• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Dec 1999; 153(4): 1513–1523.
PMCID: PMC1460845

Intron homing with limited exon homology. Illegitimate double-strand-break repair in intron acquisition by phage t4.

Abstract

The td intron of bacteriophage T4 encodes a DNA endonuclease that initiates intron homing to cognate intronless alleles by a double-strand-break (DSB) repair process. A genetic assay was developed to analyze the relationship between exon homology and homing efficiency. Because models predict exonucleolytic processing of the cleaved recipient leading to homologous strand invasion of the donor allele, the assay was performed in wild-type and exonuclease-deficient (rnh or dexA) phage. Efficient homing was supported by exon lengths of 50 bp or greater, whereas more limited exon lengths led to a precipitous decline in homing levels. However, extensive homology in one exon still supported elevated homing levels when the other exon was completely absent. Analysis of these "one-sided" events revealed recombination junctions at ectopic sites of microhomology and implicated nucleolytic degradation in illegitimate DSB repair in T4. Interestingly, homing efficiency with extremely limiting exon homology was greatly elevated in phage deficient in the 3'-5' exonuclease, DexA, suggesting that the length of 3' tails is a major determinant of the efficiency of DSB repair. Together, these results suggest that illegitimate DSB repair may provide a means by which introns can invade ectopic sites.

