Base de dados : MEDLINE
Pesquisa : B02.075.725 [Categoria DeCS]
Referências encontradas : 36 [refinar]
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  1 / 36 MEDLINE  
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[PMID]:26995682
[Au] Autor:Moran JJ; Whitmore LM; Isern NG; Romine MF; Riha KM; Inskeep WP; Kreuzer HW
[Ad] Endereço:Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA. james.moran@pnnl.gov.
[Ti] Título:Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park.
[So] Source:Extremophiles;20(3):291-9, 2016 May.
[Is] ISSN:1433-4909
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:The Norris Geyser Basin in Yellowstone National Park contains a large number of hydrothermal systems, which host microbial populations supported by primary productivity associated with a suite of chemolithotrophic metabolisms. We demonstrate that Metallosphaera yellowstonensis MK1, a facultative autotrophic archaeon isolated from a hyperthermal acidic hydrous ferric oxide (HFO) spring in Norris Geyser Basin, excretes formaldehyde during autotrophic growth. To determine the fate of formaldehyde in this low organic carbon environment, we incubated native microbial mat (containing M. yellowstonensis) from a HFO spring with (13)C-formaldehyde. Isotopic analysis of incubation-derived CO2 and biomass showed that formaldehyde was both oxidized and assimilated by members of the community. Autotrophy, formaldehyde oxidation, and formaldehyde assimilation displayed different sensitivities to chemical inhibitors, suggesting that distinct sub-populations in the mat selectively perform these functions. Our results demonstrate that electrons originally resulting from iron oxidation can energetically fuel autotrophic carbon fixation and associated formaldehyde excretion, and that formaldehyde is both oxidized and assimilated by different organisms within the native microbial community. Thus, formaldehyde can effectively act as a carbon and electron shuttle connecting the autotrophic, iron oxidizing members with associated heterotrophic members in the HFO community.
[Mh] Termos MeSH primário: Processos Autotróficos
Transporte de Elétrons
Formaldeído/metabolismo
Processos Heterotróficos
Fontes Hidrotermais/microbiologia
Sulfolobales/metabolismo
[Mh] Termos MeSH secundário: Ácidos/análise
Carbono/metabolismo
Fontes Hidrotermais/química
Ferro/análise
Oxirredução
Sulfolobales/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Acids); 1HG84L3525 (Formaldehyde); 7440-44-0 (Carbon); E1UOL152H7 (Iron)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:171013
[Lr] Data última revisão:
171013
[Sb] Subgrupo de revista:IM; S
[Da] Data de entrada para processamento:160321
[St] Status:MEDLINE
[do] DOI:10.1007/s00792-016-0821-2


  2 / 36 MEDLINE  
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[PMID]:26341207
[Au] Autor:Munson-McGee JH; Field EK; Bateson M; Rooney C; Stepanauskas R; Young MJ
[Ad] Endereço:Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA.
[Ti] Título:Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs.
[So] Source:Appl Environ Microbiol;81(22):7860-8, 2015 Nov.
[Is] ISSN:1098-5336
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of Nanoarchaeota in high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed Nanobsidianus stetteri from a more neutral YNP hot spring than to the marine Nanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP Nanoarchaeota as a Sulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate that Nanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one Nanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP Nanoarchaeota.
[Mh] Termos MeSH primário: Fontes Termais/microbiologia
Nanoarchaeota/fisiologia
Nanoarchaeota/virologia
Sulfolobales/fisiologia
[Mh] Termos MeSH secundário: Fontes Termais/virologia
Metagenômica
Nanoarchaeota/classificação
Nanoarchaeota/genética
Parques Recreativos
RNA Ribossômico 16S/genética
Análise de Célula Única
Sulfolobales/genética
Wyoming
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (RNA, Ribosomal, 16S)
[Em] Mês de entrada:1608
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150906
[St] Status:MEDLINE
[do] DOI:10.1128/AEM.01539-15


