Nucleotide sequence of the 10Sa RNA gene of the βpurple eubacterium<i>Alcaligenes eutrophus</i>

Brown, James W.; Hunt, Dirk A; Pace, Norman R.

doi:10.1093/nar/18.9.2820

Cited by 31 publications

(13 citation statements)

References 3 publications

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“…Following purification from total cellular RNA by gel filtration and electrophoresis, a single band containing RNase P RNA activity was used to probe genomic digests. The probe hybridized to single bands in genomic digests; however, clones of this DNA fragment were found to contain a gene which apparently encodes lOSa RNA (an abundant, stable RNA of unknown function that in E. coli nearly comigrates with RNase P RNA [11]), transcripts of which lacked RNase P activity (3). Inclusion of the lOSa RNA-encoding plasmid DNA (25 ,ug/m1, HindIII linearized and denatured by boiling) in the genomic hybridizations resulted in diminution of the hybridization signal from the lOSa-encoding fragments and the appearance of single novel bands, which were cloned and found to encode functional RNase P RNA.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic analysis and evolution of RNase P RNA in proteobacteria

et al. 1991

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The secondary structures of the eubacterial RNase P RNAs are being elucidated by a phylogenetic comparative approach. Sequences of genes encoding RNase P RNA from each of the recognized subgroups (a, I, y, and 8) of the proteobacteria have now been determined. These sequences allow the refinement, to nearly the base pair level, of the phylogenetic model for RNase P RNA secondary structure. Evolutionary change among the RNase P RNAs was found to occur primarily in four discrete structural domains that are peripheral to a highly conserved core structure. The new sequences were used to examine critically the proposed similarity (C. Guerrier-Takada, N. Lumelsky, and S. Altman, Science 246:1578-1584) between a portion of RNase P RNA and the "exit site" of the 23S rRNA of Escherichia cofi. Phylogenetic comparisons indicate that these sequences are not homologous and that any similarity in the structures is, at best, tenuous.RNase P cleaves leader sequences from precursor tRNAs to generate the mature 5' end of tRNA (see references 1 and 19 for reviews). In the eubacteria Bacillus subtilis and Escherichia coli, RNase P is composed of a small protein (119 amino acids) and a large RNA (-400 nucleotides). Although RNase P functions as a ribonucleoprotein in vivo, the RNA alone is an efficient and accurate catalyst at elevated concentrations of salt in vitro. RNase P contains the only RNA known to act catalytically in vivo, in the sense that each molecule of RNase P RNA acts on many substrate molecules.An accurate model for the structure of eubacterial RNase P RNA is a prerequisite for understanding the mechanism of substrate recognition, catalytic activity, and evolution of this ribozyme. A model for the secondary structure of RNase P RNA in eubacteria was originally derived by phylogenetic comparative analysis of the sequences of genes encoding RNase P RNA from several members of the y subdivision of the proteobacteria and four species of gram-positive eubacteria of the genus Bacillus (12). On the basis of the criteria used for analysis of ribosomal RNA structure (8), covariation of two base pairings within a potential continuous helix was considered proof of the occurrence of that helix. In order to increase the resolution of this model, we have cloned and sequenced the genes for RNase P RNA from a phylogenetically diverse sampling of the following additional proteobacteria: the a proteobacteria Agrobacterium tumefaciens and Rhodospirillum rubrum, the P proteobacterium Alcaligenes eutrophus, the y proteobacterium Chromatium vinosum, and the 8 proteobacterium Desulfovibrio desulfuricans (Fig. 1). Together with the previously obtained gene sequences for RNase P RNA, these analyses complete a sampling of each of the major phylogenetic branches of proteobacteria.* Corresponding author. Nucleic acid extraction. Extracts for the isolation of genomic DNAs were prepared by resuspending the cells in STE (10 mM Tris-Cl [pH 91, 100 mM NaCl, 1 mM EDTA) (15 ml/g of cells [wet weight]), treating them with lysozyme (1 mg/ml) for 5 min ...

