Secondary structure model for 23S ribosomal RNA

Noller, Harry F.; Kop, Joann; Wheaton, V. I.; Brosius, Jürgen; Gutell, Robin R.; Копылов, А. М.; Dohme, Ferdinand; Herr, Winship; Stahl, David A.; Gupta, Ramesh C.; Woese, Carl R.

doi:10.1093/nar/9.22.6167

Cited by 363 publications

(270 citation statements)

References 55 publications

Supporting

Mentioning

257

Contrasting

Unclassified

Order By: Relevance

“…Phylogenetic analysis is the most accurate method for RNA secondary structure prediction. Some structures determined by this method include tRNAs (24), ribosomal RNAs (25)(26)(27), group I and group II introns (28,29), RNAs from small nuclear ribonucleoproteins (30), hammerhead catalytic RNA (31), and RNase P RNAs (32). Further studies have confirmed these structures.…”

Section: Discussionmentioning

confidence: 91%

A conserved RNA structure ( thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria

Miranda-Ríos

Navarro²,

Soberón³

2001

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

230

153

View full text Add to dashboard Cite

The thiCOGE genes of Rhizobium etli code for enzymes involved in thiamin biosynthesis. These genes are transcribed with a 211-base untranslated leader that contains the thi box, a 38-base sequence highly conserved in the 5 regions of thiamin biosynthetic and transport genes of Gram-positive and Gram-negative organisms. A deletion analysis of thiC-lacZ fusions revealed an unexpected relationship between the degree of repression shown by the deleted derivatives and the length of the thiC sequences present in the transcript. Three regions were found to be important for regulation: (i) the thi box sequence, which is absolutely necessary for high-level expression of thiC; (ii) the region immediately upstream to the translation start codon of thiC, which can be folded into a stem-loop structure that would mask the Shine-Dalgarno sequence; and (iii) the proximal part of the coding region of thiC, which was shown to contain a putative Rho-independent terminator. A comparative phylogenetic analysis revealed a possible folding of the thi box sequence into a hairpin structure composed of a hairpin loop, two helixes, and an interior loop. Our results show that thiamin regulation of gene expression involves a complex posttranscriptional mechanism and that the thi box RNA structure is indispensable for thiCOGE expression.T hiamin pyrophosphate (TPP), also known as cocarboxylase, is the cofactor of key enzymes of carbon metabolism such as pyruvate dehydrogenase, ␣-ketoglutarate dehydrogenase, transketolase, pyruvate decarboxylase, and others. TPP is made by the enzymatic coupling of two independently synthesized precursors, 4-amino-5-hydroxymethyl-2-methyl pyrimidine pyrophosphate and 5-(2-hydroxyethyl)-4-methyl thiazole monophosphate (1).In Escherichia coli and Salmonella enterica serovar Typhimurium, several genes are known to participate in TPP biosynthesis (2). thiC and thiD are required for 4-amino-5-hydroxymethyl-2-methyl pyrimidine pyrophosphate synthesis (3, 4), whereas dxs (5, 6), thiF, thiS, thiG, thiH, and thiI are involved in 5-(2-hydroxyethyl)-4-methyl thiazole monophosphate synthesis (3,7,8). In addition, the product of the thiE gene couples 4-amino-5-hydroxymethyl-2-methyl pyrimidine pyrophosphate and 5-(2-hydroxyethyl)-4-methyl thiazole monophosphate to give thiamin monophosphate, which undergoes another phosphorylation catalyzed by the product of the thiL gene to form TPP, the biologically active form of vitamin B 1 (9, 10). A salvage enzyme (thiamin kinase) encoded by thiK, which incorporates exogenous thiamin into TPP (11), also exists. In both organisms the thi genes are located throughout the chromosome and are arranged in three operons and four single gene loci (2). thiCEFSGH, thiMD (ThiM and ThiD are involved in salvage of 5-(2-hydroxyethyl)-4-methyl thiazole and 4-amino-5-hydroxymethyl-2-methyl pyrimidine from the culture medium, respectively; ThiD also catalyzes the phosphorylation of 4-amino-5-hydroxymethyl-2-methyl pyrimidine monophosphate and thiBPQ (which code for an ABC type transport system for t...

show abstract

Section: Discussionmentioning

confidence: 91%

A conserved RNA structure ( thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria

Miranda-Ríos

Navarro²,

Soberón³

2001

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

230

153

View full text Add to dashboard Cite

show abstract

“…Shaded sequences representing mature RNAs were taken from earlier models (4,28,37,38) and the arrows represent cleavages which produce the mature ribosomal RNAs. The insert (upper right) is an estimate for the secondary structure in the ITS 2 equivalent region of Escherichia coli based on the 238…”

Section: Structure and Evolution Of The 23-45-5s Rrna Precursor Sequmentioning

confidence: 99%

“…NINA models from the laboratories of Brimacombe (37) and Noller (38). regions evolved, at least in part, through gene duplication events probably the result of unequal crossing over.…”

Section: Structure and Evolution Of The 23-45-5s Rrna Precursor Sequmentioning

confidence: 99%

Structure and evolution of the 4.5–5S ribosomal RNA intergenic region fromGlycine max(Soya bean)

