Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements

Swithers, Kristen S.; Senejani, Alireza G.; Fournier, Gregory P.; Gogarten, J. Peter

doi:10.1186/1471-2148-9-303

Cited by 47 publications

(65 citation statements)

References 69 publications

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“…In Fig. 3, viruses and hosts are ordered by their infection and susceptibility patterns, according to the number of hosts infected by one virus and to the amount of viruses (62) that are translated with the host protein and removed in the maturation of the final protein product (48). In addition, we tried to find a correlation between genetic distances and infection/susceptibility patterns for the whole host-virus interaction.…”

Section: Resultsmentioning

confidence: 99%

“…Splicing domains are located at the N and C termini of the intein and ensure its excision and ligation of its flanking sequences (extein or external protein, i.e., the host protein) (19,46,47,58). Moreover, inteins can also harbor homing endonuclease domains, particularly the dodecapeptide (DOD) motif EN1, ensuring its horizontal dispersal to intein-less alleles by recognition of a highly conserved homing site (YGDTDS on the polB sequence) (41,47,62). Although there is an excision step, experimental studies failed to find any effect of inteins on the host fitness (38,48).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Prasinoviruses of the Marine Green Alga Ostreococcus tauri Are Mainly Species Specific

Clérissi

Desdevises

Grimsley

2012

J Virol

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Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40 Ostreococcus tauri viruses on 13 independently isolated wild-type O. tauri strains, 4 wild-type O. lucimarinus strains, 1 Ostreococcus sp. ("Ostreococcus mediterraneus") clade D strain, and 1 representative species of each of two other related species of Mamiellales, Bathycoccus prasinos and Micromonas pusilla. Thirty-four out of 40 viruses infected only O. tauri, 5 could infect one other species of the Ostreococcus genus, and 1 infected two other Ostreococcus spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of Ostreococcus strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete O. tauri virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Prasinoviruses of the Marine Green Alga Ostreococcus tauri Are Mainly Species Specific

Clérissi

Desdevises

Grimsley

2012

J Virol

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“…Although other helicases also had intein insertions in the P-loop, this is not the case for the P-loops of Pols (Table 1) (16). Nevertheless, in line with inteins localizing to the conserved domains that are functionally important, inteins are inserted into either catalytic or ligand-binding sites of RNR, archaeal mini-chromosome maintenance protein (MCM) helicases and archaeal replication factor C (RFC), archaeal/eukaryotic VMA, and eukaryotic RNA polymerases (11,60,61).…”

Section: Inteins Tend To Be Located At Protein Active Sitesmentioning

confidence: 99%

Enigmatic Distribution, Evolution, and Function of Inteins

Новикова

Topilina

Belfort

2014

Journal of Biological Chemistry

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Inteins are mobile genetic elements capable of self-splicing post-translationally. They exist in all three domains of life including in viruses and bacteriophage, where they have a sporadic distribution even among very closely related species. In this review, we address this anomalous distribution from the point of view of the evolution of the host species as well as the intrinsic features of the inteins that contribute to their genetic mobility. We also discuss the incidence of inteins in functionally important sites of their host proteins. Finally, we describe instances of conditional protein splicing. These latter observations lead us to the hypothesis that some inteins have adapted to become sensors that play regulatory roles within their host protein, to the advantage of the organism in which they reside. Protein SplicingProtein splicing is a naturally occurring biochemical process that mediates the post-translational conversion of a precursor polypeptide into a mature and functional protein through the removal of an internal protein element, called an intein (Fig. 1A). The process is analogous to intron splicing at the RNA level. The protein splicing mechanism involves a series of autocatalytic peptide bond rearrangements, where the intein excises itself from the precursor polypeptide with concurrent ligation of the flanking sequences, called exteins (N-or C-exteins relative to the position of intein) (for review, see Refs. 1-3). As a result of this process, two proteins are produced from a single polypeptide product. The term intein refers to both the genetic element in the DNA or RNA and the protein splicing entity.Most inteins are expressed within a single polypeptide chain (cis-splicing inteins), but some are split into two polypeptides each containing one extein and an intein fragment (trans-splicing inteins) (4, 5). In the case of split inteins, reassociation of the fragments at a zipper-like interface (6) precedes protein splicing (Fig. 1B). Both cis-splicing and trans-splicing inteins are frequently utilized in various biotechnological applications including protein purification, modification, labeling, and posttranslational control of expressed proteins (reviewed in Refs. 7 and 8). The cis-splicing inteins often contain a distinct homing endonuclease (HEN) 2 domain (9). HEN-containing inteins are naturally occurring mobile genetic elements. The presence of a HEN provides inteins the ability to transfer their coding elements into homologous alleles at homing sites that lack the intein sequence (Fig. 1D). This HEN-mediated homing process can result in horizontal gene transfer (HGT) of inteins, by invasion of diverse species, followed by vertical transmission of inteins (10, 11). Moreover, HEN-containing inteins are involved in a so-called "homing cycle" that includes two opposing processes, precise intein loss and reinvasion of a newly formed vacant homing site. It is believed that the homing cycle allows the HEN to avoid fixation and functional decay in one locus (12).

