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  1 / 1154 MEDLINE  
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[PMID]:29179671
[Au] Autor:Hudaiberdiev S; Shmakov S; Wolf YI; Terns MP; Makarova KS; Koonin EV
[Ad] Endereço:National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
[Ti] Título:Phylogenomics of Cas4 family nucleases.
[So] Source:BMC Evol Biol;17(1):232, 2017 Nov 28.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci (solo-Cas4) and is also found in mobile genetic elements (MGE-Cas4). RESULTS: As part of our ongoing investigation of CRISPR-Cas evolution, we explored the phylogenomics of the Cas4 family. About 90% of the archaeal genomes encode Cas4 compared to only about 20% of the bacterial genomes. Many archaea encode both the CRISPR-associated form (CAS-Cas4) and solo-Cas4, whereas in bacteria, this combination is extremely rare. The solo-cas4 genes are over-represented in environmental bacteria and archaea with small genomes that typically lack CRISPR-Cas, suggesting that Cas4 could perform uncharacterized defense or repair functions in these microbes. Phylogenomic analysis indicates that both the CRISPR-associated cas4 genes are often transferred horizontally but almost exclusively, as part of the adaptation module. The evolutionary integrity of the adaptation module sharply contrasts the rampant shuffling of CRISPR-cas modules whereby a given variant of the adaptation module can combine with virtually any effector module. The solo-cas4 genes evolve primarily via vertical inheritance and are subject only to occasional horizontal transfer. The selection pressure on cas4 genes does not substantially differ between CAS-Cas4 and solo-cas4, and is close to the genomic median. Thus, cas4 genes, similarly to cas1 and cas2, evolve similarly to 'regular' microbial genes involved in various cellular functions, showing no evidence of direct involvement in virus-host arms races. A notable feature of the Cas4 family evolution is the frequent recruitment of cas4 genes by various mobile genetic elements (MGE), particularly, archaeal viruses. The functions of Cas4 in these elements are unknown and potentially might involve anti-defense roles. CONCLUSIONS: Unlike most of the other Cas proteins, Cas4 family members are as often encoded by stand-alone genes as they are incorporated in CRISPR-Cas systems. In addition, cas4 genes were repeatedly recruited by MGE, perhaps, for anti-defense functions. Experimental characterization of the solo and MGE-encoded Cas4 nucleases is expected to reveal currently uncharacterized defense and anti-defense systems and their interactions with CRISPR-Cas systems.
[Mh] Termos MeSH primário: Sistemas CRISPR-Cas/genética
Endonucleases/genética
Genômica
Família Multigênica
[Mh] Termos MeSH secundário: Archaea/enzimologia
Archaea/genética
Bactérias/enzimologia
Bactérias/genética
Sequência de Bases
Elementos de DNA Transponíveis/genética
Transferência Genética Horizontal/genética
Loci Gênicos
Genoma Arqueal
Genoma Bacteriano
Filogenia
Seleção Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Transposable Elements); EC 3.1.- (Endonucleases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1081-1


  2 / 1154 MEDLINE  
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[PMID]:28460196
[Au] Autor:Warinner C; Herbig A; Mann A; Fellows Yates JA; Weiß CL; Burbano HA; Orlando L; Krause J
[Ad] Endereço:Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de.
[Ti] Título:A Robust Framework for Microbial Archaeology.
[So] Source:Annu Rev Genomics Hum Genet;18:321-356, 2017 Aug 31.
[Is] ISSN:1545-293X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field.
[Mh] Termos MeSH primário: Archaea/isolamento & purificação
Bactérias/isolamento & purificação
DNA Antigo/análise
Metagenômica/métodos
Microbiota/genética
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Archaea/genética
Arqueologia/métodos
Bactérias/genética
Genoma Arqueal
Genoma Bacteriano
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (DNA, Ancient)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180228
[Lr] Data última revisão:
180228
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1146/annurev-genom-091416-035526


