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  • 1
    Language: English
    In: Nucleic acids research, 28 February 2017, Vol.45(4), pp.1902-1913
    Description: CRISPR-Cas (clustered regularly interspaced short palindromic repeats and the associated genes) constitute adaptive immune systems in bacteria and archaea and they provide sequence specific immunity against foreign nucleic acids. CRISPR-Cas systems are activated by viral infection. However, little is known about how CRISPR-Cas systems are activated in response to viral infection or how their expression is controlled in the absence of viral infection. Here, we demonstrate that both the transcriptional regulator Csa3b, and the type I-A interference complex Cascade, are required to transcriptionally repress the interference gene cassette in the archaeon Sulfolobus. Csa3b binds to two palindromic repeat sites in the promoter region of the cassette and facilitates binding of the Cascade to the promoter region. Upon viral infection, loading of Cascade complexes onto crRNA-matching protospacers leads to relief of the transcriptional repression. Our data demonstrate a mechanism coupling CRISPR-Cas surveillance of protospacers to transcriptional regulation of the interference gene cassette thereby allowing a fast response to viral infection.
    Keywords: Crispr-Cas Systems ; Gene Expression Regulation, Archaeal ; Transcription, Genetic ; Archaeal Proteins -- Metabolism ; Crispr-Associated Proteins -- Metabolism ; Sulfolobus -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 2
    In: Nature, 2005, Vol.436(7054), p.1101
    Description: Viruses are thought to be functionally inactive once they are outside and independent of their host cell. Here we describe an exceptional property of a newly discovered virus that infects a hyperthermophilic archaeon growing in acidic hot springs: the lemon-shaped viral particle develops a very long tail at each of its pointed ends after being released from its host cell. The process occurs only at the temperature of the host's habitat (75-90 degrees C) and it does not require the presence of the host cell, an exogenous energy source or any cofactors. This host-independent morphological development may be a strategy for viral survival in an environment that is unusually harsh and has limited host availability.
    Keywords: Virus Assembly ; Acidianus -- Virology ; Archaeal Viruses -- Growth & Development;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 3
    Language: English
    In: 2012, Vol.7(10), p.e45847
    Description: Acidianus two-tailed virus (ATV) infects crenarchaea of the genus Acidianus living in terrestrial thermal springs at extremely high temperatures and low pH. ATV is a member of the Bicaudaviridae virus family and undergoes extra-cellular development of two tails, a process that is unique in the viral world. To understand this intriguing phenomenon, we have undertaken structural studies of ATV virion proteins and here we present the crystal structure of one of these proteins, ATV . ATV forms tetramers in solution and a molecular envelope is provided for the tetramer, computed from small-angle X-ray scattering (SAXS) data. The crystal structure has properties typical of hyperthermostable proteins, including a relatively high number of salt bridges. However, the protein also exhibits flexible loops and surface pockets. Remarkably, ATV displays a new protein fold, consistent with the absence of homologues of this protein in public sequence databases.
    Keywords: Research Article ; Biology ; Virology ; Microbiology ; Computational Biology ; Developmental Biology ; Biochemistry
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Biology and Fertility of Soils, 2017, Vol.53(5), p.479(6)
    Description: To access, purchase, authenticate, or subscribe to the full-text of this article, please visit this link: http://dx.doi.org/10.1007/s00374-017-1191-3 Byline: Gisle Vestergaard (1), Stefanie Schulz (1), Anne Scholer (1), Michael Schloter (1,2) Author Affiliation: (1) Research Unit for Environmental Genomics, Helmholtz Zentrum Munchen, Ingolstadter Landstr. 1, 85764, Neuherberg, Germany (2) Chair for Soil Science, Technische Universitat Munchen, Munich, Germany Article History: Registration Date: 08/03/2017 Received Date: 12/06/2016 Accepted Date: 07/03/2017 Online Date: 16/03/2017
    Keywords: Big Data – Usage
    ISSN: 0178-2762
    E-ISSN: 14320789
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  • 5
    Language: English
    In: Journal of Bacteriology, Oct, 2008, Vol.190(19-20), p.6837(9)
