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  • 1
    Language: English
    In: Nature, 01 May 2008, Vol.453(7191), pp.120-3
    Description: The universality of ribonuclease P (RNase P), the ribonucleoprotein essential for transfer RNA (tRNA) 5' maturation, is challenged in the archaeon Nanoarchaeum equitans. Neither extensive computational analysis of the genome nor biochemical tests in cell extracts revealed the existence of this enzyme. Here we show that the conserved placement of its tRNA gene promoters allows the synthesis of leaderless tRNAs, whose presence was verified by the observation of 5' triphosphorylated mature tRNA species. Initiation of tRNA gene transcription requires a purine, which coincides with the finding that tRNAs with a cytosine in position 1 display unusually extended 5' termini with an extra purine residue. These tRNAs were shown to be substrates for their cognate aminoacyl-tRNA synthetases. These findings demonstrate how nature can cope with the loss of the universal and supposedly ancient RNase P through genomic rearrangement at tRNA genes under the pressure of genome condensation.
    Keywords: Evolution, Molecular ; Genes, Archaeal -- Genetics ; Nanoarchaeota -- Genetics ; Promoter Regions, Genetic -- Genetics ; RNA, Archaeal -- Genetics ; RNA, Transfer -- Genetics ; Ribonuclease P -- Deficiency
    ISSN: 00280836
    E-ISSN: 1476-4687
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  • 2
    In: Annals of the New York Academy of Sciences, April 2015, Vol.13411(1), pp.188-193
    Description: Profiling the RNA production in hyperthermophilic archaea revealed an abundance of small RNA–guided processes near the upper temperature limit of life. Archaea utilize the base‐pairing ability of RNA guide sequences to target ribosomal RNAs, transfer RNAs, messenger RNAs, and viral genomes. Cellular processes that are guided by small RNAs include the modification of RNA molecules, ‐splicing, gene regulation, and RNA and DNA degradation. Here, a brief overview of our knowledge on small guide RNA genes in archaeal genomes is provided and examples of their putative roles in genome evolution are described.
    Keywords: Crispr ; C/D Box Srnas ; Transfer Rna Fragments ; Virus Defense ; Genome Rearrangements ; Archaea
    ISSN: 0077-8923
    E-ISSN: 1749-6632
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  • 3
    Language: English
    In: Annals of the New York Academy of Sciences, 2015, Vol.1341(1), p.188(6)
    Description: To purchase or authenticate to the full-text of this article, please visit this link: http://onlinelibrary.wiley.com/doi/10.1111/nyas.12643/abstract Byline: Guenther Witzany, Lennart Randau Keywords: CRISPR; C/D box sRNAs; transfer RNA fragments; virus defense; genome rearrangements; archaea Profiling the RNA production in hyperthermophilic archaea revealed an abundance of small RNA-guided processes near the upper temperature limit of life. Archaea utilize the base-pairing ability of RNA guide sequences to target ribosomal RNAs, transfer RNAs, messenger RNAs, and viral genomes. Cellular processes that are guided by small RNAs include the modification of RNA molecules, trans-splicing, gene regulation, and RNA and DNA degradation. Here, a brief overview of our knowledge on small guide RNA genes in archaeal genomes is provided and examples of their putative roles in genome evolution are described.
    Keywords: Transfer RNA ; Genes ; Genomics
    ISSN: 0077-8923
    E-ISSN: 17496632
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  • 4
    In: PLoS ONE, 2014, Vol.9(8)
    Description: CRISPR-Cas systems provide immunity against viral attacks in archaeal and bacterial cells. Type I systems employ a Cas protein complex termed Cascade, which utilizes small CRISPR RNAs to detect and degrade the exogenic DNA. A small sequence motif, the PAM, marks the foreign substrates. Previously, a recombinant type I-A Cascade complex from the archaeon Thermoproteus tenax was shown to target and degrade DNA in vitro, dependent on a native PAM sequence. Here, we present the biochemical analysis of the small subunit, Csa5, of this Cascade complex. T. tenax Csa5 preferentially bound ssDNA and mutants that showed decreased ssDNA-binding and reduced Cascade-mediated DNA cleavage were identified. Csa5 oligomerization prevented DNA binding. Specific recognition of the PAM sequence was not observed. Phylogenetic analyses identified Csa5 as a universal member of type I-A systems and revealed three distinct groups. A potential role of Csa5 in R-loop stabilization is discussed.
    Keywords: Research Article ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: Journal of Bacteriology, May, 2012, Vol.194(9-10), p.2491(9)
    Description: CRISPR (clustered regularly interspaced short palindromic repeats) elements and cas (CRISPR-associated) genes are widespread in Bacteria and Archaea. The CRISPR/Cas system operates as a defense mechanism against mobile genetic elements (i.e., viruses or plasmids). Here, we investigate seven CRISPR loci in the genome of the crenarchaeon Thermoproteus tenax that include spacers with significant similarity not only to archaeal viruses but also to T. tenax genes. The analysis of CRISPR RNA (crRNA) transcription reveals transcripts of a length between 50 and 130 nucleotides, demonstrating the processing of larger crRNA precursors. The organization of identified cas genes resembles CRISPR/Cas subtype I-A, and the core cas genes are shown to be arranged on two polycistronic transcripts: cascis (cas4, cas1/2, and csa1) and cascade (csa5, cas7, cas5a, cas3, cas3?, and cas8a2). Changes in the environmental parameters such as UV-light exposure or high ionic strength modulate cas gene transcription. Two reconstitution protocols were established for the production of two discrete multipartite Cas protein complexes that correspond to their operonic gene arrangement. These data provide insights into the specialized mechanisms of an archaeal CRISPR/Cas system and allow selective functional analyses of Cas protein complexes in the future.