  3 / 1154 MEDLINE  
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[PMID]:28787424
[Au] Autor:Bowers RM; Kyrpides NC; Stepanauskas R; Harmon-Smith M; Doud D; Reddy TBK; Schulz F; Jarett J; Rivers AR; Eloe-Fadrosh EA; Tringe SG; Ivanova NN; Copeland A; Clum A; Becraft ED; Malmstrom RR; Birren B; Podar M; Bork P; Weinstock GM; Garrity GM; Dodsworth JA; Yooseph S; Sutton G; Glöckner FO; Gilbert JA; Nelson WC; Hallam SJ; Jungbluth SP; Ettema TJG; Tighe S; Konstantinidis KT; Liu WT; Baker BJ; Rattei T; Eisen JA; Hedlund B; McMahon KD; Fierer N; Knight R; Finn R; Cochrane G; Karsch-Mizrachi I; Tyson GW; Rinke C; Lapidus A; Meyer F; Yilmaz P; Parks DH; Eren AM; Genome Standards Consortium
[Ad] Endereço:Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
[Ti] Título:Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
[So] Source:Nat Biotechnol;35(8):725-731, 2017 Aug 08.
[Is] ISSN:1546-1696
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
[Mh] Termos MeSH primário: Genoma Arqueal/genética
Genômica/métodos
Metagenômica/métodos
[Mh] Termos MeSH secundário: Genoma Bacteriano/genética
Genômica/normas
Metagenômica/normas
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170821
[Lr] Data última revisão:
170821
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170809
[St] Status:MEDLINE
[do] DOI:10.1038/nbt.3893


  4 / 1154 MEDLINE  
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[PMID]:28630130
[Au] Autor:Mao D; Grogan DW
[Ad] Endereço:Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
[Ti] Título:How a Genetically Stable Extremophile Evolves: Modes of Genome Diversification in the Archaeon Sulfolobus acidocaldarius.
[So] Source:J Bacteriol;199(17), 2017 Sep 01.
[Is] ISSN:1098-5530
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In order to analyze in molecular terms how genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 × 10 , which is about 0.15% of the corresponding divergence reported for The most variable features of wild-type genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions. Natural isolates, however, also revealed large insertions/deletions and inversions, which did not occur in any of the laboratory-manipulated strains. Several of the large insertions/deletions could be attributed to the integration or excision of mobile genetic elements (MGEs), and each MGE represented a distinct system of site-specific recombination. The mode of recombination associated with one MGE, a provirus related to , was also seen in certain chromosomal inversions. Artificially induced mutations, non-MGE insertions/deletions, and small PMs exhibited different distributions over the genome, suggesting that large-scale patterning of genomes begins early in the divergence process. Unlike induced mutations, natural base pair substitutions occurred in clusters, and one cluster exhibited properties expected of nonreciprocal recombination (gene conversion) between dispersed imperfect repeats. Taken together, the results identify simple replication errors, slipped-strand events promoted by tandem repeats, homologous recombination, and rearrangements promoted by MGEs as the primary sources of genetic variation for this extremely acidophilic archaeon in its geothermal environment. The optimal growth temperatures of hyperthermophilic archaea accelerate DNA decomposition, which is expected to make DNA repair especially important for their genetic stability, yet these archaea lack certain broadly conserved types of DNA repair proteins. In this study, the genome of the extreme thermoacidophile was found to be remarkably stable, accumulating few mutations in many (though not all) laboratory manipulations and in natural populations. Furthermore, all the genetic processes that were inferred to diversify these genomes also operate in mesophilic bacteria and eukaryotes. This suggests that a common set of mechanisms produces most of the genetic variation in all microorganisms, despite the fundamental differences in physiology, DNA repair systems, and genome structure represented in the three domains of life.
[Mh] Termos MeSH primário: Evolução Molecular
Extremófilos/genética
Genoma Arqueal
Polimorfismo Genético
Sulfolobus acidocaldarius/genética
[Mh] Termos MeSH secundário: Replicação do DNA
Sequências Repetitivas Dispersas
Mutação
Recombinação Genética
Sulfolobus acidocaldarius/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170827
[Lr] Data última revisão:
170827
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170621
[St] Status:MEDLINE


  5 / 1154 MEDLINE  
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[PMID]:28628615
[Au] Autor:Cossu M; Badel C; Catchpole R; Gadelle D; Marguet E; Barbe V; Forterre P; Oberto J
[Ad] Endereço:Institute for Integrative Biology of the Cell (I2BC), Microbiology Department, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
[Ti] Título:Flipping chromosomes in deep-sea archaea.
[So] Source:PLoS Genet;13(6):e1006847, 2017 Jun.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements. We characterized the integrase from Thermococcus nautili plasmid pTN3 and showed that besides canonical site-specific reactions, it catalyzes low sequence specificity recombination reactions with the same outcome as homologous recombination events on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other known tyrosine recombinases. Through serial culturing, we showed that the integrase-mediated divergence of T. nautili strains occurs at an astonishing rate, with at least four large-scale genomic inversions appearing within 60 generations. Our results and the ubiquitous distribution of pTN3-like integrated elements suggest that a major mechanism of evolution of an entire order of Archaea results from the activity of a selfish mobile genetic element.
[Mh] Termos MeSH primário: Inversão Cromossômica/genética
Evolução Molecular
Integrases/genética
Thermococcales/genética
[Mh] Termos MeSH secundário: Genoma Arqueal
Sequências Repetitivas Dispersas/genética
Plasmídeos/genética
Recombinação Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 2.7.7.- (Integrases)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170719
[Lr] Data última revisão:
170719
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170620
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006847


