Intron mobility in the T-even phages: High frequency inheritance of group I introns promoted by intron open reading frames

Quirk, Susan M.; Bell-Pedersen, Deborah; Belfort, Marlene

doi:10.1016/0092-8674(89)90248-1

Cited by 133 publications

(98 citation statements)

References 29 publications

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“…The variable distribution of the sequences 3' to regA (Fig. 3) in the RB and T-even bacteriophages is reminiscent of the uneven distribution of introns in td, nrdB, and sun Y of the T-even phages (8,20,21). Type 1 and 2 sequences are not likely to be of intron origin, however, because unlike group 1 introns of T-even phages, they are not contained within a larger coding region; conserved base-pairing sequences (3) are not apparent, and the sequences entirely compose an open reading frame.…”

Section: Resultsmentioning

confidence: 99%

Sequence analysis of conserved regA and variable orf43.1 genes in T4-like bacteriophages

Miller

Jozwik

1990

J Bacteriol

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Bacteriophage T4 RegA protein is a translational repressor of several phage mRNAs. In the T4-related phages examined, regA nucleotide sequences are highly conserved and the inferred amino acid sequences are identical. The exceptional phage, RB69, did not produce a RegA protein reproducibly identifiable by Western blots (immunoblots) nor did it produce mRNA that hybridized to T4 regA primers. Nucleotide sequences of either 223 or 250 base pairs were identified immediately 3' to regA in RB18 and RB51 that were absent in T-even phages. Open reading frames' in these regions, designated orf43.lRBl8 and orf43.lRB59l potentially encode related proteins of 8.5 and 9.2 kilodaltons, respectively. orf43.1 sequences, detected in 13 of 27 RB bacteriophage chromosomes analyzed by polymerase chain reaction, are either RB18-or RB51-like and have flanking repeat sequences that may promote orf43.1 deletion.

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Section: Resultsmentioning

confidence: 99%

Sequence analysis of conserved regA and variable orf43.1 genes in T4-like bacteriophages

Miller

Jozwik

1990

J Bacteriol

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“…Plasmid-to-phage homing assays were performed as described by Quirk et al (18). Briefly, E. coli LMG194 cells harboring plasmids pT4(39-60ΔmobA) (donor) and either pMobA, pF-CphI, (35) or pBAD/MycHisA (the empty expression plasmid) were induced with increasing concentrations of L-arabinose on H agar plates at 30°C for 2 h. Serial dilutions of T2 phage were spotted onto the plates and incubated overnight at 30°C.…”

Section: Methodsmentioning

confidence: 99%

“…Unregulated expression of MobA is lethal to Escherichia coli (our early attempts to clone wild-type mobA failed, yielding only mutant sequences until the tightly regulated expression plasmid pBAD was used, generating plasmid pMobA). Therefore, to demonstrate horizontal transfer to phage T2, we used a twoplasmid system (18). The donor plasmid was pT4(39-60ΔmobA) (the T4 gene 39/60 locus, with codons 15-132 of mobA deleted) and wild-type MobA was provided by induction of plasmid pMobA.…”

Section: Function Of the Bypass Sequence Is Prevention Of Self-cleavamentioning

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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“…This process, termed intron ''homing,'' has been observed for introns located in a variety of mitochondrial (mt) and chloroplast genes (4-7), in nuclear rRNA genes of the slime mold Physarum (8), and in protein genes of T-even phage (9). Homing is initiated by the intron-encoded endonuclease, which makes a staggered double-strand break at its target site within a recipient intronless allele, and is thought to then proceed by the double-strand-break repair pathway (10).…”

mentioning

confidence: 99%

Explosive invasion of plant mitochondria by a group I intron

Cho

Qiu

Kuhlman

et al. 1998

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

259

204

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Group I introns are mobile, self-splicing genetic elements found principally in organellar genomes and nuclear rRNA genes. The only group I intron known from mitochondrial genomes of vascular plants is located in the cox1 gene of Peperomia, where it is thought to have been recently acquired by lateral transfer from a fungal donor. Southern-blot surveys of 335 diverse genera of land plants now show that this intron is in fact widespread among angiosperm cox1 genes, but with an exceptionally patchy phylogenetic distribution. Four lines of evidence-the intron's highly disjunct distribution, many incongruencies between intron and organismal phylogenies, and two sources of evidence from exonic coconversion tracts-lead us to conclude that the 48 angiosperm genera found to contain this cox1 intron acquired it by 32 separate horizontal transfer events. Extrapolating to the over 13,500 genera of angiosperms, we estimate that this intron has invaded cox1 genes by cross-species horizontal transfer over 1,000 times during angiosperm evolution. This massive wave of lateral transfers is of entirely recent occurrence, perhaps triggered by some key shift in the intron's invasiveness within angiosperms.Many group I introns encode site-specific endonucleases that catalyze their efficient spread from intron-containing to intronless alleles of the same gene in genetic crosses (1-3). This process, termed intron ''homing,'' has been observed for introns located in a variety of mitochondrial (mt) and chloroplast genes (4-7), in nuclear rRNA genes of the slime mold Physarum (8), and in protein genes of T-even phage (9). Homing is initiated by the intron-encoded endonuclease, which makes a staggered double-strand break at its target site within a recipient intronless allele, and is thought to then proceed by the double-strand-break repair pathway (10).The evolutionary importance of intron homing to the spread of group I introns across species barriers has been unclear, as relatively few cases of the horizontal transfer of group I introns between identical genomic sites of nonmating organisms are documented (11-17). Most of these cases involve the same genome and species belonging to the same phylum, usually fungi (11-13). Two notable exceptions are the transfer of two group I introns between identical sites of rRNA genes located in the chloroplast of a Chlamydomonas-type green alga and the mitochondrion of an Acanthamoeba-like ameboid (15).The only group I intron known from vascular plant mt genomes (which contain many group II introns) is also thought to have been acquired by homing-mediated horizontal transfer from a distantly related organism. This intron is present in the cox1 (cytochrome oxidase subunit 1) gene of the angiosperm Peperomia (16, 17) at the same location as related introns in the nonvascular plant Marchantia, the green alga Prototheca, the slime mold Dictyostelium, and several diverse fungi (see ref. 18 and references therein). This cox1 intron is thought to have been recently acquired by Peperomia, most likel...

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Intron mobility in the T-even phages: High frequency inheritance of group I introns promoted by intron open reading frames

Cited by 133 publications

References 29 publications

Sequence analysis of conserved regA and variable orf43.1 genes in T4-like bacteriophages

Sequence analysis of conserved regA and variable orf43.1 genes in T4-like bacteriophages

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

Explosive invasion of plant mitochondria by a group I intron

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