The catalytic group-I introns of the psbA gene of Chlamydomonas reinhardtii: Core structures, ORFs and evolutionary implications

Current Genetics

Volumn 36, Issue 1-2, 1999, Pages 69-78

  Holloway, Stephen P ^a,b   Deshpande, Nita N ^a   Herrin, David L ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

Chlamydomonas; Chloroplast; Evolution; Group I introns; psbA gene; Self splicing

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE T4; CHLAMYDOMONAS; CHLAMYDOMONAS REINHARDTII; CHLOROPLAST; CONTROLLED STUDY; EVOLUTION; GENE SEQUENCE; GENE STRUCTURE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE;

ALGAL PROTEINS; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CHLAMYDOMONAS REINHARDTII; CHLOROPLASTS; EVOLUTION, MOLECULAR; GENOME; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; PHOTOSYSTEM II PROTEIN COMPLEX; RNA SPLICING; RNA, CATALYTIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 0032831814     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002940050474     Document Type: Article

References (51)

1. Bao Y, Herrin DL (1993) Nucleotide sequence and secondary structure of the chloroplast group-I intron Cr.psbA-2: novel features of this self-splicing ribozyme. Nucleic Acids Res 21:1667
2. Belfort M, Roberts R (1997) Homing endonucleases: keeping the house in order. Nucleic Acids Res 25:3379-3388
3. Berry-Lowe SL, Johnson CH, Schmidt GW (1992) Nucleotide sequence of the psbB gene of Chlamydomonas reinhardtii chloroplasts. Plant Physiol 98:1541-1543
4. Buchheim MA, Turmel M, Zimmer EA, Chapman RL (1990) Phylogeny of Chlamvdomonas (Chlorophyta) based on cladistic analysis of nuclear 18S rRNA sequence data. J Phycol 26:689-699
5. Burke JM (1988) Molecular genetics of group-I introns: RNA structures and protein factors required for splicing - a review. Gene 73:273-294
6. Burke JM, Belfort M, Cech TR, Davies RW, Schweyen RJ, Shub DA, Szostak JW, Tabak HF (1987) Structural conventions for group-I introns. Nucleic Acids Res 15:7217-7221
7. Cech TR (1988) Conserved sequences and structures of group-I introns: building an active site for RNA catalysis - a review, Gene 73:259-271
8. Cech TR (1990) Self-splicing of group-I introns. Annu Rev Biochem 59:543-568
9. Côté MJ, Turmel M (1995) In vitro self-splicing reactions of chloroplast and mitochondrial group-I introns in Chlamydomonas eugametos and Chlamydomonas moewusii. Curr Genet 27:177-183
10. Deshpande NN, Bao Y, Herrin DL (1997) Evidence for light/redox-regulated splicing of psbA pre-RNAs in Chlamydomonas reinhardtii. RNA 3:37-48
11. Dujon B (1989) Group-I introns and mobile genetic elements: facts and mechanistic speculations - a review. Gene 82:91-114
12. Erickson JM, Rahire M, Rochaix JD (1984) Chlamydomonas reinhardtii gene for the 32 000 mol. wt. protein of photosystem II contains four large introns and is located entirely within the chloroplast inverted repeat. EMBO J 3:2753-2762
13. Ettl H (1976) Die Gattung Chlamydomonas Ehrenberg. Nova Hedwigia 49:1-1122
14. Gampel A, Nishikimi M, Tzagoloff A (1989) CBP2 protein promotes in vitro excision of a yeast mitochondrial group-I intron. Mol Cell Biol 9:5424-5433
15. Goodrich-Blair H, Shub DA (1994) The DNA polymerases of several HMU-bacteriophages have similar group-I introns with highly divergent open reading frames. Nucleic Acids Res 22:3715-3721
16. Goodrich-Blair H, Scarlato V, Gott JM, Xu M-Q, Shub DA (1990) A self-splicing group-I intron in the DNA polymerase gene of the Bacillus subtilis bacteriophage SP01. Cell 63:417-424
17. Gorbalenya AE (1994) Self-splicing group-I and group-II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci 3:1117-1120
18. Grube M, Gargas A, DePriest PT (1996) A small insertion in the SSU rDNA of the lichen fungus Arthonia lapidicola is a degenerate group-I intron. Curr Genet 29:582-586
19. Herrin DL, Michaels A (1985) The chloroplast 32 kDa protein is synthesized on thylakoid-bound ribosomes in Chlamydomonas reinhardtii. FEBS Lett 184:90-95
20. Herrin DL, Bao Y, Thompson AJ, Chen YF (1991) Self-splicing of the Chlamydomonas chloroplast psbA introns. Plant Cell 3:1095-1107