  6 / 1154 MEDLINE  
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[PMID]:28604660
[Au] Autor:Mukherjee S; Seshadri R; Varghese NJ; Eloe-Fadrosh EA; Meier-Kolthoff JP; Göker M; Coates RC; Hadjithomas M; Pavlopoulos GA; Paez-Espino D; Yoshikuni Y; Visel A; Whitman WB; Garrity GM; Eisen JA; Hugenholtz P; Pati A; Ivanova NN; Woyke T; Klenk HP; Kyrpides NC
[Ad] Endereço:Department of Energy, Joint Genome Institute, Walnut Creek, California, USA.
[Ti] Título:1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
[So] Source:Nat Biotechnol;35(7):676-683, 2017 Jul.
[Is] ISSN:1546-1696
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/normas
Bases de Dados Genéticas
Genoma Arqueal/genética
Genoma Bacteriano/genética
Sequenciamento de Nucleotídeos em Larga Escala/normas
Bases de Conhecimento
[Mh] Termos MeSH secundário: Sistemas de Gerenciamento de Base de Dados
Conjuntos de Dados como Assunto
Enciclopédias como Assunto
Valores de Referência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170818
[Lr] Data última revisão:
170818
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170613
[St] Status:MEDLINE
[do] DOI:10.1038/nbt.3886


  7 / 1154 MEDLINE  
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[PMID]:28602403
[Au] Autor:Carroll M; Zhou X
[Ad] Endereço:Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
[Ti] Título:Panacea in progress: CRISPR and the future of its biological research introduction.
[So] Source:Microbiol Res;201:63-74, 2017 Aug.
[Is] ISSN:1618-0623
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:The elucidation of the CRISPR (clustered, regularly interspaced, short palindromic repeats) adaptive immune system endogenous to most microbial life has culminated in progress in a diversity of scientific disciplines. The concurrently promising and eccentric nature of its theoretically plausible applications has wrought enthusiasm in the research community globally, potentiating advancements in human and animal health, ecological stability, and economic wellbeing, that would hitherto be considered the unattainable fancies of a futurist. It may be supposed that the tomes of science fiction are the true books of prophecy. Here, we narrate the scientific dialogue regarding CRISPR/Cas biotechnologies, from the happenstantial initial observation of the locus to the litany of intriguing contemporary endeavors. We discuss the mechanistic underpinnings in detail, and the corpulent body of literature on CRISPR-based biotech is digested into a germane and informative review. CRISPR applications such as microbiome engineering in order to enhance the human immune system beyond the fortitude of the wild type, bacterial genome editing in industrial and medical aspects, conquering antibiotic resistance, the development of novel antimicrobial techniques, the harvesting of solventogenic microbes, the development of antifungal therapies, and investigation of the genetic properties of fungi, are here represented, and the authors posit unconventional, and at times gainfully tangential, thoughts and concepts in order to encourage a reflective disposition towards this sophisticated device of nature: a panacea in progress, such that the most impassive and technical writing still carries the ring of poetry.
[Mh] Termos MeSH primário: Archaea/metabolismo
Bactérias/metabolismo
Proteínas Associadas a CRISPR/metabolismo
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/imunologia
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/fisiologia
Fungos/metabolismo
[Mh] Termos MeSH secundário: Animais
Anti-Infecciosos/farmacologia
Archaea/genética
Archaea/imunologia
Archaea/virologia
Bactérias/genética
Bactérias/imunologia
Bactérias/virologia
Bacteriófagos/imunologia
Resistência Microbiana a Medicamentos
Fungos/imunologia
Fungos/patogenicidade
Edição de Genes
Engenharia Genética
Genoma Arqueal
Genoma Bacteriano
Seres Humanos
Sistemas de Secreção Tipo IV/metabolismo
Sistemas de Secreção Tipo IV/fisiologia
Fatores de Virulência/isolamento & purificação
Vírus/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Anti-Infective Agents); 0 (CRISPR-Associated Proteins); 0 (Type IV Secretion Systems); 0 (Virulence Factors)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171002
[Lr] Data última revisão:
171002
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170613
[St] Status:MEDLINE


