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  • 1
    Electronic Resource
    Electronic Resource
    A guided tour: small RNA function in Archaea (2001)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 40 (2001), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: In eukaryotes, the C/D box family of small nucleolar (sno)RNAs contain complementary guide regions that are used to direct 2′-O-ribose methylation to specific nucleotide positions within rRNA during the early stages of ribosome biogenesis. Direct cDNA cloning and computational genome searches have revealed homologues of C/D box snoRNAs (called sRNAs) in prokaryotic Archaea that grow at high temperature. The guide sequences within the sRNAs indicate that they are used to direct methylation to nucleotides in both rRNAs and tRNAs. The number of sRNA genes that are detectable within currently sequenced genomes correlates with the optimal growth temperature. We suggest that archaeal sRNAs may have two functions: to guide the deposition of methyl groups at the 2′-O position of ribose, which is an important determinant in RNA structural stability, and to serve as a molecular chaperones to help orchestrate the folding of rRNAs and tRNAs at high temperature.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2001.02381.x
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  • 2
    Electronic Resource
    Electronic Resource
    Separate pathways for excision and processing of 16S and 23S rRNA from the primary rRNA operon transcript from the hyperthermophilic archaebacterium Sulfolobus acldocaldarius: similarities to eukaryotic rRNA processing (1994)
    Oxford, UK : Blackwell Publishing Ltd
    Molecular microbiology 13 (1994), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: In the hyperthermophilic archaebacterium Sulfolobus acidocaldarius, the mature 16S and 23S rRNA are generated by processing of a 5000-nucleotide transcript. Analysis of intermediates that accumulate in vivo indicates that the transcript contains 11 separate processing sites. The processing and maturation of 23S rRNA appears to follow the typical archaebacterial pathway, utilizing a bulge-helix-bulge motif within the 23S processing helix as the substrate for an excision endonuclease. The precursor 23S rRNA that is released is trimmed at its 5′ and 3′ ends to generate the mature 23S rRNA found in 50S ribosomal subunits. The pathway for processing and maturation of 16S rRNA is distinctive and does not use the bulge-helix-bulge motif in the 165 processing stem, instead, the transcript is cleaved at several novel positions in the 5′ leader and in the 3′ intercistronic sequence. The excised precursor 16S is trimmed at the 5′ end but an extra 60 nucieotides of what is normally spacer sequence is retained at the 3′ end. The elongated 16S rRNA is present in active 30S subunits. An in vitro processing system for the 16S rRNA has been established. The RNA substrate containing the entire 144-nucieotide 5′ leader and the first 72 nucleotides of 16S sequence is cleaved at the same positions observed in vivo by an endonuclease activity present in cell extract. These resuits demonstrate (i) that the 16S processing helix is neither utilized nor required for leader processing, and (ii) that complete maturation to the 5′ end of 16S rRNA can occur in the absence of concomitant ribosome assembly and in the absence of all but the first 72 nucleotides of the 16S rRNA sequence. The endonuclease activity responsible for cleavage of the 5′ leader substrate is sensitive to nuclease digestion, suggesting that it contains an essential RNA component. The cleavage sites appear to be located within regions of irregular secondary structure and have a consensus sequence of GAUUCC.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.1994.tb00418.x
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  • 3
    Electronic Resource
    Electronic Resource
    Coupling between mRNA synthesis and mRNA stability in Escherichia coli (1994)
    Oxford, UK : Blackwell Publishing Ltd
    Molecular microbiology 11 (1994), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Transiently stable products derived from the endonuclease cleavage of transcripts from the secEnusG and rplKAJLrpoBC operons have been identified. Cleavage sites for RNase III occur in the leader of the secEnusG transcript and in the L12-β intercistronic space of the rplKAJLrpoBC transcript. A single RNase E cleavage site was located in the L1-L10 intergenic space. Inactivation of RNase III and RNase E results respectively in a one- to twofold and a greater than 10-fold stabilization of five mRNA sequences from within the secE, nusG, L11-L1, L10 and β encoding cistrons. The relative amounts of each of these five mRNA sequences were found to be nearly constant when measured either in the presence or absence of cleavage by RNase III or RNase E. This clearly implies that any increases in the stability of these mRNA sequences resulting from the inactivation of processing by RNase III or RNase E are counterbalanced by changes in the mRNA synthesis rates. The mechanism that links mRNA synthesis to mRNA decay is not known.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.1994.tb00371.x
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  • 4
    Electronic Resource
    Electronic Resource
