Plasticity of the Gene Functions for DNA Replication in the T4-like Phages

Petrov, V. M.; Nolan, Justin M.; Bertrand, Claire; Levy, Dawn R.; Desplats, Carine; Krisch, Henry; Karam, J.D.

doi:10.1016/j.jmb.2006.05.071

Cited by 83 publications

(102 citation statements)

References 97 publications

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“…Because many characterized homing endonucleases have recognition and cleavage sites within protein-coding genes, transposition of free-standing endonucleases into coding regions by illegitimate DSB repair may occur at an appreciable rate (36)(37)(38). A Seg-like homing endonuclease is found associated with a split gene structure in the family B DNA polymerase (gp43) of Aeromonas salmonicida phage 25 (23,39). Related phage possess a split gene 43 separated by up to Ϸ3 kb of intervening sequence without a Seg-like endonuclease.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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 one case, a GIY-YIG family endonuclease gene disrupts DNA polymerase (28,29); in the other case, a H-N-H family endonuclease gene disrupts the large subunit of ribonucleotide reductase (30). In all three cases, the products of the split genes reunite to form enzymatically active proteins.…”

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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“…Although more than 200 T4-like phages have been examined (4), only a limited number of these phage genomes have been sequenced completely (T4-like genome database [http://phage.bioc.tulane.edu], Tulane University Health Sciences Center, New Orleans, LA). Most of the known T4-like phages specifically infect certain strains of E. coli or some other enterobacteria, but several T4-like phages can propagate in phylogenetically more distant bacteria, such as Aeromonas, Acinetobacter, Vibrio, and Cyanobacteria (4,5,8,44,62). Previous cross-genome comparisons of T4 and other T4-like phages (41,44,55,62,78) provided many interesting findings in the field of phage biology.…”

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confidence: 99%

“…Most of the known T4-like phages specifically infect certain strains of E. coli or some other enterobacteria, but several T4-like phages can propagate in phylogenetically more distant bacteria, such as Aeromonas, Acinetobacter, Vibrio, and Cyanobacteria (4,5,8,44,62). Previous cross-genome comparisons of T4 and other T4-like phages (41,44,55,62,78) provided many interesting findings in the field of phage biology. It appears that this family of phages shares a common core genome from an ancestral sequence encoding the DNA replication modules, virion structural proteins, and some conserved hypothetical proteins (7,8,62).…”

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confidence: 99%

T4-Like Genome Organization of the Escherichia coli O157:H7 Lytic Phage AR1

Liao¹,

Ng²,

Lin³

et al. 2011

J Virol

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We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. Unlike most of the other sequenced phages of O157:H7, which belong to the temperate Podoviridae and Siphoviridae families, AR1 is a T4-like phage known to efficiently infect this pathogenic bacterial strain. The 167,435-bp AR1 genome is currently the largest among all the sequenced E. coli O157:H7 phages. It carries a total of 281 potential open reading frames (ORFs) and 10 putative tRNA genes. Of these, 126 predicted proteins could be classified into six viral orthologous group categories, with at least 18 proteins of the structural protein category having been detected by tandem mass spectrometry. Comparative genomic analysis of AR1 and four other completely sequenced T4-like genomes (RB32, RB69, T4, and JS98) indicated that they share a well-organized and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. The major diverse features between these phages include the modules of distal tail fibers and the types and numbers of internal proteins, tRNA genes, and mobile elements. Codon usage analysis suggested that the presence of AR1-encoded tRNAs may be relevant to the codon usage of structural proteins. Furthermore, protein sequence analysis of AR1 gp37, a potential receptor binding protein, indicated that eight residues in the C terminus are unique to O157:H7 T4-like phages AR1 and PP01. These residues are known to be located in the T4 receptor recognition domain, and they may contribute to specificity for adsorption to the O157:H7 strain.

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Plasticity of the Gene Functions for DNA Replication in the T4-like Phages

Cited by 83 publications

References 97 publications

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

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

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

T4-Like Genome Organization of the Escherichia coli O157:H7 Lytic Phage AR1

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