1987

View full text Add to dashboard Cite

The nucleotide sequence for the 4.5-5S ribosomal DNA region from the chloroplastids of soya beans was determined as the basis of further comparative studies on the structure and evolution of this intergenic region. Comparisons with other plant sequences as well as equivalent sequences in eubacteria suggest that the longer internal transcribed spacer regions of plants have evolved, at least in part, by DNA sequence duplications and that the presence of the 4.5S rRNA in chloroplast may result from the accidental acquisition of a RNA maturation site during the evolution of longer internal transcribed spacer regions. Estimates of the secondary structures also indicate only a very limited retention of structural features and suggest that the primary role of the intergenic sequences may be to bring processed sites into close proximity. INTRODUCrIONWhile the ribosomal RNAs of chloroplasts more closely resemble those of eubacteria, the chloroplast ribosomes of flowering plants contain two low molecular weight RNA components (1-4), the commonly observed 5S RNA and a somewhat smaller 4.5S rRNA. Sequence studies indicate that all of the chloroplast rRNAs are transcribed as a common larger precursor molecule, the sequences being arranged in the order 5'-16S-23S-4.5S-5S-3' (5-7). As ribosomal RNA from many origins have been sequenced, comparisons have clearly shown (5-8) that the 4.5S rRNA sequence is not unique to plant chloroplasts; it is actually equivalent to the 3' end of the eubacterial 23S rRNA and is the result of an extra cleavage or processing step in the chlorplast rRNA precursor.Although most mature ribosomal RNAs are products from the processing of larger precursor molecules, in many instances relatively little is known about the structural features which underlie these cleavages or the enzymatic mechanisms by which these cleavages occur (e.g. ref.

show abstract

“…We show that the gene carries a transcribed spacer of approximately 147 bp which results in the production of fragmented 23S rRNA, and we demonstrate that this is a common phenomenon in C. coli and C. jejuni because many strains carry transcribed spacers of this approximate length or shorter ones and also produce fragmented 23S rRNAs. In addition, we report on the phylogenetic position of the genus Campylobacter, based on the presence of phylogenetic signatures at positions 270 and 1850 (E. coli numbering [36]) of the Campylobacter 23S rRNA, and on a phylogenetic analysis which was performed by using this C. coli 23S rRNA, a C. jejuni 23S rRNA sequence (GenBank accession number Z29326), and 53 other available complete (eu)bacterial 23S rRNA sequences. …”

mentioning

confidence: 99%

Phylogenetic and molecular characterization of a 23S rRNA gene positions the genus Campylobacter in the epsilon subdivision of the Proteobacteria and shows that the presence of transcribed spacers is common in Campylobacter spp

et al. 1994

View full text Add to dashboard Cite

The nucleotide sequence of a 23S rRNA gene of Campylobacter coli VC167 was determined. The primary sequence of the C. coli 23S rRNA was deduced, and a secondary-structure model was constructed. Comparison with Escherichia coli 23S rRNA showed a major difference in the C. coli rRNA at approximately position 1170 (E. coli numbering) in the form of an extra sequence block approximately 147 bp long. PCR analysis of 31 other strains of C. coli and C. jejuni showed that 69%o carried a transcribed spacer of either ca. 147 or ca. 37 bp.Comparison of all sequenced Campylobacter transcribed spacers showed that the Campylobacter inserts were related in sequence and percent G+C content. All Campylobacter strains carrying transcribed spacers in their 23S rRNA genes produced fragmented 23S rRNAs. Other strains which produced unfragmented 23S rRNAs did not appear to carry transcribed spacers at this position in their 23S rRNA genes. At the 1850 region (E. coli numbering), Campylobacter 23S rRNA displayed a base pairing signature most like that of the beta and gamma subdivisions of the class Proteobacteria, but in the 270 region, Campylobacter 23S rRNA displayed a helix signature which distinguished it from the alpha, beta, and gamma subdivisions. Phylogenetic analysis comparing C. coli VC167 23S rRNA and a C.jejuni TGH9011 (ATCC 43431) 23S rRNA with 53 other completely sequenced (eu)bacterial 23S rRNAs showed that the two campylobacters form a sister group to the alpha, beta, and gamma proteobacterial 23S rRNAs, a positioning consistent with the idea that the genus Campylobacter belongs to the epsilon subdivision of the class Proteobacteria.The members of the Campylobacter group of organisms are important pathogens in human and veterinary medicine. This group includes Campylobacter, Arcobacter, Helicobacter, Wolinella, and "Flexispira" spp. and has been argued to constitute a separate bacterial lineage within the class Proteobacteria (62, 63). The most recently published phylogenetic tree based on small-subunit rRNA sequences has the group positioned in the delta and epsilon subdivisions of the Proteobacteria (purple bacteria) (39). There are 11 Campylobacter species (9, 56), and the roles of several of these species in diseases of humans and animals have been well described (43). Typically, these small, nutritionally fastidious, microaerophilic, gram-negative spiral bacteria colonize moist body surfaces, including the human gingival cavity, the small intestinal mucosa, and the vaginal mucosa of bovines and this colonization leads to disease. The two most important human pathogens in the genus are Campylobacterjejuni and C. coli, which cause enteritis.In keeping with their small size and limited nutritional properties, the campylobacters have a small genome (23,37,57). At 1.7 to 1.8 Mb, the C. jejuni and C. coli genomes are only 36% of the size of the Escherichia coli chromosome (53) (23,24,27,37,57). Unlike the characteristic continuous 16S-23S (eu)bacterial rRNA operon structure seen in E. coli (35), several studies have sug...

show abstract

Secondary structure model for 23S ribosomal RNA

Cited by 363 publications

References 55 publications

A conserved RNA structure ( thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria

A conserved RNA structure ( thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria

Structure and evolution of the 4.5–5S ribosomal RNA intergenic region fromGlycine max(Soya bean)

Phylogenetic and molecular characterization of a 23S rRNA gene positions the genus Campylobacter in the epsilon subdivision of the Proteobacteria and shows that the presence of transcribed spacers is common in Campylobacter spp

Contact Info

Product

Resources

About