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Section: Resultsmentioning

confidence: 99%

Phylogenetic analysis and evolution of RNase P RNA in proteobacteria

et al. 1991

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“…From these results, we conclude that aminoacylation of the 10Sa RNA might be associated with its function, although at present we cannot exclude a possibility that only the binding of the 10Sa RNA with alanyl-tRNA synthetase is related to the function. DISCUSSION 10Sa RNA has been found in many species of microorganisms-for example, A. eutrophus (18), M. tuberculosis (19), Bacillus subtilis, and Mycoplasma (A. Muto, personal communication). In all cases, the 10Sa RNA can be drawn with a tRNA-like structure that resembles that proposed for the 10Sa RNA from E. coli.…”

Section: Resultsmentioning

confidence: 99%

A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli.

Komine

Kitabatake

Yokogawa

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

390

392

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We have determined that lOSa RNA (one of the small stable RNAs found in Escherichia cobl) has an interesting structural feature: the 5' end and the 3' end of lOSa RNA can be arranged in a s ture that is equivalent to a half-molecule (acceptor stem and TFC stem-loop) of alanine tRNA of E. coli. Primer-extension analysis of lOSa RNA extracted from a bacterial mutant with temperature-sensitive RNase P function revealed that the precursor to lOSa RNA (pre-lOSa RNA) is folded into a pre-tRNA-like structure in vivo such that it can be cleaved by RNase P to generate the 5' end of the mature 10Sa RNA. The purified 10Sa RNA can be charged with alanine in vitro. Disruption of the gene encoding lOSa RNA (ssrA) caused a reduction in the rate of cell growth, which was especaly apparent at 45C, and a reduction in motility on se d agar. These phenotypic characteristics of the deletion strain (AssrA) allowed us to investigate the effects of some mutations in lOSa RNA in vivo, although the exact function of lOSa RNA still remains unclear. When the G-U pair (G3-U357) in lOSa RNA, which may be equivalent to the determinant G-U pair of alanine tRNA, was changed to a GA or G-C pair, the ability to complement the phenotypic mutations of the AssrA strain was lost. Furthermore, this inability to complement the mutant phenotypes that was caused by the substitution of the determinant bases by a GA pair could be overcome by the introduction of a gene encoding alanyl-tRNA synthetase (aaS) on a multicopy plasmid. The evidence suggests that the proposed structural features of lOSa RNA are indeed manifested in vivo.lOSa RNA is one of the small stable RNAs that is found in Escherichia coli. It was first identified as lOS RNA, which was actually a mixture of lOSa RNA and Ml RNA (originally designated lOSb RNA) (1, 2). Subsequently, Ml RNA was shown to be a "catalytic RNA" (3), and it has been extensively studied from both a structural and a functional perspective (4). However, in contrast to Ml RNA, lOSa RNA has not been the focus of much recent attention, and very little is known about either its structure or its function.In our previous study, we found that the ssrA gene that encodes lOSa RNA of E. coli is included in the genomes of phages 438, 439, and 440 of Kohara's library (5), which corresponds to 56.5 minutes on the linkage map of the chromosome (6). We cloned a 2.2-kb fragment that covers the overlapping region of these phages into a plasmid vector and determined the nucleotide sequence of the fragment. § We also purified lOSa RNA from E. coli strain W3110 and determined its nucleotide sequence from both the 5' and the 3' end.The nucleotide sequence of the ssrA gene from E. coli has already been reported by Chauhan and Apirion (7). In comparing our sequences with the published sequence, we noticed an interesting structural feature of lOSa RNA, as presented in Fig. 2-namely, 7 nucleotides at the 5' end and 28 nucleotides at the 3' end can be arranged in a structure that is equivalent to a half-molecule of tRNA. This half-mole...

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“…The function of lOSa RNA had not previously been known. The stable RNA is made in other prokaryotes; genes for lOSa RNA from the purple bacterium Alcaligenes eutrophus and from Mycobacterium tuberculosis have been identified (7,54). These genes have more than 50% homology with ssrA; this sequence homology is especially prominent near the 3' ends of both genes and stops at the end of the core sequence we propose for attL.…”

Section: Sg20780 Cured Of the Cryptic Prophage) The Four Sg20780mentioning

confidence: 91%