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“…Like the bypass sequence, the 5′ ends of many bacteriophage introns begin with an in-frame stop codon, which is part of the base-paired stem (P1) with which all group I introns begin (21,22). Furthermore, like the insertion sites of most group I introns (12,(23)(24)(25), the bypass sequence is inserted into a highly conserved sequence of an essential protein, the Mg 2+ -binding region at the active site of type II topoisomerases (26) (Fig. 1B).…”

Section: Origin Of the Bypassmentioning

confidence: 99%

A homing endonuclease and the 50-nt ribosomal bypass sequence of phage T4 constitute a mobile DNA cassette

Bonocora

Zeng

Abel

et al. 2011

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

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Since its initial description more than two decades ago, the ribosome bypass (or "hop") sequence of phage T4 stands out as a uniquely extreme example of programmed translational frameshifting. The gene for a DNA topoisomerase subunit of T4 has been split by a 1-kb insertion into two genes that retain topoisomerase function. A second 50-nt insertion, beginning with an inphase stop codon, is inserted near the start of the newly created downstream gene 60. Instead of terminating at this stop codon, approximately half of the ribosomes skip 50 nucleotides and continue translation in a new reading frame. However, no functions, regulatory or otherwise, have been imputed for the truncated peptide that results from termination at codon 46 or for the bypass sequence itself. Moreover, how this unusual mRNA organization arose and why it is maintained have never been explained. We show here that a homing endonuclease (MobA) is encoded in the insertion that created gene 60, and the mobA gene together with the bypass sequence constitute a mobile DNA cassette. The bypass sequence provides protection against self-cleavage by the nuclease, whereas the nuclease promotes horizontal spread of the entire cassette to related bacteriophages. Group I introns frequently provide protection against self-cleavage by associated homing endonucleases. We present a scenario by which the bypass sequence, which is otherwise a unique genetic element, might have been derived from a degenerate group I intron. bacteriophage gene structure | group I intron | horizontal gene transfer | ribosomal frameshifting | mobile genetic element I n most of the phages of the T4 superfamily, the large subunit of DNA topoisomerase is a single polypeptide encoded by gene 39. However, in phage T4 this gene is disrupted by a 1-kb insertion, creating a truncated gene 39 plus a new gene (gene 60) that encodes the remainder of the topoisomerase subunit (1, 2) ( Fig. 1). Furthermore, the C terminus of the truncated gene 39 and the N terminus of the newly created gene 60 each contain additional amino acid residues (43 and 30, respectively) that were not present in the original gene 39 homologs. These two independently translated proteins interact with the small subunit (encoded by gene 52) to create an enzymatically active topoisomerase (4). A second, 50-nt insertion beginning with an inphase stop codon, is inserted into the newly created downstream gene 60 (2). Instead of terminating at this stop codon, approximately half of the ribosomes skip 50 nucleotides and continue translation in a new reading frame (5). Features involved in this remarkable process include: the stop codon, the codon at which translation resumes, a portion of the pre-hop nascent peptide, a stem-loop at the start of the bypassed sequence, a Shine/Dalgarno-like sequence within the bypassed RNA, and the structure of the bypassed mRNA (5-8).The genome sequence of phage T4 (GenBank accession no. NC_000866) indicated that the insertion into gene 39 contains two ORFs: an apparent H-N-H homing endonuclease ps...

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Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements

Cited by 47 publications

References 69 publications

Prasinoviruses of the Marine Green Alga Ostreococcus tauri Are Mainly Species Specific

Prasinoviruses of the Marine Green Alga Ostreococcus tauri Are Mainly Species Specific

Enigmatic Distribution, Evolution, and Function of Inteins

A homing endonuclease and the 50-nt ribosomal bypass sequence of phage T4 constitute a mobile DNA cassette

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