  3 / 36 MEDLINE  
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[PMID]:26292330
[Au] Autor:Zhan Z; Zhou J; Huang L
[Ad] Endereço:State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.
[Ti] Título:Site-Specific Recombination by SSV2 Integrase: Substrate Requirement and Domain Functions.
[So] Source:J Virol;89(21):10934-44, 2015 Nov.
[Is] ISSN:1098-5514
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:UNLABELLED: SSV-type integrases, encoded by fuselloviruses which infect the hyperthermophilic archaea of the Sulfolobales, are archaeal members of the tyrosine recombinase family. These integrases catalyze viral integration into and excision from a specific site on the host genome. In the present study, we have established an in vitro integration/excision assay for SSV2 integrase (Int(SSV2)). Int(SSV2) alone was able to catalyze both integration and excision reactions in vitro. A 27-bp specific DNA sequence is minimally required for the activity of the enzyme, and its flanking sequences influence the efficiency of integration by the enzyme in a sequence-nonspecific manner. The enzyme forms a tetramer through interactions in the N-terminal part (residues 1 to 80), interacts nonspecifically with DNA and performs chemical catalysis in the C-terminal part (residues 165 to 328), and appears to recognize and bind the specific site of recombination in the middle portion (residues 81 to 164). It is worth noting that an N-terminally truncated mutant of Int(SSV2) (residues 81 to 328), which corresponded to the putative product of the 3'-end sequence of the Int(SSV2) gene of the integrated SSV2 genome, was unable to form tetramers but possessed all the catalytic properties of full-length Int(SSV2) except for the slightly reduced recombination activity. Our results suggest that, unlike λ integrase, SSV-type integrases alone are capable of catalyzing viral DNA recombination with the host genome in a simple and reversible fashion. IMPORTANCE: Archaea are host to a variety of viruses. A number of archaeal viruses are able to integrate their genome into the host genome. Many known archaeal viral integrases belong to a unique type, or the SSV type, of tyrosine recombinases. SSV-type integrases catalyze viral integration into and excision from a specific site on the host genome. However, the molecular details of the recombination process have yet to be fully understood because of the lack of an established in vitro recombination assay system. Here we report an in vitro assay for integration and excision by SSV2 integrase, a member of the SSV-type integrases. We show that SSV2 integrase alone is able to catalyze both integration and excision and reveal how different parts of the target DNA and the enzyme serve their roles in these processes. Therefore, our results provide mechanistic insights into a simple recombination process catalyzed by an archaeal integrase.
[Mh] Termos MeSH primário: DNA Nucleotidiltransferases/metabolismo
Fuselloviridae/enzimologia
Integrases/fisiologia
Filogenia
Sulfolobales/virologia
Integração Viral/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Cromatografia em Gel
Análise por Conglomerados
Ensaio de Desvio de Mobilidade Eletroforética
Técnicas In Vitro
Modelos Genéticos
Dados de Sequência Molecular
Oligonucleotídeos/genética
Reação em Cadeia da Polimerase
Ligação Proteica
Análise de Sequência de DNA
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Oligonucleotides); EC 2.7.7.- (DNA Nucleotidyltransferases); EC 2.7.7.- (Integrases); EC 2.7.7.- (Site-specific recombinase)
[Em] Mês de entrada:1601
[Cu] Atualização por classe:160501
[Lr] Data última revisão:
160501
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150821
[St] Status:MEDLINE
[do] DOI:10.1128/JVI.01637-15


