Phylogenetic relationships among group II intron ORFs

Zimmerly, Steven

doi:10.1093/nar/29.5.1238

Cited by 178 publications

(241 citation statements)

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“…Phylogenetic analysis of the most frequently observed intron S1396, a group II intron, revealed that it was probably acquired both vertically and horizontally within the family. This feature is well known among group II introns (46)(47)(48)(49). Comparative sequence analysis of intron S1396 generally reflects the phylogeny suggested by 16S rRNA sequence analysis at species level (Table S1 and Fig.…”

Section: Discussionsupporting

confidence: 72%

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.

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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.

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Section: Discussionsupporting

confidence: 72%

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.

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“…Full sequences of E.c.I1 and E.c.I3 were obtained by PCR amplification of the introns based on predicted flanking exon sequences and host strains (Ferat et al+, 1994), followed by cloning and sequencing (see Material and Methods)+ Based on the completed sequences, all five introns can be described+ E.c.I1, E.c.I2, and E.c.I3 are related to each other and belong to the previously defined subclass "bacterial class D+" (Intron subclasses are based on phylogenetic groupings of the intron-encoded ORFs, but each subclass also has a distinct intron secondary structure; Toor et al+, 2001;Zimmerly et al+, 2001+) Typical of bacterial class D, the introns are IIB-like in RNA structure (Fig+ 1A,B), and the ORFs lack a Zn domain+ Although the Zn domain is required for mobility of Lactococcus Ll+ltrB (Cousineau et al+, 1998), many bacterial introns do not contain Zn domains and at least one of these is efficiently mobile nevertheless (Martinez-Abarca & Toro, 2000a)+ E.c.I1 and E.c.I2 are 67% identical in DNA sequence, whereas E.c.I3 is much less related, with 44% identity to E.c.I2 over its ORF+ E.c.I1 sequence from ECOR43 has a stop codon in RT domain 6 and a frame shift in domain X, suggesting loss of mobility and splicing functions+ E.c.I1 and E.c.I2 are inserted into an ISEc1 element, which is itself contained within an Recombination hot spot (Rhs) element (Ferat et al+, 1994)+ ISEc1 was previously called an H-repeat, but has been renamed ISEc1 because of its resemblance to IS elements (Mahillon & Chandler, 1998)+ The Rhs element is an ;6-kb DNA found in five copies in the sequenced K-12 genome+ There are at least eight varieties of Rhs elements (A-H), whose core sequences are .70% identical, but which differ in organization and lengths of spacer elements (Zhao et al+, 1993;Bachellier et al+, 1996;Wang et al+, 1998)+ At the 39 terminus of most Rhs elements is an ISEc1 copy, which is flanked by 11 bp inverted repeats+ E.c.I1 is inserted 4 bp after the upstream inverted repeat, whereas E.c.I2 is inserted near the 39 end of the ISEc1 ORF+ E.c.I3 is also located in an IS element, IS679+ E.c.I4 belongs to the subclass "bacterial class A," and its only other relative is the essentially identical intron in the closely related bacterium Shigella (99+4% identity)+ A possible secondary structure is shown in Figure 1C+ According to information in the databases, the intron has two homing sites in IS629 and IS911 elements, which share only 60% identity (Fig+ 2D)+ (We use the term "homing site" to denote the insertion site for all five introns in this study+ Although homing has not been experimentally demonstrated, it is suggested because the introns are repeatedly found within the same flanking sequences+)…”

Section: Completion Of Sequencing Of Two Introns and Description Of Amentioning

confidence: 99%

The dispersal of five group II introns among natural populations of Escherichia coli

Dai

Zimmerly

2002

RNA

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Group II introns are self-splicing RNAs that also act as retroelements in bacteria, mitochondria, and chloroplasts. Group II introns were identified in Escherichia coli in 1994, but have not been characterized since, and, instead, other bacterial group II introns have been studied for splicing and mobility properties. Despite their apparent intractability, at least five distinct group II introns exist naturally in E. coli strains. To illuminate their function and learn how the introns have dispersed in their natural host, we have investigated their distribution in the ECOR reference collection. Two introns were cloned and sequenced to complete their partial sequences. Unexpectedly, southern blots showed all ECOR strains to contain fragments and/or full-length copies of group II introns, with some strains containing up to 15 intron copies. One intron, E.c.I4, has two natural homing sites in IS629 and IS911 elements, and the intron can be present in one, both, or neither homing site in a given strain. Nearly all strains that contain full-length introns also contain unfilled homing sites, suggesting either that mobility is highly inefficient or that most full-length copies are nonfunctional. The data indicate independent mobility of the introns, as well as mobility via the host DNA elements, and overall, the pattern of intron distribution resembles that of IS elements.

