estuarine and lagoon ecosystems, supporting an important role for these photosystems in all aquatic environments influenced by sunlight.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2008
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Cold Spring Harbor Laboratory ; 2009
    In:  Genome Research Vol. 19, No. 5 ( 2009-05), p. 744-756
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 19, No. 5 ( 2009-05), p. 744-756
    Abstract: The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call “species” is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept—by which is meant a genetic and ecological theory of speciation—might best explain species existence and rationalize a species definition, if we could agree on one. We review existing theories and some relevant data. We conclude that microbiologists now understand in some detail the various genetic, population, and ecological processes that effect the evolution of prokaryotes. There will be on occasion circumstances under which these, working together, will form groups of related organisms sufficiently like each other that we might all agree to call them “species,” but there is no reason that this must always be so. Thus, there is no principled way in which questions about prokaryotic species, such as how many there are, how large their populations are, or how globally they are distributed, can be answered. These questions can, however, be reformulated so that metagenomic methods and thinking will meaningfully address the biological patterns and processes whose understanding is our ultimate target.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2009
    detail.hit.zdb_id: 1483456-X
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2021
    In:  The ISME Journal Vol. 15, No. 10 ( 2021-10), p. 2853-2864
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 15, No. 10 ( 2021-10), p. 2853-2864
    Abstract: All environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities used DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. The preferential eDNA consumption and differential growth under various nutrient availability regimes were associated with substantial shifts in the taxonomic composition and diversity of microcosm communities. Therefore, we conjecture that in salterns the microbial community assembly is driven by the available resources, including eDNA.
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2299378-2
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