  4 / 36 MEDLINE  
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[PMID]:26148716
[Au] Autor:van Wolferen M; Ma X; Albers SV
[Ad] Endereço:Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, Freiburg, Germany.
[Ti] Título:DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales.
[So] Source:J Bacteriol;197(18):2941-51, 2015 Sep.
[Is] ISSN:1098-5530
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:UNLABELLED: The ups operon of Sulfolobus species is highly induced upon UV stress. Previous studies showed that the pili encoded by this operon are involved in cellular aggregation, which is essential for subsequent DNA exchange between cells, resulting in homologous recombination. The presence of this pilus system increases the fitness of Sulfolobus cells under UV light-induced stress conditions, as the transfer of DNA takes place in order to repair UV-induced DNA lesions via homologous recombination. Four conserved genes (saci_1497 to saci_1500) which encode proteins with putative DNA processing functions are present downstream of the ups operon. In this study, we show that after UV treatment the cellular aggregation of strains with saci_1497, saci_1498, and saci_1500 deletions is similar to that of wild-type strains; their survival rates, however, were reduced and similar to or lower than those of the pilus deletion strains, which could not aggregate anymore. DNA recombination assays indicated that saci_1498, encoding a ParB-like protein, plays an important role in DNA transfer. Moreover, biochemical analysis showed that the endonuclease III encoded by saci_1497 nicks UV-damaged DNA. In addition, RecQ-like helicase Saci_1500 is able to unwind homologous recombination intermediates, such as Holliday junctions. Interestingly, a saci_1500 deletion mutant was more sensitive to UV light but not to the replication-stalling agents hydroxyurea and methyl methanesulfonate, suggesting that Saci_1500 functions specifically in the UV damage pathway. Together these results suggest a role of Saci_1497 to Saci_1500 in the repair or transfer of DNA that takes place after UV-induced damage to the genomic DNA of Sulfolobus acidocaldarius. IMPORTANCE: Sulfolobales species increase their fitness after UV stress by a UV-inducible pilus system that enables high rates of DNA exchange between cells. Downstream of the pilus operon, three genes that seem to play a role in the repair or transfer of the DNA between Sulfolobus cells were identified, and their possible functions are discussed. Next to the previously described role of UV-inducible pili in the exchange of DNA, we have thereby increased our knowledge of DNA transfer at the level of DNA processing. This paper therefore contributes to the overall understanding of the DNA exchange mechanism among Sulfolobales cells.
[Mh] Termos MeSH primário: Proteínas de Bactérias/metabolismo
Regulação Bacteriana da Expressão Gênica/efeitos da radiação
Estresse Fisiológico/efeitos da radiação
Sulfolobales/metabolismo
Sulfolobales/efeitos da radiação
Raios Ultravioleta
[Mh] Termos MeSH secundário: Proteínas de Bactérias/genética
DNA Bacteriano
Sulfolobales/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (DNA, Bacterial)
[Em] Mês de entrada:1511
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150708
[St] Status:MEDLINE
[do] DOI:10.1128/JB.00344-15


  5 / 36 MEDLINE  
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[PMID]:25142282
[Au] Autor:Xie W; Zhang CL; Wang J; Chen Y; Zhu Y; de la Torre JR; Dong H; Hartnett HE; Hedlund BP; Klotz MG
[Ad] Endereço:State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China; Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
[Ti] Título:Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables.
[So] Source:Environ Microbiol;17(5):1600-14, 2015 May.
[Is] ISSN:1462-2920
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community.
[Mh] Termos MeSH primário: Archaea/metabolismo
Sedimentos Geológicos/microbiologia
Éteres de Glicerila/metabolismo
Fontes Termais/microbiologia
Lipídeos de Membrana/metabolismo
[Mh] Termos MeSH secundário: Archaea/genética
Desulfurococcales/genética
Desulfurococcales/isolamento & purificação
Meio Ambiente
Éteres de Glicerila/análise
Concentração de Íons de Hidrogênio
Lipídeos de Membrana/análise
Oxigênio/metabolismo
Filogenia
RNA Ribossômico 16S/genética
Estações do Ano
Microbiologia do Solo
Sulfolobales/genética
Sulfolobales/isolamento & purificação
Temperatura Ambiente
Thermoplasmales/genética
Thermoplasmales/isolamento & purificação
Tibet
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Glyceryl Ethers); 0 (Membrane Lipids); 0 (RNA, Ribosomal, 16S); S88TT14065 (Oxygen)
[Em] Mês de entrada:1510
[Cu] Atualização por classe:150427
[Lr] Data última revisão:
150427
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140822
[St] Status:MEDLINE
[do] DOI:10.1111/1462-2920.12595


  6 / 36 MEDLINE  
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[PMID]:24560724
[Au] Autor:Di Giulio M
[Ad] Endereço:Laboratory for Molecular Evolution, Institute of Genetics and Biophysics 'Adriano Buzzati Traverso', CNR, Via P. Castellino, 111, 80131 Naples, Italy. Electronic address: massimo.digiulio@ibbr.cnr.it.
[Ti] Título:The split genes of Nanoarchaeum equitans have not originated in its lineage and have been merged in another Nanoarchaeota: a reply to Podar et al.
[So] Source:J Theor Biol;349:167-9, 2014 May 21.
[Is] ISSN:1095-8541
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:I reply to the suggestion of Podar et al. (2013) that the split genes of Nanoarchaeun equitans are a derived character, showing that their analysis is mistaken. In particular, I show that the split genes both proteins and tRNAs have not been split in N. equitans and have been on the contrary merged in the nanoarchaeon sequenced recently by Podar et al. (2013). This implies that the main argument of Podar et al. (2013) that there should be: "a unique propensity for splitting in the Nanoarchaeota that is most dramatically manifested in the Nanoarchaeum equitans lineage" is false. On the other hand, the analysis seems to favor the hypothesis that the split genes are an ancestral character. This would strengthen to greater extent a model for the origin of the tRNA molecule.
[Mh] Termos MeSH primário: Proteínas Arqueais/genética
Genoma Arqueal
Nanoarchaeota/fisiologia
Sulfolobales/fisiologia
Simbiose
[Pt] Tipo de publicação:COMMENT; LETTER; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Archaeal Proteins)
[Em] Mês de entrada:1501
[Cu] Atualização por classe:140331
[Lr] Data última revisão:
140331
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140225
[St] Status:MEDLINE


