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. 1992 Jul 15;89(14):6658–6662. doi: 10.1073/pnas.89.14.6658

Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage.

M Sharma 1, R L Ellis 1, D M Hinton 1
PMCID: PMC49561  PMID: 1631169

Abstract

The bacteriophage T4 segA gene lies in a genetically unmapped region between the gene beta gt (beta-glucosyltransferase) and uvsX (recombination protein) and encodes a protein of 221 amino acids. We have found that the first 100 amino acids of the SegA protein are highly similar to the N termini of four other predicted T4 proteins, also of unknown function. Together these five proteins, SegA-E (similar to endonucleases of group I introns), contain regions of similarity to the endonuclease I-Tev I, which is encoded by the mobile group I intron of the T4 td gene, and to putative endonucleases of group I introns present in the mitochondria of Neurospora crassa, Podospora anserina, and Saccharomyces douglasii. Intron-encoded endonucleases are required for the movement (homing) of the intron DNA into an intronless gene, cutting at or near the site of intron insertion. Our in vitro assays indicate that SegA, like I-Tev I, is a Mg(2+)-dependent DNA endonuclease that has preferred sites for cutting. Unlike the I-Tev I gene, however, there is no evidence that segA (or the other seg genes) resides within introns. Thus, it is possible that segA encodes an endonuclease that is involved in the movement of the endonuclease-encoding DNA rather than in the homing of an intron.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adhya S., Gottesman M. Promoter occlusion: transcription through a promoter may inhibit its activity. Cell. 1982 Jul;29(3):939–944. doi: 10.1016/0092-8674(82)90456-1. [DOI] [PubMed] [Google Scholar]
  2. Belfort M. Phage T4 introns: self-splicing and mobility. Annu Rev Genet. 1990;24:363–385. doi: 10.1146/annurev.ge.24.120190.002051. [DOI] [PubMed] [Google Scholar]
  3. Belfort M. Self-splicing introns in prokaryotes: migrant fossils? Cell. 1991 Jan 11;64(1):9–11. doi: 10.1016/0092-8674(91)90201-9. [DOI] [PubMed] [Google Scholar]
  4. 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. doi: 10.1093/nar/18.13.3763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Broida J., Abelson J. Sequence organization and control of transcription in the bacteriophage T4 tRNA region. J Mol Biol. 1985 Oct 5;185(3):545–563. doi: 10.1016/0022-2836(85)90071-3. [DOI] [PubMed] [Google Scholar]
  6. Burger G., Werner S. The mitochondrial URF1 gene in Neurospora crassa has an intron that contains a novel type of URF. J Mol Biol. 1985 Nov 20;186(2):231–242. doi: 10.1016/0022-2836(85)90100-7. [DOI] [PubMed] [Google Scholar]
  7. Chu F. K., Maley G. F., Maley F., Belfort M. Intervening sequence in the thymidylate synthase gene of bacteriophage T4. Proc Natl Acad Sci U S A. 1984 May;81(10):3049–3053. doi: 10.1073/pnas.81.10.3049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chu F. K., Maley G. F., West D. K., Belfort M., Maley F. Characterization of the intron in the phage T4 thymidylate synthase gene and evidence for its self-excision from the primary transcript. Cell. 1986 Apr 25;45(2):157–166. doi: 10.1016/0092-8674(86)90379-x. [DOI] [PubMed] [Google Scholar]
  9. Chu F. K., Maley G., Pedersen-Lane J., Wang A. M., Maley F. Characterization of the restriction site of a prokaryotic intron-encoded endonuclease. Proc Natl Acad Sci U S A. 1990 May;87(9):3574–3578. doi: 10.1073/pnas.87.9.3574. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Colleaux L., D'Auriol L., Galibert F., Dujon B. Recognition and cleavage site of the intron-encoded omega transposase. Proc Natl Acad Sci U S A. 1988 Aug;85(16):6022–6026. doi: 10.1073/pnas.85.16.6022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Colleaux L., Michel-Wolwertz M. R., Matagne R. F., Dujon B. The apocytochrome b gene of Chlamydomonas smithii contains a mobile intron related to both Saccharomyces and Neurospora introns. Mol Gen Genet. 1990 Sep;223(2):288–296. doi: 10.1007/BF00265065. [DOI] [PubMed] [Google Scholar]
  12. Collins R. A., Reynolds C. A., Olive J. The self-splicing intron in the Neurospora apocytochrome b gene contains a long reading frame in frame with the upstream exon. Nucleic Acids Res. 1988 Feb 11;16(3):1125–1134. doi: 10.1093/nar/16.3.1125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Cummings D. J., Domenico J. M., Michel F. DNA sequence and organization of the mitochondrial ND1 gene from Podospora anserina: analysis of alternate splice sites. Curr Genet. 1988 Sep;14(3):253–264. doi: 10.1007/BF00376746. [DOI] [PubMed] [Google Scholar]
