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. 1994 Apr 11;22(7):1167–1171. doi: 10.1093/nar/22.7.1167

Evidence for a group II intron in Escherichia coli inserted into a highly conserved reading frame associated with mobile DNA sequences.

V Knoop 1, A Brennicke 1
PMCID: PMC523638  PMID: 8165129

Abstract

The distribution of group II introns in the living world is an important aspect of the hypothesis which postulates their evolutionary relation to the nuclear spliceosome. As an alternative to the restricted experimental approaches towards their identification we devised a strategy to recognize group II introns in sequence data. By this approach we identified a locus on a plasmid in the bacterium Escherichia coli. Modelling of the derived RNA secondary structure reveals the presence of perfectly conserved domains V and VI as typical features of group II introns. An intron internal reading frame upstream of domain V is homologous to group II intron encoded maturases. A reading frame downstream of the predicted 3'-splice site is highly similar to a small polypeptide encoded in the central part of the Agrobacterium tumefaciens T-DNA. With the TBLASTN algorithm a set of plasmid-borne insertion sequences in Agrobacteria and Rhizobia and surprisingly also in a Yersinia pseudotuberculosis strain was identified which contain this highly conserved reading frame.

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Selected References

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

  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. Bonnard G., Vincent F., Otten L. Sequence and distribution of IS866, a novel T region-associated insertion sequence from Agrobacterium tumefaciens. Plasmid. 1989 Jul;22(1):70–81. doi: 10.1016/0147-619x(89)90037-1. [DOI] [PubMed] [Google Scholar]
  3. Bölin I., Wolf-Watz H. The plasmid-encoded Yop2b protein of Yersinia pseudotuberculosis is a virulence determinant regulated by calcium and temperature at the level of transcription. Mol Microbiol. 1988 Mar;2(2):237–245. doi: 10.1111/j.1365-2958.1988.tb00025.x. [DOI] [PubMed] [Google Scholar]
  4. Chandler M., Fayet O. Translational frameshifting in the control of transposition in bacteria. Mol Microbiol. 1993 Feb;7(4):497–503. doi: 10.1111/j.1365-2958.1993.tb01140.x. [DOI] [PubMed] [Google Scholar]
  5. Chapdelaine Y., Bonen L. The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces. Cell. 1991 May 3;65(3):465–472. doi: 10.1016/0092-8674(91)90464-a. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Endoh H., Hirayama T., Aoyama T., Oka A. Characterization of the virA gene of the agropine-type plasmid pRiA4 of Agrobacterium rhizogenes. FEBS Lett. 1990 Oct 1;271(1-2):28–32. doi: 10.1016/0014-5793(90)80364-o. [DOI] [PubMed] [Google Scholar]
  8. Ferat J. L., Michel F. Group II self-splicing introns in bacteria. Nature. 1993 Jul 22;364(6435):358–361. doi: 10.1038/364358a0. [DOI] [PubMed] [Google Scholar]
  9. Fox T. D., Leaver C. J. The Zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons. Cell. 1981 Nov;26(3 Pt 1):315–323. doi: 10.1016/0092-8674(81)90200-2. [DOI] [PubMed] [Google Scholar]
  10. Kanemoto R. H., Powell A. T., Akiyoshi D. E., Regier D. A., Kerstetter R. A., Nester E. W., Hawes M. C., Gordon M. P. Nucleotide sequence and analysis of the plant-inducible locus pinF from Agrobacterium tumefaciens. J Bacteriol. 1989 May;171(5):2506–2512. doi: 10.1128/jb.171.5.2506-2512.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kemmerer E. C., Wu R. The Pisum sativum mitochondrial gene encoding cytochrome oxidase subunit I has an unusual transcription pattern. Gene. 1990 May 14;89(2):157–162. doi: 10.1016/0378-1119(90)90001-8. [DOI] [PubMed] [Google Scholar]
  12. Knoop V., Schuster W., Wissinger B., Brennicke A. Trans splicing integrates an exon of 22 nucleotides into the nad5 mRNA in higher plant mitochondria. EMBO J. 1991 Nov;10(11):3483–3493. doi: 10.1002/j.1460-2075.1991.tb04912.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lamattina L., Grienenberger J. M. RNA editing of the transcript coding for subunit 4 of NADH dehydrogenase in wheat mitochondria: uneven distribution of the editing sites among the four exons. Nucleic Acids Res. 1991 Jun 25;19(12):3275–3282. doi: 10.1093/nar/19.12.3275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Machida Y., Sakurai M., Kiyokawa S., Ubasawa A., Suzuki Y., Ikeda J. E. Nucleotide sequence of the insertion sequence found in the T-DNA region of mutant Ti plasmid pTiA66 and distribution of its homologues in octopine Ti plasmid. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7495–7499. doi: 10.1073/pnas.81.23.7495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns--a review. Gene. 1989 Oct 15;82(1):5–30. doi: 10.1016/0378-1119(89)90026-7. [DOI] [PubMed] [Google Scholar]
  16. Michiels T., Cornelis G. Nucleotide sequence and transcription analysis of yop51 from Yersinia enterocolitica W22703. Microb Pathog. 1988 Dec;5(6):449–459. doi: 10.1016/0882-4010(88)90006-x. [DOI] [PubMed] [Google Scholar]
  17. Mohr G., Perlman P. S., Lambowitz A. M. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res. 1993 Nov 11;21(22):4991–4997. doi: 10.1093/nar/21.22.4991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Oda K., Yamato K., Ohta E., Nakamura Y., Takemura M., Nozato N., Akashi K., Kanegae T., Ogura Y., Kohchi T. Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J Mol Biol. 1992 Jan 5;223(1):1–7. doi: 10.1016/0022-2836(92)90708-r. [DOI] [PubMed] [Google Scholar]
  19. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sharp P. A. "Five easy pieces". Science. 1991 Nov 1;254(5032):663–663. doi: 10.1126/science.1948046. [DOI] [PubMed] [Google Scholar]
  21. Slightom J. L., Durand-Tardif M., Jouanin L., Tepfer D. Nucleotide sequence analysis of TL-DNA of Agrobacterium rhizogenes agropine type plasmid. Identification of open reading frames. J Biol Chem. 1986 Jan 5;261(1):108–121. [PubMed] [Google Scholar]
  22. Wabiko H. Sequence analysis of an insertion element, IS1131, isolated from the nopaline-type Ti plasmid of Agrobacterium tumefaciens. Gene. 1992 May 15;114(2):229–233. doi: 10.1016/0378-1119(92)90579-e. [DOI] [PubMed] [Google Scholar]
  23. Wissinger B., Schuster W., Brennicke A. Trans splicing in Oenothera mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences. Cell. 1991 May 3;65(3):473–482. doi: 10.1016/0092-8674(91)90465-b. [DOI] [PubMed] [Google Scholar]
  24. de Haan L. A., Willshaw G. A., van der Zeijst B. A., Gaastra W. The nucleotide sequence of a regulatory gene present on a plasmid in an enterotoxigenic Escherichia coli strain of serotype O167:H5. FEMS Microbiol Lett. 1991 Oct 15;67(3):341–346. doi: 10.1111/j.1574-6968.1991.tb04487.x. [DOI] [PubMed] [Google Scholar]

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