A group II intron in a conjugative transposon from the gram-positive bacterium, Clostridium difficile

Mullany, Peter; Pallen, Mark J.; Wilks, Mark; Stephen, J.; Tabaqchali, Soad

doi:10.1016/0378-1119(96)00511-2

Cited by 76 publications

(82 citation statements)

References 16 publications

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“…Our Consensus ----------------------------AY-------GA-------- Q------------p-F---s---RP--S---A-------------W-- D----FD---H-------------------I---L-A-------------- diverse bacterial groups. The possibility for intron dissemination via horizontal transfer exists in bacteria, as all the bacterial group I1 introns found so far are associated with insertion sequence elements (Ferat et al, 1994;, a conjugative transposon (Mullany et al, 1996), a lactococcal conjugative plasmid (Mills et al, 1996) and a lactococcal chromosomal sex factor (Shearman et al, 1996).…”

Section: Discussionmentioning

confidence: 99%

Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis

et al. 1997

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Pseudomonas alcaligenes NClB 9867 (strain P25X), which grows on 2,5-xylenol and harbours the plasmid RP4, was mated with a plasmid-free derivative of Pseudomonas putida NClB 9869, strain RA713, which cannot grow on 2,5-xylenol. Some RA713 transconjugants, initially selected on 2,5-xylenol, were found to carry RP4 plasmids that had acquired additional fragments (designated Xln) which ranged in size from 2 kb to approximately 26 kb. Instability of DNA inserts in RP4::Xln hybrid plasmids was observed. The smallest insert present in a stable RP4::Xln6 hybrid plasmid, termed Xln6, yielded multiple bands when it was used as a probe with digested P25X chromosomal DNA. Sequence analysis of Xln6 led to the discovery of an open reading frame with homology to the maturases of group II introns. The Xln6 insert also exhibited several features characteristic of a group II intron. These included the presence of the consensus sequence GUGYG at the 5' end and RAY at the 3' end of the intron. RNA secondary structure modelling of Xln6 also revealed the presence of perfectly conserved domains V and VI. Differences were detected in the Xln6 hybridization profiles of several P25X catabolic mutants that have lost the ability to grow on 2,5-xylenol. In these mutants the loss of 2,5-xylenol degradative ability could be due to genome rearrangements mediated by sequences related to the Xln6 group II intron. This is the f i r s t reported group II intron isolated from Pseudomonas spp. and the first time that the mobility of a bacterial group II intron has been demonstrated.

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Section: Discussionmentioning

confidence: 99%

Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis

et al. 1997

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“…Although there are fewer known examples of group II introns than of group I introns in bacteria, one trend is immediately clear: most group II introns are inserted in, or associated with, other mobile genetic elements (23,32,48,56,59,80) ( Table 2). The best studied bacterial group II intron, the Ll.LtrB intron of L. lactis ML3, is inserted in the conjugative relaxase gene essential for transfer of the plasmid pRS01 (56).…”

Section: Where Are Group I and Ii Introns Found?mentioning

confidence: 99%

Barriers to Intron Promiscuity in Bacteria

2000

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2"The field of bacterial viruses is a fine playground for serious children who ask ambitious questions."Max DelbruckThe first bacterial intron, a self-splicing group I intron, was found to interrupt the thymidylate synthase (td) gene of the Escherichia coli phage T4 (11). The second and third bacterial group I introns were found to interrupt the aerobic (nrdB) and anaerobic (nrdD [initially named sunY]) ribonucleotide reductases of phage T4 (29,90), and another group I intron was soon discovered in the DNA polymerase gene of SPO1, a Bacillus phage (25). From this (admittedly) small sampling of phage genomes, one might have naively expected that group I introns would be abundant in phage or bacterial genomes, especially since subsequent laboratory experiments demonstrated that group I introns could propagate themselves (by a process called homing) throughout populations of intron-minus alleles with near 100% efficiency (5, 68). That a similar homing phenomenon had also been previously demonstrated for a group I intron in the large rRNA gene of yeast mitochondria (34) gave additional support to the notion that group I introns should be able to spread efficiently throughout populations. However, this expected outcome has never been realized in natural phage populations; some phage populations harbor many introns, while other related phage populations are strangely lacking in any introns whatsoever (Table 1). Why do group I introns have an unusual distribution in phage and bacterial genomes, and what potential barriers might exist to prevent their spread?A similar question might be asked of group II introns in bacteria. Much was made of the initial finding of group II introns in bacteria, as their discovery added fuel to the debate concerning the evolutionary origins of eukaryotic spliceosomal introns (22, 70) which have both structural and functional similarities to group II introns (53,79,84). Yet, the number of group II introns in bacteria is small, many of which are inferred only from database matches to reverse transcriptases or maturases encoded within known introns (13,41,73,89), and only two have been shown to splice or be mobile in vivo (48,49,55,80) (Table 2). While group II intron homing is mechanistically distinct from group I intron homing, the principle is similar; group II introns home from intron-containing to intronless alleles. Many elegant biochemical and genetic experiments have unraveled the complexities of bacterial group II intron homing (14,48,49), and based on these results, there seems no a priori reason why group II introns should not be able to spread efficiently through populations of intron-minus alleles. The paucity of bacterial group II introns becomes even more perplexing given the recent demonstration of group II intron transposition to novel chromosomal sites (15). That group II introns are abundant in mitochondrial and chloroplast genomes (52) and present in bacterial genomes but at lower levels (and absent in phages) only adds to the mystery surrounding the lack of group II intro...