  14. Cummings D. J., MacNeil I. A., Domenico J., Matsuura E. T. Excision-amplification of mitochondrial DNA during senescence in Podospora anserina. DNA sequence analysis of three unique "plasmids". J Mol Biol. 1985 Oct 20;185(4):659–680. doi: 10.1016/0022-2836(85)90052-x. [DOI] [PubMed] [Google Scholar]
  15. Delahodde A., Goguel V., Becam A. M., Creusot F., Perea J., Banroques J., Jacq C. Site-specific DNA endonuclease and RNA maturase activities of two homologous intron-encoded proteins from yeast mitochondria. Cell. 1989 Feb 10;56(3):431–441. doi: 10.1016/0092-8674(89)90246-8. [DOI] [PubMed] [Google Scholar]
  16. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Dujon B. Group I introns as mobile genetic elements: facts and mechanistic speculations--a review. Gene. 1989 Oct 15;82(1):91–114. doi: 10.1016/0378-1119(89)90034-6. [DOI] [PubMed] [Google Scholar]
  18. Dujon B. Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci. Cell. 1980 May;20(1):185–197. doi: 10.1016/0092-8674(80)90246-9. [DOI] [PubMed] [Google Scholar]
  19. Dürrenberger F., Rochaix J. D. Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility. EMBO J. 1991 Nov;10(11):3495–3501. doi: 10.1002/j.1460-2075.1991.tb04913.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ehrenman K., Pedersen-Lane J., West D., Herman R., Maley F., Belfort M. Processing of phage T4 td-encoded RNA is analogous to the eukaryotic group I splicing pathway. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5875–5879. doi: 10.1073/pnas.83.16.5875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Formosa T., Alberts B. M. Purification and characterization of the T4 bacteriophage uvsX protein. J Biol Chem. 1986 May 5;261(13):6107–6118. [PubMed] [Google Scholar]
  22. Fujisawa H., Yonesaki T., Minagawa T. Sequence of the T4 recombination gene, uvsX, and its comparison with that of the recA gene of Escherichia coli. Nucleic Acids Res. 1985 Oct 25;13(20):7473–7481. doi: 10.1093/nar/13.20.7473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Hall D. H., Povinelli C. M., Ehrenman K., Pedersen-Lane J., Chu F., Belfort M. Two domains for splicing in the intron of the phage T4 thymidylate synthase (td) gene established by nondirected mutagenesis. Cell. 1987 Jan 16;48(1):63–71. doi: 10.1016/0092-8674(87)90356-4. [DOI] [PubMed] [Google Scholar]
  24. Hinton D. M. Altered expression of the bacteriophage T4 gene 41 (primase-helicase) in an Escherichia coli rho mutant. J Biol Chem. 1989 Aug 25;264(24):14440–14446. [PubMed] [Google Scholar]
  25. Hinton D. M., Nossal N. G. Bacteriophage T4 DNA replication protein 61. Cloning of the gene and purification of the expressed protein. J Biol Chem. 1985 Oct 15;260(23):12858–12865. [PubMed] [Google Scholar]
  26. Hinton D. M., Nossal N. G. Cloning of the bacteriophage T4 uvsX gene and purification and characterization of the T4 uvsX recombination protein. J Biol Chem. 1986 Apr 25;261(12):5663–5673. [PubMed] [Google Scholar]
  27. Hinton D. M., Silver L. L., Nossal N. G. Bacteriophage T4 DNA replication protein 41. Cloning of the gene and purification of the expressed protein. J Biol Chem. 1985 Oct 15;260(23):12851–12857. [PubMed] [Google Scholar]
  28. Hinton D. M. Transcript analyses of the uvsX-40-41 region of bacteriophage T4. Changes in the RNA as infection proceeds. J Biol Chem. 1989 Aug 25;264(24):14432–14439. [PubMed] [Google Scholar]
  29. Hinton D. M. Transcription from a bacteriophage T4 middle promoter using T4 motA protein and phage-modified RNA polymerase. J Biol Chem. 1991 Sep 25;266(27):18034–18044. [PubMed] [Google Scholar]
  30. Infanger A., Bertrand H. Inversions and recombinations in mitochondrial DNA of the (SG-1) cytoplasmic mutant in two Neurospora species. Curr Genet. 1986;10(8):607–617. doi: 10.1007/BF00418128. [DOI] [PubMed] [Google Scholar]
  31. Jacquier A., Dujon B. An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene. Cell. 1985 Jun;41(2):383–394. doi: 10.1016/s0092-8674(85)80011-8. [DOI] [PubMed] [Google Scholar]
