Bacterial ribosomal RNA in pieces

Evguenieva‐Hackenberg, Elena

doi:10.1111/j.1365-2958.2005.04662.x

Cited by 63 publications

(59 citation statements)

References 56 publications

(115 reference statements)

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“…1). Unlike with introns, the IVS is excised from the RNA without exon ligation, a cleavage process mediated by RNase III (8), resulting in a fragmented but functional rRNA. Moreover, unlike with other obligate intracellular bacteria, which have few or no insertion sequencespresumably due to limited opportunities for lateral gene transfer-C. burnetii's genome possesses a large number of insertion sequence elements (29 full-length and 3 degenerate).…”

Section: Discussionmentioning

confidence: 99%

The Unusual 23S rRNA Gene of Coxiella burnetii : Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical ΩG

et al. 2007

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We describe the presence and characteristics of two self-splicing group I introns in the sole 23S rRNA gene of Coxiella burnetii. The two group I introns, Cbu.L1917 and Cbu.L1951, are inserted at sites 1917 and 1951 (Escherichia coli numbering), respectively, in the 23S rRNA gene of C. burnetii. Both introns were found to be self-splicing in vivo and in vitro even though the terminal nucleotide of Cbu.L1917 is adenine and not the canonical conserved guanine, termed ⍀G, found in Cbu.L1951 and all other group I introns described to date. Predicted secondary structures for both introns were constructed and revealed that Cbu.L1917 and Cbu.L1951 were group IB2 and group IA3 introns, respectively. We analyzed strains belonging to eight genomic groups of C. burnetii to determine sequence variation and the presence or absence of the elements and found both introns to be highly conserved (>99%) among them. Although phylogenetic analysis did not identify the specific identities of donors, it indicates that the introns were likely acquired independently; Cbu.L1917 was acquired from other bacteria like Thermotoga subterranea and Cbu.L1951 from lower eukaryotes like Acanthamoeba castellanii. We also confirmed the fragmented nature of mature 23S rRNA in C. burnetii due to the presence of an intervening sequence. The presence of three selfish elements in C. burnetii's 23S rRNA gene is very unusual for an obligate intracellular bacterium and suggests a recent shift to its current lifestyle from a previous niche with greater opportunities for lateral gene transfer.Group I introns are a distinct class of catalytic RNAs (ribozymes) that are considered a legacy of a primordial RNA world (40). They are able to self-splice by means of a two-step transesterification reaction using a guanosine molecule as a cofactor. The catalytic structure that is conserved among all group I introns consists of a specific arrangement of about 10 paired elements (P) that are capped by loops and connected by junctions (J) (38). The core of each intron is comprised of two separately folding helical domains made up of P4-P5-P6 and P3-P7-P9. The P4-P6 domain structurally supports the P3-P9 domain, which contains the active site (17). Splice sites are determined by helix P1, which pairs with the 5Ј substrate strand (5Ј exon), and by helix P10, which pairs with the 3Ј substrate strand (3Ј exon). A conserved G · U wobble pair contributes to the recognition of the 5Ј splice site, whereas the 3Ј splice site is recognized in part by a conserved terminal guanine, termed ⍀G (23). Based on conserved secondary-structure characteristics, group I introns are further classified into 13 subgroups (23, 34). These selfish genetic elements are distributed widely in nature, albeit with a bias towards fungi, plants, and red or green algae (14). Although group I introns are abundant in mitochondria and chloroplasts of lower eukaryotes, they are relatively rare in bacteria and until recently were unknown in bacterial structural RNAs. Group I introns in 23S rRNA genes have been...

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Section: Discussionmentioning

confidence: 99%

The Unusual 23S rRNA Gene of Coxiella burnetii : Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical ΩG

et al. 2007

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“…Similarly, it is reported that tRNA cleavage is a response to stresses in the Eukaryota (15,56), and cancer-or ageassociated changes in fragmented tRNAs have been observed (27,32). Recently, rRNA fragmentation has become another topic of interest (16,39), although the functions of fragmented rRNAs remain unclear. Papers that report unique RNA regulatory sequences, called riboswitches, in prokaryotic cells also are accumulating (49).…”

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confidence: 99%

Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation

Murakami

Fujishima

Tomita

et al. 2012

Appl Environ Microbiol

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Studies of small noncoding RNAs (sRNAs) have been conducted predominantly using culturable organisms, and the acquisition of further information about sRNAs from global environments containing uncultured organisms now is very important. In this study, hot spring water (57°C, pH 8.1) was collected directly from the underground environment at depths of 250 to 1,000 m in Yunohama, Japan, and small RNA sequences obtained from the environment were analyzed. A phylogenetic analysis of both archaeal and bacterial 16S rRNA gene sequences was conducted, and the results suggested the presence of unique species in the environment, corresponding to the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) group and three new Betaproteobacteria. A metatranscriptomic analysis identified 64,194 (20,057 nonredundant) cDNA sequences. Of these cDNAs, 90% were either tRNAs, tRNA fragments, rRNAs, or rRNA fragments, whereas 2,181 reads (10%) were classified as previously uncharacterized putative candidate sRNAs. Among these, 15 were particularly abundant, 14 of which showed no sequence similarity to any known noncoding RNA, and at least six of which form very stable RNA secondary structures. The analysis of a large number of tRNA fragments suggested that unique relationships exist between the anticodons of the tRNAs and the sites of tRNA degradation. Previous bacterial tRNA degradation studies have been limited to specific organisms, such as Escherichia coli and Streptomyces coelicolor, and the current results suggest that specific tRNA decay occurs more frequently than previously expected.

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“…The rrn operon is one of the most widely studied operons in the bacterial genome having been studied at the level of ribosome structure (Gutell, Lee, & Cannone, 2002;Wimberly et al, 2000), ribosomal RNA (rRNA) gene transcription (Condon, Squires, & Squires, 1995;Evguenieva-Hackenberg, 2005), rRNA gene organisation (Martín, Barreiro, González-Lavado, & Barriuso, 2003), rrn operon organisation at the level of the bacterial whole genome (Gurtler & Grando, 2013) and the use of the 16S rRNA gene sequence in evolutionary and phylogenetic studies, pioneered by Woese (1987). Indeed, the 16S rRNA gene sequence database is the cornerstone of evolutionary phylogenetics and bacterial taxonomy (Amann, Ludwig, & Schleifer, 1995;Baker, Smith, & Cowan, 2003;Woese, 1987).…”

Section: Introductionmentioning

confidence: 99%

Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequences

Gürtler

Subrahmanyam

Shekar

et al. 2014

Methods in Microbiology

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Bacterial ribosomal RNA in pieces

Cited by 63 publications

References 56 publications

The Unusual 23S rRNA Gene of Coxiella burnetii : Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical ΩG

The Unusual 23S rRNA Gene of Coxiella burnetii : Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical ΩG

Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation

Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequences

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