Intervening sequence with conserved open reading frame in eubacterial 23S rRNA genes.

Ralph, David; McClelland, Michael

doi:10.1073/pnas.90.14.6864

Cited by 53 publications

(56 citation statements)

References 25 publications

(44 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Intervening sequences, in contrast to introns, cannot self-splice from precursor RNA and, upon removal by cellular maturation enzymes, leave the ribosomal RNA fragmented (3)(4)(5)(6)(7). In this study, we also showed that true selfsplicing introns can be present in bacterial 16S rRNA genes, leading to the conclusion that the 16S rRNA genes of bacteria can indeed be far longer than ∼1,500 nucleotides.…”

Section: Discussionsupporting

confidence: 53%

“…The possibility that the 16S rRNA gene may not have a conserved size has not been sufficiently considered in designing and applying techniques for diversity studies, even though elongations of 16S rRNA genes due to intervening sequences have been reported before (3)(4)(5)(6)(7). Intervening sequences, in contrast to introns, cannot self-splice from precursor RNA and, upon removal by cellular maturation enzymes, leave the ribosomal RNA fragmented (3)(4)(5)(6)(7).…”

Section: Discussionmentioning

confidence: 99%

“…In the past decades, these techniques have become fundamental tools in molecular ecology, and the 16S rRNA gene is the most frequently sequenced and analyzed gene today. The universality of this gene has never been questioned, even though in some studies unusual 16S rRNA genes, which contained, e.g., intervening sequences, were encountered (3)(4)(5)(6)(7).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Salman

Amann

Shub³

et al. 2012

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

View full text Add to dashboard Cite

The gene encoding the small subunit rRNA serves as a prominent tool for the phylogenetic analysis and classification of Bacteria and Archaea owing to its high degree of conservation and its fundamental function in living organisms. Here we show that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis , regularly contain numerous self-splicing introns of variable length. The 16S rRNA genes can thus be enlarged to up to 3.5 kb. Remarkably, introns have never been identified in bacterial 16S rRNA genes before, although they are the most frequently sequenced genes today. This may be caused in part by a bias during the PCR amplification step that discriminates against longer homologs, as we show experimentally. Such length heterogeneity of 16S rRNA genes has so far never been considered when constructing 16S rRNA-based clone libraries, even though an elongation of rRNA genes due to intervening sequences has been reported previously. The detection of elongated 16S rRNA genes has profound implications for common methods in molecular ecology and may cause systematic biases in several techniques. In this study, catalyzed reporter deposition–fluorescence in situ hybridization on both ribosomes and rRNA precursor molecules as well as in vitro splicing experiments were performed and confirmed self-splicing of the introns. Accordingly, the introns do not inhibit the formation of functional ribosomes.

show abstract

Section: Discussionsupporting

confidence: 53%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Salman

Amann

Shub³

et al. 2012

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

View full text Add to dashboard Cite

show abstract

“…2 and 3A). Similar sequence blocks have been shown to be present at this position in the 23S rRNA genes from a variety of bacteria (3,20,44,47,52,60) and chloroplasts (59), and these extra sequence blocks in the 23S rRNA genes have been termed intervening sequences (3) or transcribed spacers (60).…”

Section: Resultsmentioning

confidence: 85%

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

“…The presence of IVSs resulting in such 23S rRNA fragmentation was first described for Salmonella enterica serovars Typhimurium and Arizonae (5), for which it was shown that the IVS was excised posttranscriptionally by endoribonuclease RNase III without religation (5). IVSs have been identified in and characterized for other bacteria, including Yersinia enterocolitica (37), Coxiella burnetii (2), Helicobacter (18), and Haemophilus (39), Brucella (4), Leptospira (35), Proteus, and Providencia (27) spp. Horizontal gene transfer has been postulated to underlie the dissemination of IVSs (34,36).…”

mentioning

confidence: 99%

The Absence of Intervening Sequences in 23S rRNA Genes of Campylobacter coli Isolates from Turkeys Is a Unique Attribute of a Cluster of Related Strains Which Also Lack Resistance to Erythromycin

Chan

Miller

Mandrell

et al. 2007

Appl Environ Microbiol

View full text Add to dashboard Cite

Certain Campylobacter strains harbor a transcribed intervening sequence (IVS) in their 23S rRNA genes. Following transcription, the IVS is excised, leading to fragmentation of the 23S rRNA. The origin and possible functions of the IVS are unknown. Furthermore, the distribution of IVS-harboring strains within Campylobacter populations is poorly understood. In this study, 104 strains of Campylobacter coli from turkeys, representing 27 different multilocus sequence typing-based sequence types (STs), were characterized in terms of IVS content and erythromycin susceptibility. Sixty-nine strains harbored IVSs in all three 23S rRNA genes, whereas the other 35 strains lacked IVSs from at least one of the genes. The STs of the latter strains belonged to an unusual cluster of C. coli STs (cluster II), earlier found primarily in turkey strains and characterized by the presence of the C. jejuni aspA103 allele. The majority (66/69) of strains harboring IVSs in all three 23S rRNA genes were resistant to erythromycin, whereas none of the 35 strains with at least one IVS-free 23S rRNA gene were resistant. Cluster II strains could be transformed to erythromycin resistance with genomic DNA from C. coli that harbored IVS and the A2075G transition in the 23S rRNA gene, associated with resistance to erythromycin in Campylobacter. Erythromycin-resistant transformants harbored both the A2075 transition and IVS. The findings suggest that the absence of IVS in C. coli from turkeys is characteristic of a unique clonal group of erythromycin-susceptible strains and that IVS can be acquired by these strains via natural transformation to erythromycin resistance.

show abstract

Intervening sequence with conserved open reading frame in eubacterial 23S rRNA genes.

Cited by 53 publications

References 25 publications

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

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

The Absence of Intervening Sequences in 23S rRNA Genes of Campylobacter coli Isolates from Turkeys Is a Unique Attribute of a Cluster of Related Strains Which Also Lack Resistance to Erythromycin

Contact Info

Product

Resources

About