    The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus (2005)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 55 (2005), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Archaeal L7Ae is a multifunctional protein that binds to a distinctive K-turn motif in RNA and is found as a component in the large subunit of the ribosome, and in ribose methylation and pseudouridylation guide RNP particles. A collection of L7Ae-associated small RNAs were isolated from Sulfolobus solfataricus cell extracts and used to construct a cDNA library; 45 distinct cDNA sequences were characterized and divided into six groups. Group 1 contained six RNAs that exhibited the features characteristic of the canonical C/D box archaeal sRNAs, two RNAs that were atypical C/D box sRNAs and one RNA representative of archaeal H/ACA sRNA family. Group 2 contained 13 sense strand RNA sequences that were encoded either within, or overlapping annotated open reading frames (ORFs). Group 3 contained three sequences form intergenic regions. Group 4 contained antisense sequences from within or overlapping sense strand ORFs or antisense sequences to C/D box sRNAs. More than two-thirds of these sequences possessed K-turn motifs. Group 5 contained two sequences corresponding to internal regions of 7S RNA. Group 6 consisted of 11 sequences that were fragments from the 5′ or 3′ ends of 16S and 23S ribosomal RNA and from seven different tRNAs. Our data suggest that S. solfataricus contains a plethora of small RNAs. Most of these are bound directly by the L7Ae protein; the others may well be part of larger, transiently stable RNP complexes that contain the L7Ae protein as core component.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.2005.04505.x
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  • 5
    Electronic Resource
    Electronic Resource
    RNA-modifying machines in archaea (2003)
    Oxford, UK : Blackwell Publishing Ltd.
    Molecular microbiology 48 (2003), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: It has been known for nearly half a century that coding and non-coding RNAs (mRNA, and tRNAs and rRNAs respectively) play critical roles in the process of information transfer from DNA to protein. What is both surprising and exciting, are the discoveries in the last decade that cells, particularly eukaryotic cells, contain a plethora of non-coding RNAs and that these RNAs can either possess catalytic activity or can function as integral components of dynamic ribonucleoprotein machines. These machines appear to mediate diverse, complex and essential processes such as intron excision, RNA modification and editing, protein targeting, DNA packaging, etc. Archaea have been shown to possess RNP complexes; some of these are authentic homologues of the eukaryotic complexes that function as machines in the processing, modification and assembly of rRNA into ribosomal subunits. Deciphering how these RNA-containing machines function will require a dissection and analysis of the component parts, an understanding of how the parts fit together and an ability to reassemble the parts into complexes that can function in vitro. This article summarizes our current knowledge about small-non-coding RNAs in Archaea, their roles in ribosome biogenesis and their relationships to the complexes that have been identified in eukaryotic cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2003.03483.x
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  • 6
    Electronic Resource
    Electronic Resource
    RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea (2004)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 54 (2004), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Archaea use ribonucleoprotein (RNP) machines similar to those found in the eukaryotic nucleolus to methylate ribose residues in nascent ribosomal RNA. The archaeal complex required for this 2′-O-ribose-methylation consists of the C/D box sRNA guide and three proteins, the core RNA-binding aL7a protein, the aNop56 protein and the methyltransferase aFib protein. These RNP machines were reconstituted in vitro from purified recombinant components, and shown to have methylation activity when provided with a simple target oligonucleotide, complementary to the sRNA guide sequence. To obtain a better understanding of the versatility and specificity of this reaction, the activity of reconstituted particles on more complex target substrates, including 5S RNA, tRNAGln and ‘double target’ oligonucleotides that exhibit either direct or reverse complementarity to both the D′ and D box guides, has been examined. The natural 5S and tRNAGln substrates were efficiently methylated in vitro, as long as the complementarity between guide and target was about 10 base pairs in length, and lacked mismatches. Maximal activity of double guide sRNAs required that both methylation sites be present in cis on the target RNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.2004.04319.x
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  • 7
    Electronic Resource
    Electronic Resource
    Stringent control of the transcriptional activities of ribosomal protein genes in E. coli (1975)
    [s.l.] : Nature Publishing Group