  8 / 1154 MEDLINE  
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[PMID]:28520982
[Au] Autor:Qi L; Yue L; Feng D; Qi F; Li J; Dong X
[Ad] Endereço:State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, PR China.
[Ti] Título:Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis.
[So] Source:Nucleic Acids Res;45(12):7285-7298, 2017 Jul 07.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively. A predominant uridine downstream PSSs served as a processing signature. Remarkably, 5΄P-seq detected overrepresented uPSS and iPSS in the polycistronic operons encoding ribosomal proteins, and the majority upstream and proximal ribosome binding sites, suggesting a regulatory role of processing on translation initiation. The processed transcripts showed increased stability and translation efficiency. Particularly, processing within the tricistronic transcript of rplA-rplJ-rplL enhanced the translation of rplL, which can provide a driving force for the 1:4 stoichiometry of L10 to L12 in the ribosome. Growth-associated mRNA processing intensities were also correlated with the cellular ribosomal protein levels, thereby suggesting that mRNA processing is involved in tuning growth-dependent ribosome synthesis. In conclusion, our findings suggest that mRNA processing-mediated post-transcriptional regulation is a potential mechanism of ribosomal protein synthesis and stoichiometry.
[Mh] Termos MeSH primário: Proteínas Arqueais/genética
Genoma Arqueal
Mathanococcus/genética
Methanosarcinaceae/genética
Processamento Pós-Transcricional do RNA
RNA Mensageiro/genética
Proteínas Ribossômicas/genética
[Mh] Termos MeSH secundário: Proteínas Arqueais/metabolismo
Sequência de Bases
Clonagem Molecular
Escherichia coli/genética
Escherichia coli/metabolismo
Expressão Gênica
Mathanococcus/metabolismo
Methanosarcinaceae/metabolismo
Conformação de Ácido Nucleico
Iniciação Traducional da Cadeia Peptídica
Isoformas de Proteínas/genética
Isoformas de Proteínas/metabolismo
RNA Mensageiro/química
RNA Mensageiro/metabolismo
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Proteínas Ribossômicas/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (Protein Isoforms); 0 (RNA, Messenger); 0 (Recombinant Proteins); 0 (Ribosomal Proteins); 70815-33-7 (ribosomal protein L7-L12)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171017
[Lr] Data última revisão:
171017
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170519
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx454


  9 / 1154 MEDLINE  
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[PMID]:28502981
[Au] Autor:Wagner A; Whitaker RJ; Krause DJ; Heilers JH; van Wolferen M; van der Does C; Albers SV
[Ad] Endereço:Molecular Biology of Archaea, Institute of Biology II - Microbiology, Albert Ludwigs University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany.
[Ti] Título:Mechanisms of gene flow in archaea.
[So] Source:Nat Rev Microbiol;15(8):492-501, 2017 Aug.
[Is] ISSN:1740-1534
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution.
[Mh] Termos MeSH primário: Archaea/genética
Fluxo Gênico
Genoma Arqueal
[Mh] Termos MeSH secundário: Evolução Molecular
Transferência Genética Horizontal
Genes Bacterianos
Genômica
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170720
[Lr] Data última revisão:
170720
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170516
[St] Status:MEDLINE
[do] DOI:10.1038/nrmicro.2017.41


  10 / 1154 MEDLINE  
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[PMID]:28418097
[Au] Autor:Ahlgren NA; Chen Y; Needham DM; Parada AE; Sachdeva R; Trinh V; Chen T; Fuhrman JA
[Ad] Endereço:Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
[Ti] Título:Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems.
[So] Source:Environ Microbiol;19(6):2434-2452, 2017 Jun.
[Is] ISSN:1462-2920
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes. The PT modification genes and an adjacent putative restriction enzyme (RE) operon likely form a restriction modification (RM) system for defence from foreign DNA. PacBio sequencing showed >98% methylation at two motifs, and inferred PT guanine modification of 19% of possible TGCA sites. Metagenomic recruitment also reveals the putative virus region and PT modification and RE genes are present in 18-26%, 9-14% and <1.5% of natural populations at 150 m with ≥85% identity to strain SPOT01. The presence of multiple probable RM systems in a highly streamlined genome suggests a surprising importance for defence from foreign DNA for dilute populations that infrequently encounter viruses or other cells. This new strain provides new insights into the ecology, including viral interactions, of this important group of marine microbes.
[Mh] Termos MeSH primário: Archaea
DNA Arqueal/genética
Genoma Arqueal/genética
Vírus/genética
[Mh] Termos MeSH secundário: Organismos Aquáticos/genética
Archaea/classificação
Archaea/genética
Archaea/virologia
Sequência de Bases
Metagenômica
RNA Ribossômico 16S/genética
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Archaeal); 0 (RNA, Ribosomal, 16S)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171109
[Lr] Data última revisão:
171109
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170419
[St] Status:MEDLINE
[do] DOI:10.1111/1462-2920.13768



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