    Keywords: Crenarchaeota -- Genetic Aspects ; Operons -- Chemical Properties ; Transcription (Genetics) -- Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: PLoS ONE, August 22, 2014, Vol.9(8)
    Description: CRISPR-Cas systems provide immunity against viral attacks in archaeal and bacterial cells. Type I systems employ a Cas protein complex termed Cascade, which utilizes small CRISPR RNAs to detect and degrade the exogenic DNA. A small sequence motif, the PAM, marks the foreign substrates. Previously, a recombinant type I-A Cascade complex from the archaeon Thermoproteus tenax was shown to target and degrade DNA in vitro, dependent on a native PAM sequence. Here, we present the biochemical analysis of the small subunit, Csa5, of this Cascade complex. T. tenax Csa5 preferentially bound ssDNA and mutants that showed decreased ssDNA-binding and reduced Cascade-mediated DNA cleavage were identified. Csa5 oligomerization prevented DNA binding. Specific recognition of the PAM sequence was not observed. Phylogenetic analyses identified Csa5 as a universal member of type I-A systems and revealed three distinct groups. A potential role of Csa5 in R-loop stabilization is discussed.
    Keywords: Oligomers – Chemical Properties ; Oligomers – Analysis ; DNA Binding – Chemical Properties ; DNA Binding – Analysis ; Phylogeny – Chemical Properties ; Phylogeny – Analysis ; DNA – Chemical Properties ; DNA – Analysis
    ISSN: 1932-6203
    Source: Cengage Learning, Inc.
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  • 7
    Language: English
    In: PLoS ONE, 2011, Vol.6(5), p.e19235
    Description: Among the seven different sigma factors in E. coli σ 70 has the highest concentration and affinity for the core RNA polymerase. The E. coli protein Rsd is regarded as an anti-sigma factor, inhibiting σ 70 -dependent transcription at the onset of stationary growth. Although binding of Rsd to σ 70 has been shown and numerous structural studies on Rsd have been performed the detailed mechanism of action is still unknown. ; We have performed studies to unravel the function and regulation of Rsd expression and . Cross-linking and affinity binding revealed that Rsd is able to interact with σ, with the core enzyme of RNA polymerase and is able to form dimers in solution. Unexpectedly, we find that Rsd does also interact with σ, the stationary phase-specific sigma factor. This interaction was further corroborated by gel retardation and footprinting studies with different promoter fragments and σ- or σ-containing RNA polymerase in presence of Rsd. Under competitive transcription conditions, in presence of both sigma factors, a selective inhibition of σ-dependent transcription was prevailing, however. Analysis of expression revealed that the nucleoid-associated proteins H-NS and FIS, StpA and LRP bind to the regulatory region of the promoters. Furthermore, the major promoter P2 was shown to be down-regulated by RpoS, the stationary phase-specific sigma factor and the transcription factor DksA, while induction of the stringent control enhanced promoter activity. Most notably, the -dependent methylation of a cluster of GATC sites turned out to be important for efficient transcription. ; The results contribute to a better understanding of the intricate mechanism of Rsd-mediated sigma factor specificity changes during stationary phase.
    Keywords: Research Article ; Biology ; Genetics And Genomics ; Microbiology ; Molecular Biology
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: PLoS ONE, 2012, Vol.7(4), p.e35321
    Description: Aminoacyl tRNA synthetases play a central role in protein synthesis by charging tRNAs with amino acids. Yeast mitochondrial lysyl tRNA synthetase (Msk1), in addition to the aminoacylation of mitochondrial tRNA, also functions as a chaperone to facilitate the import of cytosolic lysyl tRNA. In this report, we show that human mitochondrial Kars (lysyl tRNA synthetase) can complement the growth defect associated with the loss of yeast Msk1 and can additionally facilitate the in vitro import of tRNA into mitochondria. Surprisingly, the import of lysyl tRNA can occur independent of Msk1 in vivo . This suggests that an alternative mechanism is present for the import of lysyl tRNA in yeast.
    Keywords: Research Article ; Biology ; Microbiology ; Molecular Biology ; Cell Biology ; Biochemistry
    E-ISSN: 1932-6203
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  • 9
    Language: English
    In: New BIOTECHNOLOGY, 25 July 2016, Vol.33, pp.S64-S64
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.nbt.2016.06.944 Byline: Lennart Randau Author Affiliation: Max Planck Institute for Terrestrial Microbiology, Germany
    Keywords: Engineering ; Biology
    ISSN: 1871-6784
    E-ISSN: 1876-4347
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  • 10
    Language: English
    In: Science, 21 May 2009, Vol.324(5, 2009)
    Description: All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the cytidine deaminase-like superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs. Journal Article.
    Keywords: Materials Science Basic Biological Sciences General And Miscellaneous//Mathematics, Computing, And Information Sciencecrystal Structure ; Cytidine ; Deamination ; Enzymes ; Genes ; Harbors ; Transfer Rna ; Uridine ; National Synchrotron Light Source;
    ISSN: 00368075
    E-ISSN: 10959203
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