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. 1994 Sep 11;22(18):3715–3721. doi: 10.1093/nar/22.18.3715

The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames.

H Goodrich-Blair 1, D A Shub 1
PMCID: PMC308352  PMID: 7937082

Abstract

A previous report described the discovery of a group I, self-splicing intron in the DNA polymerase gene of the Bacillus subtilis bacteriophage SPO1 (1). In this study, the DNA polymerase genes of three close relatives of SPO1: SP82, 2C and phi e, were also found to be interrupted by an intron. All of these introns have group I secondary structures that are extremely similar to one another in primary sequence. Each is interrupted by an open reading frame (ORF) that, unlike the intron core or exon sequences, are highly diverged. Unlike the relatives of Escherichia coli bacteriophage T4, most of which do not have introns (2), this intron seems to be common among the relatives of SPO1.

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Selected References

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  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Braithwaite D. K., Ito J. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 1993 Feb 25;21(4):787–802. doi: 10.1093/nar/21.4.787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cech T. R. Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review. Gene. 1988 Dec 20;73(2):259–271. doi: 10.1016/0378-1119(88)90492-1. [DOI] [PubMed] [Google Scholar]
  4. Cech T. R. Self-splicing of group I introns. Annu Rev Biochem. 1990;59:543–568. doi: 10.1146/annurev.bi.59.070190.002551. [DOI] [PubMed] [Google Scholar]
  5. Cummings D. J., Michel F., McNally K. L. DNA sequence analysis of the 24.5 kilobase pair cytochrome oxidase subunit I mitochondrial gene from Podospora anserina: a gene with sixteen introns. Curr Genet. 1989 Dec;16(5-6):381–406. doi: 10.1007/BF00340719. [DOI] [PubMed] [Google Scholar]
  6. GREEN D. M. INFECTIVITY OF DNA ISOLATED FROM BACILLUS SUBTILIS BACTERIOPHAGE, SP82. J Mol Biol. 1964 Dec;10:438–451. doi: 10.1016/s0022-2836(64)80065-6. [DOI] [PubMed] [Google Scholar]
  7. Gage L. P., Geiduschek E. P. RNA synthesis during bacteriophage SPO1 development: six classes of SPO1 RNA. J Mol Biol. 1971 Apr 28;57(2):279–297. doi: 10.1016/0022-2836(71)90346-9. [DOI] [PubMed] [Google Scholar]
  8. Garriga G., Lambowitz A. M. RNA splicing in neurospora mitochondria: self-splicing of a mitochondrial intron in vitro. Cell. 1984 Dec;39(3 Pt 2):631–641. doi: 10.1016/0092-8674(84)90470-7. [DOI] [PubMed] [Google Scholar]
  9. Goodrich-Blair H., Scarlato V., Gott J. M., Xu M. Q., Shub D. A. A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1. Cell. 1990 Oct 19;63(2):417–424. doi: 10.1016/0092-8674(90)90174-d. [DOI] [PubMed] [Google Scholar]
  10. Gott J. M., Shub D. A., Belfort M. Multiple self-splicing introns in bacteriophage T4: evidence from autocatalytic GTP labeling of RNA in vitro. Cell. 1986 Oct 10;47(1):81–87. doi: 10.1016/0092-8674(86)90368-5. [DOI] [PubMed] [Google Scholar]
  11. Lambowitz A. M., Belfort M. Introns as mobile genetic elements. Annu Rev Biochem. 1993;62:587–622. doi: 10.1146/annurev.bi.62.070193.003103. [DOI] [PubMed] [Google Scholar]
  12. Lawrie J. M., Downard J. S., Whiteley H. R. Bacillus subtilis bacteriophages SP82, SPO1, and phie: a comparison of DNAs and of peptides synthesized during infection. J Virol. 1978 Sep;27(3):725–737. doi: 10.1128/jvi.27.3.725-737.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 1990 Dec 5;216(3):585–610. doi: 10.1016/0022-2836(90)90386-Z. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. 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]
  16. ROMIG W. R., BRODETSKY A. M. Isolation and preliminary characterization of bacteriophages for Bacillus subtilis. J Bacteriol. 1961 Jul;82:135–141. doi: 10.1128/jb.82.1.135-141.1961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Roscoe D. H., Tucker R. G. The biosynthesis of 5-hydroxymethyldeoxyuridylic acid in bacteriophage-infected Bacillus subtilis. Virology. 1966 May;29(1):157–166. doi: 10.1016/0042-6822(66)90205-4. [DOI] [PubMed] [Google Scholar]
  18. Scarlato V., Gargano S. The DNA polymerase-encoding gene of Bacillus subtilis bacteriophage SPO1. Gene. 1992 Sep 1;118(1):109–113. doi: 10.1016/0378-1119(92)90256-o. [DOI] [PubMed] [Google Scholar]
  19. Sharma M., Ellis R. L., Hinton D. M. Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage. Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6658–6662. doi: 10.1073/pnas.89.14.6658. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Shub D. A., Goodrich-Blair H. Protein introns: a new home for endonucleases. Cell. 1992 Oct 16;71(2):183–186. doi: 10.1016/0092-8674(92)90345-d. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Sjöberg B. M., Hahne S., Mathews C. Z., Mathews C. K., Rand K. N., Gait M. J. The bacteriophage T4 gene for the small subunit of ribonucleotide reductase contains an intron. EMBO J. 1986 Aug;5(8):2031–2036. doi: 10.1002/j.1460-2075.1986.tb04460.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Trinkl H., Wolf K. The mosaic cox1 gene in the mitochondrial genome of Schizosaccharomyces pombe: minimal structural requirements and evolution of group I introns. Gene. 1986;45(3):289–297. doi: 10.1016/0378-1119(86)90027-2. [DOI] [PubMed] [Google Scholar]
  24. Truffaut N., Revet B., Soulie M. O. Etude comparative des DNA de phages 2C, SP8*, SP82, phi e, SP01 et SP50. Eur J Biochem. 1970 Aug;15(2):391–400. doi: 10.1111/j.1432-1033.1970.tb01020.x. [DOI] [PubMed] [Google Scholar]
  25. Weise F., Chai S., Lüder G., Alonso J. C. Nucleotide sequence and complementation studies of the gene 35 region of the Bacillus subtilis bacteriophage SPP1. Virology. 1994 Aug 1;202(2):1046–1049. doi: 10.1006/viro.1994.1436. [DOI] [PubMed] [Google Scholar]
  26. Young P., Ohman M., Xu M. Q., Shub D. A., Sjöberg B. M. Intron-containing T4 bacteriophage gene sunY encodes an anaerobic ribonucleotide reductase. J Biol Chem. 1994 Aug 12;269(32):20229–20232. [PubMed] [Google Scholar]
  27. Zuker M., Jaeger J. A., Turner D. H. A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res. 1991 May 25;19(10):2707–2714. doi: 10.1093/nar/19.10.2707. [DOI] [PMC free article] [PubMed] [Google Scholar]

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