Full Text

The Full Text of this article is available as a PDF (439K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bautz FA, Bautz EK. Transformation in phage T4: minmal recognition length between donor and recipient DNA. Genetics. 1967 Dec;57(4):887–895. [PMC free article] [PubMed]
  • Belfort M, Perlman PS. Mechanisms of intron mobility. J Biol Chem. 1995 Dec 22;270(51):30237–30240. [PubMed]
  • Belfort M, Reaban ME, Coetzee T, Dalgaard JZ. Prokaryotic introns and inteins: a panoply of form and function. J Bacteriol. 1995 Jul;177(14):3897–3903. [PMC free article] [PubMed]
  • Bell-Pedersen D, Quirk SM, Aubrey M, Belfort M. A site-specific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4. Gene. 1989 Oct 15;82(1):119–126. [PubMed]
  • Bell-Pedersen D, Quirk S, Clyman J, Belfort M. Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications. Nucleic Acids Res. 1990 Jul 11;18(13):3763–3770. [PMC free article] [PubMed]
  • Bryk M, Quirk SM, Mueller JE, Loizos N, Lawrence C, Belfort M. The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target. EMBO J. 1993 May;12(5):2141–2149. [PMC free article] [PubMed]
  • Bryk M, Belisle M, Mueller JE, Belfort M. Selection of a remote cleavage site by I-tevI, the td intron-encoded endonuclease. J Mol Biol. 1995 Mar 24;247(2):197–210. [PubMed]
  • Chandry PS, Belfort M. Activation of a cryptic 5' splice site in the upstream exon of the phage T4 td transcript: exon context, missplicing, and mRNA deletion in a fidelity mutant. Genes Dev. 1987 Nov;1(9):1028–1037. [PubMed]
  • Chang AC, Cohen SN. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. [PMC free article] [PubMed]
  • Cho Y, Qiu YL, Kuhlman P, Palmer JD. Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14244–14249. [PMC free article] [PubMed]
  • Clyman J, Belfort M. Trans and cis requirements for intron mobility in a prokaryotic system. Genes Dev. 1992 Jul;6(7):1269–1279. [PubMed]
  • Dujon B. Group I introns as mobile genetic elements: facts and mechanistic speculations--a review. Gene. 1989 Oct 15;82(1):91–114. [PubMed]
  • Gauss P, Gayle M, Winter RB, Gold L. The bacteriophage T4 dexA gene: sequence and analysis of a gene conditionally required for DNA replication. Mol Gen Genet. 1987 Jan;206(1):24–34. [PubMed]
  • George JW, Kreuzer KN. Repair of double-strand breaks in bacteriophage T4 by a mechanism that involves extensive DNA replication. Genetics. 1996 Aug;143(4):1507–1520. [PMC free article] [PubMed]
  • Gruber H, Kern G, Gauss P, Gold L. Effect of DNA sequence and structure on nuclease activity of the DexA protein of bacteriophage T4. J Bacteriol. 1988 Dec;170(12):5830–5836. [PMC free article] [PubMed]
  • Hall DH, Tessman I, Karlström O. Linkage of T4 genes controlling a series of steps in pyrimidine biosynthesis. Virology. 1967 Mar;31(3):442–448. [PubMed]
  • Hobbs LJ, Nossal NG. Either bacteriophage T4 RNase H or Escherichia coli DNA polymerase I is essential for phage replication. J Bacteriol. 1996 Dec;178(23):6772–6777. [PMC free article] [PubMed]
  • Hollingsworth HC, Nossal NG. Bacteriophage T4 encodes an RNase H which removes RNA primers made by the T4 DNA replication system in vitro. J Biol Chem. 1991 Jan 25;266(3):1888–1897. [PubMed]
  • Hsieh P, Camerini-Otero CS, Camerini-Otero RD. The synapsis event in the homologous pairing of DNAs: RecA recognizes and pairs less than one helical repeat of DNA. Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6492–6496. [PMC free article] [PubMed]
  • Huang YJ, Parker MM, Belfort M. Role of exonucleolytic degradation in group I intron homing in phage T4. Genetics. 1999 Dec;153(4):1501–1512. [PMC free article] [PubMed]
  • King SR, Richardson JP. Role of homology and pathway specificity for recombination between plasmids and bacteriophage lambda. Mol Gen Genet. 1986 Jul;204(1):141–147. [PubMed]
  • Kreuzer KN, Saunders M, Weislo LJ, Kreuzer HW. Recombination-dependent DNA replication stimulated by double-strand breaks in bacteriophage T4. J Bacteriol. 1995 Dec;177(23):6844–6853. [PMC free article] [PubMed]
  • Parker MM, Court DA, Preiter K, Belfort M. Homology requirements for double-strand break-mediated recombination in a phage lambda-td intron model system. Genetics. 1996 Jul;143(3):1057–1068. [PMC free article] [PubMed]
  • Pribnow D, Sigurdson DC, Gold L, Singer BS, Napoli C, Brosius J, Dull TJ, Noller HF. rII cistrons of bacteriophage T4. DNA sequence around the intercistronic divide and positions of genetic landmarks. J Mol Biol. 1981 Jul 5;149(3):337–376. [PubMed]
  • Lambowitz AM, Belfort M. Introns as mobile genetic elements. Annu Rev Biochem. 1993;62:587–622. [PubMed]
  • Quirk SM, Bell-Pedersen D, Belfort M. Intron mobility in the T-even phages: high frequency inheritance of group I introns promoted by intron open reading frames. Cell. 1989 Feb 10;56(3):455–465. [PubMed]
  • Quirk SM, Bell-Pedersen D, Tomaschewski J, Rüger W, Belfort M. The inconsistent distribution of introns in the T-even phages indicates recent genetic exchanges. Nucleic Acids Res. 1989 Jan 11;17(1):301–315. [PMC free article] [PubMed]
  • Rosenberg M, Ho YS, Shatzman A. The use of pKc30 and its derivatives for controlled expression of genes. Methods Enzymol. 1983;101:123–138. [PubMed]
  • Salinas F, Jiang H, Kodadek T. Homology dependence of UvsX protein-catalyzed joint molecule formation. J Biol Chem. 1995 Mar 10;270(10):5181–5186. [PubMed]
  • Mosig G. Recombination and recombination-dependent DNA replication in bacteriophage T4. Annu Rev Genet. 1998;32:379–413. [PubMed]
  • Selick HE, Kreuzer KN, Alberts BM. The bacteriophage T4 insertion/substitution vector system. A method for introducing site-specific mutations into the virus chromosome. J Biol Chem. 1988 Aug 15;263(23):11336–11347. [PubMed]
  • Mosig G, Colowick NE, Pietz BC. Several new bacteriophage T4 genes, mapped by sequencing deletion endpoints between genes 56 (dCTPase) and dda (a DNA-dependent ATPase-helicase) modulate transcription. Gene. 1998 Nov 26;223(1-2):143–155. [PubMed]
  • Shub DA, Gott JM, Xu MQ, Lang BF, Michel F, Tomaschewski J, Pedersen-Lane J, Belfort M. Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes. Proc Natl Acad Sci U S A. 1988 Feb;85(4):1151–1155. [PMC free article] [PubMed]
  • Singer BS, Gold L, Gauss P, Doherty DH. Determination of the amount of homology required for recombination in bacteriophage T4. Cell. 1982 Nov;31(1):25–33. [PubMed]
  • Mueller JE, Clyman J, Huang YJ, Parker MM, Belfort M. Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by way of multiple pathways. Genes Dev. 1996 Feb 1;10(3):351–364. [PubMed]
  • Wiberg JS. Mutants of bacteriophage T4 unable to cause breakdown of host DNA. Proc Natl Acad Sci U S A. 1966 Mar;55(3):614–621. [PMC free article] [PubMed]
  • Woodworth DL, Kreuzer KN. Bacteriophage T4 mutants hypersensitive to an antitumor agent that induces topoisomerase-DNA cleavage complexes. Genetics. 1996 Jul;143(3):1081–1090. [PMC free article] [PubMed]
  • Mueller JE, Smith D, Belfort M. Exon coconversion biases accompanying intron homing: battle of the nucleases. Genes Dev. 1996 Sep 1;10(17):2158–2166. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...