  7 / 36 MEDLINE  
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[PMID]:23710131
[Au] Autor:Satoh T; Watanabe K; Yamamoto H; Yamamoto S; Kurosawa N
[Ad] Endereço:Division of Environmental Engineering for Symbiosis, Graduate School of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan. stomoko76@soka.gr.jp
[Ti] Título:Archaeal community structures in the solfataric acidic hot springs with different temperatures and elemental compositions.
[So] Source:Archaea;2013:723871, 2013.
[Is] ISSN:1472-3654
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Archaeal 16S rRNA gene compositions and environmental factors of four distinct solfataric acidic hot springs in Kirishima, Japan were compared. The four ponds were selected by differences of temperature and total dissolved elemental concentration as follows: (1) Pond-A: 93°C and 1679 mg L(-1), (2) Pond-B: 66°C and 2248 mg L(-1), (3) Pond-C: 88°C and 198 mg L(-1), and (4) Pond-D: 67°C and 340 mg L(-1). In total, 431 clones of 16S rRNA gene were classified into 26 phylotypes. In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured thermoacidic spring clone group. In contrast to Pond-B and Pond-D, much less diverse archaeal clones were detected in Pond-A and Pond-C showing higher temperatures. However, dominant groups in these ponds were also different from each other. The members of the order Sulfolobales shared 89% of total clones in Pond-A, and the uncultured crenarchaeal groups shared 99% of total Pond-C clones. Therefore, species compositions and biodiversity were clearly different among the ponds showing different temperatures and dissolved elemental concentrations.
[Mh] Termos MeSH primário: Archaea/classificação
Archaea/genética
Fontes Termais/microbiologia
Consórcios Microbianos
[Mh] Termos MeSH secundário: Sequência de Bases
Biodiversidade
DNA Arqueal/genética
Genes Arqueais
Japão
Consórcios Microbianos/genética
Dados de Sequência Molecular
Filogenia
RNA Ribossômico 16S/genética
Análise de Sequência de DNA
Sulfolobales/classificação
Sulfolobales/genética
Temperatura Ambiente
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Archaeal); 0 (RNA, Ribosomal, 16S)
[Em] Mês de entrada:1311
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130528
[St] Status:MEDLINE
[do] DOI:10.1155/2013/723871


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[PMID]:23607726
[Au] Autor:Huang Q; Jiang H; Briggs BR; Wang S; Hou W; Li G; Wu G; Solis R; Arcilla CA; Abrajano T; Dong H
[Ad] Endereço:Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA.
[Ti] Título:Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines.
[So] Source:FEMS Microbiol Ecol;85(3):452-64, 2013 Sep.
[Is] ISSN:1574-6941
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The microbial diversity was investigated in sediments of six acidic to circumneutral hot springs (Temperature: 60-92 °C, pH 3.72-6.58) in the Philippines using an integrated approach that included geochemistry and 16S rRNA gene pyrosequencing. Both bacterial and archaeal abundances were lower in high-temperature springs than in moderate-temperature ones. Overall, the archaeal community consisted of sequence reads that exhibited a high similarity (nucleotide identity > 92%) to phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea. The bacterial community was composed of sequence reads moderately related (nucleotide identity > 90%) to 17 phyla, with Aquificae and Firmicutes being dominant. These phylogenetic groups were correlated with environmental conditions such as temperature, dissolved sulfate and calcium concentrations in spring water, and sediment properties including total nitrogen, pyrite, and elemental sulfur. Based on the phylogenetic inference, sulfur metabolisms appear to be key physiological functions in these hot springs. Sulfobacillus (within phylum Firmicutes) along with members within Sulfolobales were abundant in two high-temperature springs (> 76 °C), and they were hypothesized to play an important role in regulating the sulfur cycling under high-temperature conditions. The results of this study improve our understanding of microbial diversity and community composition in acidic to circumneutral terrestrial hot springs and their relationships with geochemical conditions.
[Mh] Termos MeSH primário: Archaea/classificação
Bactérias/classificação
Fontes Termais/microbiologia
[Mh] Termos MeSH secundário: Archaea/genética
Archaea/isolamento & purificação
Bactérias/genética
Bactérias/isolamento & purificação
Biodiversidade
Crenarchaeota/genética
Crenarchaeota/isolamento & purificação
Fontes Termais/química
Temperatura Alta
Filipinas
Filogenia
RNA Ribossômico 16S/genética
Sulfolobales/genética
Sulfolobales/isolamento & purificação
Sulfolobales/metabolismo
Enxofre/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (RNA, Ribosomal, 16S); 70FD1KFU70 (Sulfur)
[Em] Mês de entrada:1311
[Cu] Atualização por classe:131121
[Lr] Data última revisão:
131121
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130424
[St] Status:MEDLINE
[do] DOI:10.1111/1574-6941.12134