  32. Kaliman A. V., Khasanova M. A., Kryukov V. M., Tanyashin V. I., Bayev A. A. The nucleotide sequence of the region of bacteriophage T4 inh(lip)-hoc genes. Nucleic Acids Res. 1990 Jul 25;18(14):4277–4277. doi: 10.1093/nar/18.14.4277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  34. Lambowitz A. M. Infectious introns. Cell. 1989 Feb 10;56(3):323–326. doi: 10.1016/0092-8674(89)90232-8. [DOI] [PubMed] [Google Scholar]
  35. Macreadie I. G., Scott R. M., Zinn A. R., Butow R. A. Transposition of an intron in yeast mitochondria requires a protein encoded by that intron. Cell. 1985 Jun;41(2):395–402. doi: 10.1016/s0092-8674(85)80012-x. [DOI] [PubMed] [Google Scholar]
  36. Mannella C. A., Lambowitz A. M. Unidirectional gene conversion associated with two insertions in neurospora crassa mitochondrial DNA. Genetics. 1979 Nov;93(3):645–654. doi: 10.1093/genetics/93.3.645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Marshall P., Lemieux C. Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos. Gene. 1991 Aug 15;104(2):241–245. doi: 10.1016/0378-1119(91)90256-b. [DOI] [PubMed] [Google Scholar]
  38. Michel F., Dujon B. Genetic exchanges between bacteriophage T4 and filamentous fungi? Cell. 1986 Aug 1;46(3):323–323. doi: 10.1016/0092-8674(86)90651-3. [DOI] [PubMed] [Google Scholar]
  39. Mota E. M., Collins R. A. Independent evolution of structural and coding regions in a Neurospora mitochondrial intron. Nature. 1988 Apr 14;332(6165):654–656. doi: 10.1038/332654a0. [DOI] [PubMed] [Google Scholar]
  40. Muscarella D. E., Ellison E. L., Ruoff B. M., Vogt V. M. Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum. Mol Cell Biol. 1990 Jul;10(7):3386–3396. doi: 10.1128/mcb.10.7.3386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Muscarella D. E., Vogt V. M. A mobile group I intron in the nuclear rDNA of Physarum polycephalum. Cell. 1989 Feb 10;56(3):443–454. doi: 10.1016/0092-8674(89)90247-x. [DOI] [PubMed] [Google Scholar]
  42. Nakagawa K., Morishima N., Shibata T. A maturase-like subunit of the sequence-specific endonuclease endo.SceI from yeast mitochondria. J Biol Chem. 1991 Jan 25;266(3):1977–1984. [PubMed] [Google Scholar]
  43. Perlman P. S., Butow R. A. Mobile introns and intron-encoded proteins. Science. 1989 Dec 1;246(4934):1106–1109. doi: 10.1126/science.2479980. [DOI] [PubMed] [Google Scholar]
  44. Quirk S. M., 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. doi: 10.1016/0092-8674(89)90248-1. [DOI] [PubMed] [Google Scholar]
  45. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Shibata T., Watabe H., Kaneko T., Iino T., Ando T. On the nucleotide sequence recognized by a eukaryotic site-specific endonuclease, Endo.SceI from yeast. J Biol Chem. 1984 Aug 25;259(16):10499–10506. [PubMed] [Google Scholar]
  47. Shub D. A., Gott J. M., Xu M. Q., Lang B. F., 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. doi: 10.1073/pnas.85.4.1151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. doi: 10.1016/0092-8674(83)90331-8. [DOI] [PubMed] [Google Scholar]
  49. Séraphin B., Simon M., Faye G. The mitochondrial reading frame RF3 is a functional gene in Saccharomyces uvarum. J Biol Chem. 1987 Jul 25;262(21):10146–10153. [PubMed] [Google Scholar]
  50. Tian G. L., Michel F., Macadre C., Slonimski P. P., Lazowska J. Incipient mitochondrial evolution in yeasts. II. The complete sequence of the gene coding for cytochrome b in Saccharomyces douglasii reveals the presence of both new and conserved introns and discloses major differences in the fixation of mutations in evolution. J Mol Biol. 1991 Apr 20;218(4):747–760. doi: 10.1016/0022-2836(91)90263-6. [DOI] [PubMed] [Google Scholar]
  51. Wenzlau J. M., Saldanha R. J., Butow R. A., Perlman P. S. A latent intron-encoded maturase is also an endonuclease needed for intron mobility. Cell. 1989 Feb 10;56(3):421–430. doi: 10.1016/0092-8674(89)90245-6. [DOI] [PubMed] [Google Scholar]
  52. Wernette C. M., Saldahna R., Perlman P. S., Butow R. A. Purification of a site-specific endonuclease, I-Sce II, encoded by intron 4 alpha of the mitochondrial coxI gene of Saccharomyces cerevisiae. J Biol Chem. 1990 Nov 5;265(31):18976–18982. [PubMed] [Google Scholar]
  53. Wilson J. H., Kim J. S., Abelson J. N. Bacteriophage T4 transfer RNA. 3. Clustering of the genes for the T4 transfer RNA's. J Mol Biol. 1972 Nov 28;71(3):547–556. doi: 10.1016/s0022-2836(72)80022-6. [DOI] [PubMed] [Google Scholar]

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