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“…It has also been assigned to phylogenetic bacterial class D (17,18) on the basis of the internally encoded (ORF within DIV) reverse transcriptasematurase (intron-encoded protein (IEP)). This group II intron is excised, both in vivo and in vitro, as an intron lariat (16,19).…”

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confidence: 99%

Relevance of the Branch Point Adenosine, Coordination Loop, and 3′ Exon Binding Site for in Vivo Excision of the Sinorhizobium meliloti Group II Intron RmInt1

Molina-Sánchez¹,

Barrientos‐Durán²,

Toro

2011

Journal of Biological Chemistry

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Excision of the bacterial group II intron RmInt1 has been demonstrated in vivo, resulting in the formation of both intron lariat and putative intron RNA circles. We show here that the bulged adenosine in domain VI of RmInt1 is required for splicing via the branching pathway, but branch site mutants produce small numbers of RNA molecules in which the first G residue of the intron is linked to the last C residue. Mutations in the coordination loop in domain I reduced splicing efficiency, but branched templates clearly predominated among splicing products. We also found that a single substitution at the EBS3 position (G329C), preventing EBS3-IBS3 pairing, resulted in the production of 50 to 100 times more RNA molecules in which the 5 and 3 extremities were joined. We provide evidence that these intron molecules may correspond to both, intron circles linked by a 2-5 phosphodiester bond, and tandem, head-to-tail intron copies.Group II introns are large catalytic RNAs with a conserved secondary structure consisting of six domains arranged around a central wheel (1). Group II introns may self-splice via several different pathways (Fig. 1). The main splicing pathway in group II introns involves two sequential trans-esterification reactions. In the first, the 2Ј-hydroxyl of a bulged adenosine near the end of the intron, in domain VI, triggers a nucleophilic attack on the 5Ј splice site. In the second reaction, the 2Ј-5Ј branched product is released as a lariat when the free 3Ј-OH at the end of the 5Ј exon attacks the 3Ј splice junction joining the two exons (2-5). In ai5␥, a yeast mitochondrial group IIB intron, the functional group II intron branch site consists of the bulged adenosine, the wobble pairs (G-U) flanking this residue and, possibly, the purine-enriched sequence in domain VI on the strand opposite the bulged nucleotide (6 -8). Recent studies have reported the presence, within domain I of group IIB introns, of a branch site receptor known as a coordination loop (9), which is required for trans-esterification (8), but these findings have been called into question (10). This coordination loop has been identified as a key element for exon ligation, as it positions the exon and intron binding sequences, the EBS3-IBS3 base pair and the EBS1-IBS1 helix, in an appropriate conformation for reaction (9). There is also an alternative splicing pathway, the first step of which involves hydrolysis. The ligated exons and linear intron are then generated in a standard second step (11-13). An additional excision reaction, in which the intron is excised as a putative circle, has also been proposed for some group II introns (14 -16). In this case, prior release of the 3Ј exon from the precursor molecules, presumably via a transsplicing mechanism, seems to be required for the generation of a putative 2Ј-5Ј ligated circular intron. The origin and function of such intron circles in vivo remains unknown.RmInt1 is a mobile subclass IIB3 intron (17). It has also been assigned to phylogenetic bacterial class D (17, 18) on the basis o...

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Phylogenetic relationships among group II intron ORFs

Cited by 178 publications

References 45 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

The dispersal of five group II introns among natural populations of Escherichia coli

Relevance of the Branch Point Adenosine, Coordination Loop, and 3′ Exon Binding Site for in Vivo Excision of the Sinorhizobium meliloti Group II Intron RmInt1

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