  9 / 36 MEDLINE  
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[PMID]:23607440
[Au] Autor:Podar M; Makarova KS; Graham DE; Wolf YI; Koonin EV; Reysenbach AL
[Ad] Endereço:Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA. podarm@ornl.gov
[Ti] Título:Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.
[So] Source:Biol Direct;8:9, 2013 Apr 22.
[Is] ISSN:1745-6150
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. CONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. REVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia.
[Mh] Termos MeSH primário: Proteínas Arqueais/genética
Genoma Arqueal
Nanoarchaeota/fisiologia
Sulfolobales/fisiologia
Simbiose
[Mh] Termos MeSH secundário: Proteínas Arqueais/metabolismo
Evolução Biológica
Evolução Molecular
Dados de Sequência Molecular
Nanoarchaeota/genética
Filogenia
Reação em Cadeia da Polimerase
Homologia de Sequência
Sulfolobales/genética
Wyoming
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., INTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Archaeal Proteins)
[Em] Mês de entrada:1307
[Cu] Atualização por classe:161019
[Lr] Data última revisão:
161019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130424
[St] Status:MEDLINE
[do] DOI:10.1186/1745-6150-8-9


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[PMID]:23403393
[Au] Autor:Shah SA; Erdmann S; Mojica FJ; Garrett RA
[Ad] Endereço:Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
[Ti] Título:Protospacer recognition motifs: mixed identities and functional diversity.
[So] Source:RNA Biol;10(5):891-9, 2013 May.
[Is] ISSN:1555-8584
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Protospacer adjacent motifs (PAMs) were originally characterized for CRISPR-Cas systems that were classified on the basis of their CRISPR repeat sequences. A few short 2-5 bp sequences were identified adjacent to one end of the protospacers. Experimental and bioinformatical results linked the motif to the excision of protospacers and their insertion into CRISPR loci. Subsequently, evidence accumulated from different virus- and plasmid-targeting assays, suggesting that these motifs were also recognized during DNA interference, at least for the recently classified type I and type II CRISPR-based systems. The two processes, spacer acquisition and protospacer interference, employ different molecular mechanisms, and there is increasing evidence to suggest that the sequence motifs that are recognized, while overlapping, are unlikely to be identical. In this article, we consider the properties of PAM sequences and summarize the evidence for their dual functional roles. It is proposed to use the terms protospacer associated motif (PAM) for the conserved DNA sequence and to employ spacer acqusition motif (SAM) and target interference motif (TIM), respectively, for acquisition and interference recognition sites.
[Mh] Termos MeSH primário: Archaea/genética
Bactérias/genética
Sistemas CRISPR-Cas/genética
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas
Motivos de Nucleotídeos
[Mh] Termos MeSH secundário: Archaea/metabolismo
Bactérias/metabolismo
Sequência de Bases
DNA Intergênico
DNA Viral/genética
Escherichia coli/genética
Escherichia coli/metabolismo
Dados de Sequência Molecular
Plasmídeos
Sulfolobales/genética
Sulfolobales/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Intergenic); 0 (DNA, Viral)
[Em] Mês de entrada:1401
[Cu] Atualização por classe:150219
[Lr] Data última revisão:
150219
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130214
[St] Status:MEDLINE
[do] DOI:10.4161/rna.23764



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