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“…The group II introns of bacteria have been identified in cyanobacteria (Calothrix spp. ), proteobacteria (Azotobacter vinelandii and E. coli [9]), and gram-positive bacteria (L. lactis and Clostridium difficile [27,35]). Most of the eubacterial group II introns are found in genes on plasmids or associated with conjugal transfer (7).…”

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confidence: 99%

Group I Self-Splicing Intron in the recA Gene of Bacillus anthracis

Choi

Park

2002

J Bacteriol

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Self-splicing introns are rarely found in bacteria and bacteriophages. They are classified into group I and II according to their structural features and splicing mechanisms. While the group I introns are occasionally found in protein-coding regions of phage genomes and in several tRNA genes of cyanobacteria and proteobacteria, they had not been found in protein-coding regions of bacterial genomes. Here we report a group I intron in the recA gene of Bacillus anthracis which was initially found by DNA sequencing as an intervening sequence (IVS). By using reverse transcriptase PCR, the IVS was shown to be removable from the recA precursor mRNA for RecA that was being translated in E. coli. The splicing was visualized in vitro with labeled free GTP, indicating that it is a group I intron, which is also implied by its predicted secondary structure. The RecA protein of B. anthracis expressed in E. coli was functional in its ability to complement a recA defect. When recA-negative E. coli cells were irradiated with UV, the Bacillus RecA reduced the UV susceptibility of the recA mutant, regardless of the presence of intron.While most of the introns found in eukaryotes and archaebacteria require functions of several proteins for their processing, introns found in eubacterial species are removed by selfsplicing. There are two types of self-splicing introns, classified according to their structures and splicing mechanisms. The processing of group I introns is initiated by a transesterification reaction mediated by an exogenous guanosine cofactor, generating ligated exon with a free intron bearing the guanosine at its 5Ј end (2, 32). The splicing of group II intron is similar to that of eukaryotic pre-mRNA, in which the 5Ј splice site is attacked by a 2Ј OH group of a bulged nucleotide, resulting in a lariat structure joined with a 2Ј-5Ј bond. Subsequently, the cleaved 5Ј exon attacks the 3Ј splice site, resulting in exon ligation and release of the intron lariat (14, 32).Despite a lack of overall primary sequence conservation, the group I introns contain blocks of conserved nucleotide sequence elements (P, Q, R, and S), forming an active center with a secondary structure consisting of characteristic stemloops P1 through P10 (2,22,23). There are also extra sequences, often including open reading frames (ORFs), which are located in loops peripheral to the catalytic intron core. The group II introns contain a different secondary structure, consisting of six conserved pairings emanating from a central wheel (24). In both introns, sequence conservations are confined to small regions of nucleotide residues. The products of internal ORFs of these introns usually play a role in splicing (in which case they are called maturases) or mobility of the intron (also referred to as "homing") (17, 32).The bacterial group I introns are found in several tRNA genes of cyanobacteria and purple proteobacteria (16,28,38).

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A group II intron in a conjugative transposon from the gram-positive bacterium, Clostridium difficile

Cited by 76 publications

References 16 publications

Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis

Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis

Barriers to Intron Promiscuity in Bacteria

Group I Self-Splicing Intron in the recA Gene of Bacillus anthracis

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