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. 1991 Dec 11;19(23):6491–6497. doi: 10.1093/nar/19.23.6491

A mixed group II/group III twintron in the Euglena gracilis chloroplast ribosomal protein S3 gene: evidence for intron insertion during gene evolution.

D W Copertino 1, D A Christopher 1, R B Hallick 1
PMCID: PMC329205  PMID: 1721702

Abstract

The splicing of a 409 nucleotide intron from the Euglena gracilis chloroplast ribosomal protein S3 gene (rps3) was examined by cDNA cloning and sequencing, and northern hybridization. Based on the characterization of a partially spliced pre-mRNA, the intron was characterized as a 'mixed' twintron, composed of a 311 nucleotide group II intron internal to a 98 nucleotide group III intron. Twintron excision is via a 2-step sequential splicing pathway, with removal of the internal group II intron preceding excision of the external group III intron. Based on secondary structural analysis of the twintron, we propose that group III introns may represent highly degenerate versions of group II introns. The existence of twintrons is interpreted as evidence that group II introns were inserted during the evolution of Euglena chloroplast genes from a common ancestor with eubacteria, archaebacteria, cyanobacteria, and other chloroplasts.

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Selected References

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  1. Augustin S., Müller M. W., Schweyen R. J. Reverse self-splicing of group II intron RNAs in vitro. Nature. 1990 Jan 25;343(6256):383–386. doi: 10.1038/343383a0. [DOI] [PubMed] [Google Scholar]
  2. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2247–2249. doi: 10.1093/nar/19.suppl.2247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2241–2245. doi: 10.1093/nar/19.suppl.2241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Barker W. C., George D. G., Hunt L. T., Garavelli J. S. The PIR protein sequence database. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2231–2236. doi: 10.1093/nar/19.suppl.2231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Boynton J. E., Gillham N. W., Harris E. H., Hosler J. P., Johnson A. M., Jones A. R., Randolph-Anderson B. L., Robertson D., Klein T. M., Shark K. B. Chloroplast transformation in Chlamydomonas with high velocity microprojectiles. Science. 1988 Jun 10;240(4858):1534–1538. doi: 10.1126/science.2897716. [DOI] [PubMed] [Google Scholar]
  6. Casanova J. L., Pannetier C., Jaulin C., Kourilsky P. Optimal conditions for directly sequencing double-stranded PCR products with sequenase. Nucleic Acids Res. 1990 Jul 11;18(13):4028–4028. doi: 10.1093/nar/18.13.4028. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cavalier-Smith T. Intron phylogeny: a new hypothesis. Trends Genet. 1991 May;7(5):145–148. [PubMed] [Google Scholar]
  8. Christopher D. A., Cushman J. C., Price C. A., Hallick R. B. Organization of ribosomal protein genes rpl23, rpl2, rps19, rpl22 and rps3 on the Euglena gracilis chloroplast genome. Curr Genet. 1988 Sep;14(3):275–285. doi: 10.1007/BF00376748. [DOI] [PubMed] [Google Scholar]
  9. Christopher D. A., Hallick R. B. Complex RNA maturation pathway for a chloroplast ribosomal protein operon with an internal tRNA cistron. Plant Cell. 1990 Jul;2(7):659–671. doi: 10.1105/tpc.2.7.659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Christopher D. A., Hallick R. B. Euglena gracilis chloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III. Nucleic Acids Res. 1989 Oct 11;17(19):7591–7608. doi: 10.1093/nar/17.19.7591. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Copertino D. W., Favreau M. R., Hallick R. B. Transverse gradient gel electrophoresis: a gel system for resolving complex mixtures of lariat and linear RNA molecules. Nucleic Acids Res. 1990 Dec 25;18(24):7451–7452. doi: 10.1093/nar/18.24.7451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Copertino D. W., Hallick R. B. Group II twintron: an intron within an intron in a chloroplast cytochrome b-559 gene. EMBO J. 1991 Feb;10(2):433–442. doi: 10.1002/j.1460-2075.1991.tb07965.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Darnell J. E., Doolittle W. F. Speculations on the early course of evolution. Proc Natl Acad Sci U S A. 1986 Mar;83(5):1271–1275. doi: 10.1073/pnas.83.5.1271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dorit R. L., Schoenbach L., Gilbert W. How big is the universe of exons? Science. 1990 Dec 7;250(4986):1377–1382. doi: 10.1126/science.2255907. [DOI] [PubMed] [Google Scholar]
  15. Douglas S. E., Turner S. Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor. J Mol Evol. 1991 Sep;33(3):267–273. doi: 10.1007/BF02100678. [DOI] [PubMed] [Google Scholar]
  16. Fukuzawa H., Kohchi T., Sano T., Shirai H., Umesono K., Inokuchi H., Ozeki H., Ohyama K. Structure and organization of Marchantia polymorpha chloroplast genome. III. Gene organization of the large single copy region from rbcL to trnI(CAU). J Mol Biol. 1988 Sep 20;203(2):333–351. doi: 10.1016/0022-2836(88)90003-4. [DOI] [PubMed] [Google Scholar]
