Compilation of small ribosomal subunit RNA sequences

Dams, Erna; Hendriks, Lydia; Peer, Yves Van de; Neefs, Jean-Marc; Smits, Guido F.; Vandenbempt, I.; Wächter, Rupert De

doi:10.1093/nar/16.suppl.r87

Cited by 254 publications

(178 citation statements)

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“…At position 1198, clone OMl contained a G residue instead of the high G+ C signature A residue, though it is noted that a G residue at this position is the bacterial consensus, and is found in a minor percentage (< 15%) of high G+C Gram-positive bacteria. A portion of the helix in variable region 9 (V9, positions 1410-1435, 1466-1490Dams et al 1988) was also reported by Woese as a high G+C Gram-positive rRNA signature (Woese 1987). In the secondary structural model for clone OMl, nucleotide sequence and base pairing within this helix was consistent with the high G+C Gram-positive signature (Fig.…”

Section: Resultssupporting

confidence: 74%

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Rappé

Kemp

Giovannoni

1997

Limnology & Oceanography

222

195

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The phylogenetic diversity of a continental-shelf picoplankton community was examined by analyzing 16s ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial-specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near Cape Hatteras, North Carolina, served as the source of bulk nucleic acids used in this study. A large proportion of the 169 rDNA clones recovered (33%) were related to plastid 16s r-RNA genes, including plastids from both chromophyte and chlorophyte algae. Most bacterial gene clones (75% of bacterial clones, 50% of the total) were closely related to r-RNA gene lineages that had been discovered previously in clone libraries from opcnocean marine habitats, including the SARI36 cluster (y-Proteobacteria), SAR83, SARll, and SAR116 clusters (all a-Proteobacteria), as well as the marine Gram-positive cluster (high G+C Gram-positive). Most of the remaining bacterial clones recovered were phylogenetically related to the y and /3 subclasses of the Proteobacteria, including an rDNA lineage within the type 1 methylotroph clade of the p subclass. The abundance of plastid rDNAs and the lack of cyanobacterial-related clones, as well as the presence of P-Proteobacteria, are features of this coastal picoplankton gene clone library that distinguish it from similar studies of oligotrophic open-ocean sites. Overall, however, these data indicate that a limited number of as yet uncultured bacterioplankton lineages, related to those previously observed in the open ocean, can account for most cells in this coastal marine bacterioplankton assemblage.

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Section: Resultssupporting

confidence: 74%

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Rappé

Kemp

Giovannoni

1997

Limnology & Oceanography

222

195

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“…This extended type of mRNA recognition with 3' and 5'-terminal sequences of 16S rRNA pairing on adjacent regions of mRNA would imply neighbourhood of the two termini, but in contrast to our model would also imply melting of helices 1 (positions 9-13) and 2 (positions [18][19][20] during mRNA recognition.…”

Section: Discussioncontrasting

confidence: 67%

“…From this situation and by taking into account the possibility of rearrangements and/or partial melting of helical regions, an interaction of the two terminal regions by base pairing appears sterically possible. Therefore, and in view of the large amount of sequence information available from the compilation of more than one hundred small subunit RNA (DNA) primary structures (18), we have undertaken a systematic screening for complementary sequences between the two termini of small subunit rRNAs. This has led us to the detection of highly conserved sequences which allow formation of 5 or 6 base pairs between the two terminal regions.…”

Section: Introductionmentioning

confidence: 99%

Alternative base pairing between 5′- and 3′-terminal sequences of small subunit RNA may provide the basis of a conformational switch of the small ribosomal subunit

1990

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The compiled sequences of small subunit ribosomal RNAs have been screened for base complementary between 5'-and 3-terminal regions. Highly conserved complementary sequences are found which allow formation of a helix between the two ends of 5 or 6 base pairs. This helix is composed of sequences from the loop region of the first 5'-terminal stem and from sequences immediately distal to the last stem (the Me2A-stem) of the 3' terminus and therefore allows a coaxial stacking with either of these two flanking stems.

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“…Interestingly, a 14-nucleotide sequence from the instability element of the inherently unstable MAT~I mRNA ) is also complementary to the same region of 18S rRNA (for review, see . Clearly, these interactions are only hypothetical and must be weighed in light of models suggesting that this region of rRNA may be involved in intramolecular base-pairing (Dams et al 1988). However, this premise merits attention because substantive evidence has emerged in recent years that rRNA has a functional role in translation (Dahlberg 1989;Noller 1991) and the processes of translation and turnover are intimately linked (see above).…”

Section: Mrna Translation and Mrna Turnover Are Intimately Linked: Pomentioning

confidence: 99%

mRNA destabilization triggered by premature translational termination depends on at least three cis-acting sequence elements and one trans-acting factor.

Peltz¹,

Brown²,

Jacobson³

1993

Genes Dev.

286

349

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Nonsense mutations in a gene can accelerate the decay rate of the mRNA transcribed from that gene, a phenomenon we describe as nonsense-mediated mRNA decay. Using amber (UAG) mutants of the yeast PGK1 gene as a model system, we find that nonsense-mediated mRNA decay is position dependent, that is, nonsense mutations within the initial two-thirds of the PGKl-coding region accelerate the decay rate of the PGK1 transcript ~<12-fold, whereas nonsense mutations within the carboxy-terminal third of the coding region have no effect on mRNA decay. Moreover, we find that this position effect reflects (1) a requirement for sequences 3' to the nonsense mutation that may be necessary for translational reinitiation or pausing, and (2) the presence of an additional sequence that, when translated, inactivates the nonsense-mediated mRNA decay pathway. This stabilizing element is positioned within the coding region such that it constitutes the boundary between nonsense mutations that do or do not affect mRNA decay. Rapid decay of PGK1 nonsense-containing transcripts is also dependent on the status of the UPF1 gene. Regardless of the position of an amber codon in the PGK1 gene, deletion of the UPF1 gene restores wild-type decay rates to nonsense-containing PGK1 transcripts.

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Compilation of small ribosomal subunit RNA sequences

Abstract: Helix numbering system Helices are given a different number if separated by a multibranched loop (e.g. helices 9 and 10), by a pseudoknot loop (e.g. helices 1 and 2), or by a single stranded area that does not * To whom correspondence should be addressed k.

Cited by 254 publications

References 1 publication

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Alternative base pairing between 5′- and 3′-terminal sequences of small subunit RNA may provide the basis of a conformational switch of the small ribosomal subunit

mRNA destabilization triggered by premature translational termination depends on at least three cis-acting sequence elements and one trans-acting factor.

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