    Nature 255 (1975), S. 460-465 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The stringent control system regulates the expression of not only rRNA genes but also r-protein genes. The regulation of r-protein genes takes place by a mechanism which determines the amount of r-protein mRNA available for translation. Presumably this mechanism operates at the level of initiation ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/255460a0
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  • 8
    Electronic Resource
    Electronic Resource
    RNA Polymerase of Aquifex pyrophilus: Implications for the Evolution of the Bacterial rpoBC Operon and Extremely Thermophilic Bacteria (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 528-541 
    Details
    ISSN: 1432-1432
    Keywords: Key words: DNA-directed RNA polymerase —rpoBC operon — Extreme thermophiles —Aquifex pyrophilus—Thermotoga maritima—Mycoplasmatales— Molecular evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. A 16,226-bp fragment from the genome of Aquifex pyrophilus was sequenced, containing the genes for ribosomal proteins L1, L10, and L7/12 (rplAJL), DNA-directed RNA polymerase subunits β and β′(rpoBC), alanyl-tRNA synthetase (alaS), and subunit A of proteinase Clp (clpA). Enzymatic activity and extreme thermostability of purified A. pyrophilus RNA polymerase were verified. Transcription initiation on a DNA construct harboring the T7 A1 promoter was demonstrated by elongation of a 32P-labeled trinucleotide. Phylogenetic analyses of the two largest subunits of bacterial RNA polymerases (β and β′) showed overall consistency with the 16S rRNA-based phylogeny, except for the positions of the hyperthermophiles A. pyrophilus and Thermotoga maritima and for the location of the root of the domain Bacteria. In the phylogenies for both RNA polymerase subunits β and β′, A. pyrophilus was placed within the Gram-negative bacteria below the ε subdivision of the Proteobacteria. No support was found for the 16S rRNA-based hypothesis that A. pyrophilus might be the deepest branch of the Bacteria, but the cell wall–less mycoplasmas were found with a high confidence at the root of the Bacteria phylogenies. This raised doubts not only about whether the original Bacteria were indeed like the hyperthermophiles, but also concerning the value of single-gene phylogenies for hypotheses about the evolution of organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006496
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular phylogenies based on ribosomal protein L11, L1, L10, and L12 sequences (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 405-419 
    Details
    ISSN: 1432-1432
    Keywords: Molecular phylogeny ; Universal tree ; Ribosomal proteins ; Evolution ; Archaebacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Available sequences that correspond to the E. coli ribosomal proteins L11, L1, L10, and L12 from eubacteria, archaebacteria, and eukaryotes have been aligned. The alignments were analyzed qualitatively for shared structural features and for conservation of deletions or insertions. The alignments were further subjected to quantitative phylogenetic analysis, and the amino acid identity between selected pairs of sequences was calculated. In general, eubacteria, archaebacteria, and eukaryotes each form coherent and well-resolved nonoverlapping phylogenetic domains. The degree of diversity of the four proteins between the three groups is not uniform. For L11, the eubacterial and archaebacterial proteins are very similar whereas the eukaryotic L11 is clearly less similar. In contrast, in the case of the L12 proteins and to a lesser extent the L10 proteins, the archaebacterial and eukaryotic proteins are similar whereas the eubacterial proteins are different. The eukaryotic L1 equivalent protein has yet to be identified. If the root of the universal tree is near or within the eubacterial domain, our ribosomal protein-based phylogenies indicate that archaebacteria are monophyletic. The eukaryotic lineage appears to originate either near or within the archaebacterial domain.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163157
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  • 10
    Electronic Resource
    Electronic Resource
    The effects of the relA gene on the synthesis of aminoacyl-tRNA synthetases and other transcription and translation proteins in Escherichia coli B (1976)
    Springer
    Molecular genetics and genomics 149 (1976), S. 291-296 
    Details
    ISSN: 1617-4623
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The effects of a partial restriction of valyl-tRNA aminoacylation on the synthesis of aminoacyl-tRNA synthetases, ribosomal proteins, and other translation and transcription proteins were examined in otherwise isogenic stringent (relA +) and relaxed (relA1) derivatives of E. coli B. The synthesis of individual ribosomal proteins, elongation factor G, and to a lesser extent elongation factors Tu and Ts, and the valyl- and arginyl-tRNA synthetases was found to be subject to the influence of the stringent control system. The synthesis of the α and β subunits of RNA polymerase and several of the aminoacyl-tRNA synthetases, in contrast, is either not subject to the influence of the stringent control system, or is subject to additional regulatory constraints.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00268530
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