  17. Gingrich J. C., Hallick R. B. The Euglena gracilis chloroplast ribulose-1,5-bisphosphate carboxylase gene. I. Complete DNA sequence and analysis of the nine intervening sequences. J Biol Chem. 1985 Dec 25;260(30):16156–16161. [PubMed] [Google Scholar]
  18. Guthrie C. Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science. 1991 Jul 12;253(5016):157–163. doi: 10.1126/science.1853200. [DOI] [PubMed] [Google Scholar]
  19. Higgins D. G., Sharp P. M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988 Dec 15;73(1):237–244. doi: 10.1016/0378-1119(88)90330-7. [DOI] [PubMed] [Google Scholar]
  20. Jacquier A., Michel F. Multiple exon-binding sites in class II self-splicing introns. Cell. 1987 Jul 3;50(1):17–29. doi: 10.1016/0092-8674(87)90658-1. [DOI] [PubMed] [Google Scholar]
  21. Jarrell K. A., Dietrich R. C., Perlman P. S. Group II intron domain 5 facilitates a trans-splicing reaction. Mol Cell Biol. 1988 Jun;8(6):2361–2366. doi: 10.1128/mcb.8.6.2361. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kao J. S., Wu M., Chiang Y. M. Cloning and characterization of chloroplast ribosomal protein-encoding genes, rpl16 and rps3, of the marine macro-algae, Gracilaria tenuistipitata. Gene. 1990 Jun 15;90(2):221–226. doi: 10.1016/0378-1119(90)90183-r. [DOI] [PubMed] [Google Scholar]
  23. Kuhsel M. G., Strickland R., Palmer J. D. An ancient group I intron shared by eubacteria and chloroplasts. Science. 1990 Dec 14;250(4987):1570–1573. doi: 10.1126/science.2125748. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  26. McLaughlin W. E., Larrinua I. M. The sequence of the maize plastid encoded rps3 locus. Nucleic Acids Res. 1987 Jun 11;15(11):4689–4689. doi: 10.1093/nar/15.11.4689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Michalowski C. B., Pfanzagl B., Löffelhardt W., Bohnert H. J. The cyanelle S10 spc ribosomal protein gene operon from Cyanophora paradoxa. Mol Gen Genet. 1990 Nov;224(2):222–231. doi: 10.1007/BF00271555. [DOI] [PubMed] [Google Scholar]
  28. Michel F., Dujon B. Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members. EMBO J. 1983;2(1):33–38. doi: 10.1002/j.1460-2075.1983.tb01376.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Michel F., Jacquier A., Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 1982 Oct;64(10):867–881. doi: 10.1016/s0300-9084(82)80349-0. [DOI] [PubMed] [Google Scholar]
  30. Michel F., Lang B. F. Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses. Nature. 1985 Aug 15;316(6029):641–643. doi: 10.1038/316641a0. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. Morden C. W., Golden S. S. Sequence analysis and phylogenetic reconstruction of the genes encoding the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase from the chlorophyll b-containing prokaryote Prochlorothrix hollandica. J Mol Evol. 1991 May;32(5):379–395. doi: 10.1007/BF02101278. [DOI] [PubMed] [Google Scholar]
  33. Ohkubo S., Muto A., Kawauchi Y., Yamao F., Osawa S. The ribosomal protein gene cluster of Mycoplasma capricolum. Mol Gen Genet. 1987 Dec;210(2):314–322. doi: 10.1007/BF00325700. [DOI] [PubMed] [Google Scholar]
  34. Peebles C. L., Perlman P. S., Mecklenburg K. L., Petrillo M. L., Tabor J. H., Jarrell K. A., Cheng H. L. A self-splicing RNA excises an intron lariat. Cell. 1986 Jan 31;44(2):213–223. doi: 10.1016/0092-8674(86)90755-5. [DOI] [PubMed] [Google Scholar]
  35. Rogers J. H. How were introns inserted into nuclear genes? Trends Genet. 1989 Jul;5(7):213–216. doi: 10.1016/0168-9525(89)90084-x. [DOI] [PubMed] [Google Scholar]
  36. Sugiura M. The chloroplast chromosomes in land plants. Annu Rev Cell Biol. 1989;5:51–70. doi: 10.1146/annurev.cb.05.110189.000411. [DOI] [PubMed] [Google Scholar]
  37. Tanaka M., Wakasugi T., Sugita M., Shinozaki K., Sugiura M. Genes for the eight ribosomal proteins are clustered on the chloroplast genome of tobacco (Nicotiana tabacum): similarity to the S10 and spc operons of Escherichia coli. Proc Natl Acad Sci U S A. 1986 Aug;83(16):6030–6034. doi: 10.1073/pnas.83.16.6030. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Wessler S. R., Baran G., Varagona M. The maize transposable element Ds is spliced from RNA. Science. 1987 Aug 21;237(4817):916–918. doi: 10.1126/science.3039661. [DOI] [PubMed] [Google Scholar]
  39. Xu M. Q., Kathe S. D., Goodrich-Blair H., Nierzwicki-Bauer S. A., Shub D. A. Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science. 1990 Dec 14;250(4987):1566–1570. doi: 10.1126/science.2125747. [DOI] [PubMed] [Google Scholar]
  40. Zhou D. X., Quigley F., Massenet O., Mache R. Cotranscription of the S10- and spc-like operons in spinach chloroplasts and identification of three of their gene products. Mol Gen Genet. 1989 Apr;216(2-3):439–445. doi: 10.1007/BF00334388. [DOI] [PubMed] [Google Scholar]
  41. Zurawski G., Zurawski S. M. Structure of the Escherichia coli S10 ribosomal protein operon. Nucleic Acids Res. 1985 Jun 25;13(12):4521–4526. doi: 10.1093/nar/13.12.4521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. van der Veen R., Arnberg A. C., van der Horst G., Bonen L., Tabak H. F., Grivell L. A. Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell. 1986 Jan 31;44(2):225–234. doi: 10.1016/0092-8674(86)90756-7. [DOI] [PubMed] [Google Scholar]

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