Inteins: Structure, Function, and Evolution

Gogarten, J. Peter; Senejani, Alireza G.; Zhaxybayeva, Olga; Olendzenski, Lorraine; Hilario, Elena

doi:10.1146/annurev.micro.56.012302.160741

Cited by 199 publications

(222 citation statements)

References 102 publications

(153 reference statements)

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“…A few phycodnavirus genomes have been found to harbor inteins, which are parasitic genetic elements that typically insert themselves within the conserved motifs of the essential genes of their hosts (Gogarten et al, 2002). Inteins are translated and transcribed with their host protein and then extract themselves autocatalytically before the final conformation of the mature protein (Gogarten and Hilario, 2006).…”

Section: Introductionmentioning

confidence: 99%

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

2008

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Viruses in the family Phycodnaviridae infect autotrophic protists in aquatic environments. Application of a PCR assay targeting the DNA polymerase of viruses in this family has revealed that phycodnaviruses are quite diverse and appear to be widespread, but a limited number of environments have been examined so far. In this study, we examined the sequence diversity among viral DNA pol genes amplified by PCR from subtropical coastal waters of O'ahu, Hawai'i. A total of 18 novel prasinovirus-like sequences were detected along with two other divergent sequences that differ at the genus-level relative to other sequences in the family. Of the 20 new sequence types reported here, three were serendipitously found to contain protein introns, or inteins. Sequence analysis of the inteins suggested that all three have self-splicing domains and are apparently capable of removing themselves from the translated polymerase protein. Two of the three also appear to be 'active', meaning they encode all the motifs necessary for a complete dodecapeptide homing endonuclease, and are therefore capable of horizontal transfer. A subsequent PCR survey of our samples with intein-specific primers suggested that intein-containing phycodnaviruses are common in this environment. A search for similar sequences in metagenomic data sets from other oceans indicated that viral inteins are also widespread, but how these genetic parasites might be influencing the ecology and evolution of phycodnaviruses remains unclear.

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Section: Introductionmentioning

confidence: 99%

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

2008

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“…1). Homing endonucleases are often encoded within self-splicing introns and inteins (2)(3)(4), but many bacterial and phage genomes possess a significant number of so-called freestanding homing endonucleases that are not encoded within introns or inteins (5,6). Free-standing endonucleases do not have the benefit of a self-splicing element to minimize their impact on host gene structure and function and, thus, are found at genomic insertion sites that are of low impact, such as intergenic regions.…”

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confidence: 99%

Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase that retains function

Friedrich

Torrents

Gibb

et al. 2007

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

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In bacterial and phage genomes, coding regions are sometimes interrupted by self-splicing introns or inteins, which can encode mobility-promoting homing endonucleases. Homing endonuclease genes are also found free-standing (not intron-or intein-encoded) in phage genomes where they are inserted in intergenic regions. One example is the HNH family endonuclease, mobE, inserted between the large (nrdA) and small (nrdB) subunit genes of aerobic ribonucleotide reductase (RNR) of T-even phages T4, RB2, RB3, RB15, and LZ7. Here, we describe an insertion of mobE into the nrdA gene of Aeromonas hydrophila phage Aeh1. The insertion creates a unique genes-in-pieces arrangement, where nrdA is split into two independent genes, nrdA-a and nrdA-b, each encoding cysteine residues that correspond to the active-site residues of uninterrupted NrdA proteins. Remarkably, the mobE insertion does not inactivate NrdA function, although the insertion is not a self-splicing intron or intein. We copurified the NrdA-a, NrdA-b, and NrdB proteins as complex from Aeh1-infected cells and also showed that a reconstituted complex has RNR activity. Class I RNR activity in phage Aeh1 is thus assembled from separate proteins that interact to form a composite active site, demonstrating that the mobE insertion is phenotypically neutral in that its presence as an intervening sequence does not disrupt the function of the surrounding gene.bacteriophage Aeh1 ͉ gene structure ͉ intervening sequence H oming endonucleases are a distinctive class of site-specific DNA endonucleases that promote the lateral transfer of their own coding region and flanking DNA between genomes by a recombination-dependent process termed homing (reviewed in ref. 1). Homing endonucleases are often encoded within self-splicing introns and inteins (2-4), but many bacterial and phage genomes possess a significant number of so-called freestanding homing endonucleases that are not encoded within introns or inteins (5, 6). Free-standing endonucleases do not have the benefit of a self-splicing element to minimize their impact on host gene structure and function and, thus, are found at genomic insertion sites that are of low impact, such as intergenic regions. In T4-like phages that infect Escherichia coli and related bacteria, free-standing endonucleases are more abundant than intron-encoded versions (6-9) and promote their spread to phage genomes lacking the endonuclease by an intronless homing pathway (10-12).As a consequence of their abundance in T4-like phages, free-standing endonucleases represent a significant source of genetic variation by promoting recombination between genomes. Many characterized homing endonucleases have recognition sites that lie in genes that function in DNA metabolism, including those that encode aerobic and anaerobic ribonucleotide reductases (RNRs) (13). Three classes of RNRs have been described to date, based on required metallocofactors used to generate a radical intermediate and on structural differences (14). Prokaryotic class Ia aerobic enzymes, typifi...