    Description: A newly characterized archaeal rudivirus Stygiolobus rod-shaped virus (SRV), which infects a hyperthermophilic Stygiolobus species, was isolated from a hot spring in the Azores, Portugal. Its virions are rod-shaped, 702 ([+ or -] 50) by 22 ([+ or -] 3) nm in size, and nonenveloped and carry three tail fibers at each terminus. The linear double-stranded DNA genome contains 28,096 bp and an inverted terminal repeat of 1,030 bp. The SRV shows morphological and genomic similarities to the other characterized rudiviruses Sulfolobus rod-shaped virus 1 (SIRV1), SIRV2, and Acidianus rod-shaped virus 1, isolated from hot acidic springs of Iceland and Italy. The single major rudiviral structural protein is shown to generate long tubular structures in vitro of similar dimensions to those of the virion, and we estimate that the virion constitutes a single, superhelical, doublestranded DNA embedded into such a protein structure. Three additional minor conserved structural proteins are also identified. Ubiquitous rudiviral proteins with assigned functions include glycosyl transferases and a S-adenosylmethionine-dependent methyltransferase, as well as a Holliday junction resolvase, a transcriptionally coupled helicase and nuclease implicated in DNA replication. Analysis of matches between known crenarchaeal chromosomal CRISPR spacer sequences, implicated in a viral defense system, and rudiviral genomes revealed that about 10% of the 3,042 unique acidothermophile spacers yield significant matches to rudiviral genomes, with a bias to highly conserved protein genes, consistent with the widespread presence of rudiviruses in hot acidophilic environments. We propose that the 12-bp indels which are commonly found in conserved rudiviral protein genes may be generated as a reaction to the presence of the host CRISPR defense system.
    Keywords: Bacteriophages -- Physiological Aspects ; Bacteriophages -- Genetic Aspects ; Bacteriophages -- Research ; Cellular Immunity -- Physiological Aspects ; Cellular Immunity -- Genetic Aspects ; Cellular Immunity -- Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: RNA Biology, 01 February 2014, Vol.11(2), pp.156-167
    Description: CRISPR adaptive immune systems were analyzed for all available completed genomes of archaea, which included representatives of each of the main archaeal phyla. Initially, all proteins encoded within, and proximal to, CRISPR-cas loci were clustered...
    Keywords: Crispr ; Cas ; Type I ; Type III ; Archaea ; Anatomy & Physiology
    ISSN: 1547-6286
    E-ISSN: 1555-8584
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  • 7
    Language: English
    In: Trends in Microbiology, 2011, Vol.19(11), pp.549-556
    Description: CRISPR (clustered regularly interspaced short palindromic repeats)-based immune systems are essentially modular with three primary functions: the excision and integration of new spacers, the processing of CRISPR transcripts to yield mature CRISPR RNAs (crRNAs), and the targeting and cleavage of foreign nucleic acid. The primary target appears to be the DNA of foreign genetic elements, but the CRISPR/Cmr system that is widespread amongst archaea also specifically targets and cleaves RNA . The archaeal CRISPR systems tend to be both diverse and complex. Here we examine evidence for exchange of functional modules between archaeal systems that is likely to contribute to their diversity, particularly of their nucleic acid targeting and cleavage functions. The molecular constraints that limit such exchange are considered. We also summarize mechanisms underlying the dynamic nature of CRISPR loci and the evidence for intergenomic exchange of CRISPR systems.
    Keywords: Biology
    ISSN: 0966-842X
    E-ISSN: 1878-4380
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  • 8
    Language: English
    In: PLoS ONE, 01 January 2017, Vol.12(9), p.e0184119
    Description: In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 9
    Language: English
    In: Biology and Fertility of Soils, 2017, Vol.53(5), pp.485-489
    Description: The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of PCR-amplified marker genes by next-generation sequencing. While these high-throughput methods offer...
    Keywords: Life Sciences ; Next-Generation Sequencing ; Amplicon Sequencing ; 16s Rrna ; Sequencing Depth ; Bioinformatics ; Agriculture ; Biology ; Ecology
    ISSN: 0178-2762
    E-ISSN: 1432-0789
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  • 10
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 13 March 2018, Vol.115(11), pp.2670-2675
    Description: Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: () a physico-chemical characterization of the soil habitability after an exceptional rain event, () identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], () measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and () microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity.
    Keywords: Mars ; Aridity ; Biomarker ; Habitat ; Microbial Activity ; Ecosystem ; Soil Microbiology ; Bacteria -- Isolation & Purification
    ISBN: 1714341115
    ISSN: 00278424
    E-ISSN: 1091-6490
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