New insight into RNase P RNA structure from comparative analysis of the archaeal RNA

Harris, J. Kirk; Haas, Elizabeth S.; Williams, Daniel J.; Frank, Daniel N.; Brown, James W.

doi:10.1017/s1355838201001777

Cited by 101 publications

(129 citation statements)

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“…RNase P RNA: The structure derived by sequence comparison contains two long-range pseudoknots [5,18]. Our prediction is based on 8 bacterial sequences.…”

Section: Resultsmentioning

confidence: 99%

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Prediction of consensus RNA secondary structures including pseudoknots

Witwer

Hofacker²,

Stadler³

2004

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to five different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly, and more than 85% of the base pairs were identified.

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“…RNase P RNA: The structure derived by sequence comparison contains two long-range pseudoknots [5,18]. Our prediction is based on 8 bacterial sequences.…”

Section: Resultsmentioning

confidence: 99%

“…Comparative sequence analysis revealed conserved pseudoknots e.g. in rRNAs [6], RNase P RNAs [5,18], and tmRNA [47].…”

Section: Introductionmentioning

confidence: 99%

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Prediction of consensus RNA secondary structures including pseudoknots

Witwer

Hofacker²,

Stadler³

2004

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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“…New sequences were aligned to selected available type A sequences, representing all possible groups in the domain Bacteria, from an alignment in the RNase P database (Brown, 1999) using GeneDoc version 2.6 (Nicholas & Nicholas, 1997) and were manually edited. Secondary structures were determined and drawn based on the E. coli structure deduced by Harris et al (2001) and refined using the alignment and by comparison with other bacterial structures. The alignment was then edited again, based on the determined secondary structure.…”

Section: Methodsmentioning

confidence: 99%

“…Secondly, it is useful for inferring the functional significance of different regions within the RNA molecule from the nature of the structural variation. Planctomycete RNase P RNA sequence data have only been available for Pirellula staleyi, Planctomyces maris (Haas & Brown, 1998) and some environmental clone sequences Harris et al, 2001) and, more recently, the first complete genome sequence for a planctomycete has become available for a Pirellula strain (Glöckner et al, 2003), but this does not adequately represent the diversity of even the cultured species, which extends to members of the genera Gemmata and Isosphaera.Comparison of planctomycete RNase P RNA sequences with those of other bacteria will enable us to determine whether the unique position of these organisms is reflected by any unique features of their RNase P RNA.In this study, the sequence information on planctomycete RNase P RNA was expanded to include ten new sequences to cover all four genera for which pure cultures exist. The RNase P RNA sequences of the species studied were compared both within the phylum and with sequences of other bacteria by analysis of predicted secondary structure and by phylogenetics.…”

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confidence: 99%

Comparative analysis of ribonuclease P RNA of the planctomycetes

Butler

Fuerst

2004

International Journal of Systematic and Evolutionary Microbiology

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The planctomycetes, order Planctomycetales, are a distinct phylum of domain Bacteria. Genes encoding the RNA portion of ribonuclease P (RNase P) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpB gene sequences encoding RNase P RNA were generated by a conserved primer PCR strategy for Planctomyces brasiliensis, Planctomyces limnophilus, Pirellula marina, Pirellula staleyi strain ATCC 35122, Isosphaera pallida, one other Isosphaera strain, Gemmata obscuriglobus and three other strains of the Gemmata group. These sequences were aligned against reference bacterial sequences and secondary structures of corresponding RNase P RNAs deduced by a comparative approach. P12 helices were found to be highly variable in length, as were helices P16.1 and P19, when present. RNase P RNA secondary structures of Gemmata isolates were found to have unusual features relative to other planctomycetes, including a long P9 helix and an insert in the P13 helix not found in any other member of domain Bacteria. These unique features are consistent with other unusual properties of this genus, distinguishing it from other bacteria. Phylogenetic analyses indicate that relationships between planctomycetes derived from RNase P RNA are consistent with 16S rRNA-based analyses. INTRODUCTIONRibonuclease P (RNase P) is the most widespread ribonuclease (Condon & Putzer, 2002), found in all organisms so far examined (Altman et al., 1989) except the bacterial species 'Aquifex aeolicus' (Condon & Putzer, 2002), and also found within the subcellular compartments of eukaryotes known to synthesize tRNA (Frank & Pace, 1998). It is one of the key enzymes involved in the processing of tRNA, responsible for the generation of the 59 termini of mature tRNA (Altman, 1975), via a single endonucleolytic cleavage (Deutscher, 1984). Due to its universal existence, it is most likely an ancient enzyme, possibly descended from the postulated 'RNA world', prior to the development of protein-directed catalysis (Brown & Pace, 1991;Jeffares et al., 1998). In bacteria, the RNase P molecule is composed of a small protein and a large RNA moiety (Pace & Brown, 1995), the latter of which is capable of in vitro catalysis (Guerrier-Takada et al., 1983). RNase P RNA molecules in bacteria can generally be divided into two structurally separate classes: type A, the most common form, and type B, which is found in the low-G+C Gram-positive bacteria . Type A is distinguished by the presence of helix P6 and the absence of helix P5.1. A third intermediate type, type C, has been observed in the green nonsulfur bacteria (Haas & Brown, 1998). RNase P RNA has proven useful for phylogenetic analysis of the Chlamydiales (Herrmann et al., 2000), Prochlorococcus (Schön et al., 2002), the LL-2,6-diaminopimelic acid-containing actinomycetes (Yoon & Park, 2000), Bartonella (Pitulle et al., 2002) and Vibrio core species (Maeda et al., 2001), among others.The phylum Planctomycetes (Garrity et al., 2001) comprises a distinct group of the do...

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RNA Secondary Structures

Hofacker

Stadler

2006

Encyclopedia of Molecular Cell Biology and Molecular Medicine

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New insight into RNase P RNA structure from comparative analysis of the archaeal RNA

Cited by 101 publications

References 50 publications

Prediction of consensus RNA secondary structures including pseudoknots

Prediction of consensus RNA secondary structures including pseudoknots

Comparative analysis of ribonuclease P RNA of the planctomycetes

RNA Secondary Structures

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