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“…Their sporadic phylogenetic distributions suggest lateral gene transfer through intein homing (16,17). Inteins generally share only low levels of sequence similarity, but they share striking similarities in structure, reaction mechanism, and evolution (4,18,19,21). It is thought that inteins first originated with just the splicing domain and then acquired the endonuclease domain, with the latter conferring genetic mobility to the intein.…”

mentioning

confidence: 99%

Synthetic Two-piece and Three-piece Split Inteins for Protein trans-Splicing

Sun

Yang

Liu

2004

Journal of Biological Chemistry

111

109

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Inteins are protein-intervening sequences that can self-excise and concomitantly splice together the flanking polypeptides. Two-piece split inteins capable of protein trans-splicing have been found in nature and engineered in laboratories, but they all have a similar split site corresponding to the endonuclease domain of the intein. Can inteins be split at other sites and do transsplicing? After testing 13 split sites engineered into a Ssp DnaB mini-intein, we report the finding of three new split sites that each produced a two-piece split intein capable of protein trans-splicing. These three functional split sites are located in different loop regions between ␤-strands of the intein structure, and one of them is just 11 amino acids from the beginning of the intein. Because different inteins have similar structures and similar ␤-strands, these new split sites may be generalized to other inteins. We have also demonstrated for the first time that a three-piece split intein could function in protein trans-splicing. These findings have implications for intein structure-function, evolution, and uses in biotechnology.An intein is a protein-intervening sequence that catalyzes a protein-splicing reaction in which the intein sequence is precisely excised and its flanking sequences (N-and C-exteins) join with a peptide bond to produce the mature host protein (spliced protein) (1). The mechanism of protein splicing typically has four steps: two acyl rearrangements at the two splicing junctions, a trans-esterification between the two junctions, and a cyclization of the Asn residue at the C-terminal junction (2-4). Crystal structures of inteins revealed a splicing domain consisting of 11-12 ␤-strands and forming a compact horseshoe shape with the splicing junctions located in the central cleft (5-11). A majority of inteins also have a homing endonuclease domain inserted in the splicing domain sequence (12). These bifunctional inteins are ϳ350 -550 amino acids (aa) 1 long, although some extra large inteins are up to 1650 aa long and also contain tandem repeats (13,14). Nearly 200 intein and inteinlike sequences have been found in a wide variety of host proteins and in microorganisms belonging to bacteria, Archaea, and eukaryotes (12,15). Their sporadic phylogenetic distributions suggest lateral gene transfer through intein homing (16,17). Inteins generally share only low levels of sequence similarity, but they share striking similarities in structure, reaction mechanism, and evolution (4,18,19,21). It is thought that inteins first originated with just the splicing domain and then acquired the endonuclease domain, with the latter conferring genetic mobility to the intein. During intein evolution, however, some inteins lost their endonuclease domain to become mini-inteins consisting of just the ϳ130-aa protein-splicing domain plus a linker sequence of various lengths in place of the endonuclease domain (12,22).An interesting event of intein evolution is the loss of sequence continuity in some inteins, which apparently produced ...

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Inteins: Structure, Function, and Evolution

Cited by 199 publications

References 102 publications

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase that retains function

Synthetic Two-piece and Three-piece Split Inteins for Protein trans-Splicing

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