21. Jaeger L, Westhof E, Michel F (1991) Function of P11, a tertiary base pairing in self-splicing introns of subgroup IA. J Mol Biol 221:1153-1164
22. Jaeger L, Michel F, Westhof E (1994) Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J Mol Biol 236:1271-1276
23. Jaeger L, Michel F, Westhof E (1996) The structure of group-I ribozymes. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology, vol 10. Springer-Verlag, Berlin, pp 33-52
24. Johnson CH, Schmidt GW (1993) The psbB gene cluster of the Chlamydomonas reinhardtii chloroplast: sequence and transcriptional analyses of psbN and psbH. Plant Mol Biol 22:645-658
25. Kumar S, Koichiro T, Nei M (1993) MEGA: molecular evolutionary genetics analysis, v1.0. Pennsylvania State University, University Park, Pennsylvania, USA
26. Lambowitz AM, Belfort M (1993) Introns as mobile genetic elements. Annu Rev Biochem 62:587-622
27. Lambowitz AM, Perlman PS (1990) Involvement of aminoacyltRNA synthetases and other proteins in group-I and group-II intron splicing. Trends Biochem Sci 15:440-444
28. Loizos N, Tillier ERM, Belfort M (1994) Evolution of mobile group-I introns: recognition of intron sequences by an intronencoded endonuclease. Proc Natl Acad Sci USA 91:11983-11987
29. Lonergan KM, Gray MW (1994) The ribosomal RNA gene region in Acanthamoeba castellani mitochondrial DNA. A case of evolutionary transfer of introns between mitochondria and plastids. J Mol Biol 239:476-499
30. Michel F, Westhof E (1990) Modelling of the three-dimensional architecture of group-I catalytic introns based on comparative sequence analysis. J Mol Biol 216:585-610
31. Mueller JE, Bryk M, Loizos N, Belfort M (1993) Homing endonucleases. In: Nucleases, 2nd edn. Cold Spring Harbor Laboratory Press, New York
32. Newman SM, Harris EH, Johnson AM, Boynton JE, Gillham NW (1992) Non-random distribution of chloroplast recombination events in Chlamydomonas reinhardtii: evidence for a hotspot and an adjacent cold region. Genetics 132:413-429
33. Palmer JD, Boynton JE, Gillham NW, Harris EH (1985) Evolution and recombination of the large inverted repeat in Chlamydomonas chloroplast DNA. In: Molecular biology of the photosynthetic apparatus. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
34. Paquin B, O'Kelly CJ, Lang BF (1995) Intron-encoded open reading frame of the GIY-YIG subclass in a plastid gene. Curr Genet 28:97-99
35. Roberts K (1974) Crystalline glycoprotein cell walls of algae: their structure, composition and assembly. Phil Trans R Soc Lond B Biol Sci 268:129-146
36. Rochaix JD, Rahire M, Michel F (1985) The chloroplast ribosomal intron of Chlamydomonas reinhardtii codes for a polypeptide related to mitochondrial maturases. Nucleic Acids Res 13:975-984
37. Saldanha R, Mohr G, Belfort M, Lambowitz AM (1993) Group-I and group-II introns. FASEB J 7:15-24
38. Schlösser UG (1984) Species-specific sporangium autolysin (cell-wall-dissolving enzymes) in the genus Chlamydomonas. In: Irvine DEG, John D (eds) The systematics of green algae. Academic Press, London, pp 409-418
39. Schneider M, Rochaix JD (1986) Sequence organization of the chloroplast ribosomal spacer of Chlamydomonas reinhardtii: uninterrupted tRNA-Ala and tRNA-Ile genes and extensive secondary structure. Plant Mol Biol 6:265-270
40. Schneider M, Darlix JL, Erickson J, Rochaix JD (1985) Sequence organization of repetitive elements in the flanking regions of the chloroplast ribosomal unit of Chlamydomonas reinhardtii. Nucleic Acids Res 13:8531-8541
41. Sharma M, Ellis RL, Hinton DM (1992) 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 Sei USA 89:6658-6662
42. Shub DA, Gott JM, Xu MQ, Lang BF, Michel F, Tomaschewski J, Pedersen-Lane J and Belfort M (1988) Structural conservation among three homologous introns of bacteriophage T4 and the group-I introns of eucaryotes. Proc Natl Acad Sci USA 85:1151-1155
43. Shub DA, Goodrich-Blair H and Eddy SR (1994) Amino-acid sequence motif of group-I intron endonucleases is conserved in open reading frames of group-II introns. Trends Biochem Sci 19:402-404
44. Sturm NR, Kuras R, Büschlen S, Sakamoto W, Kindle KL, Stern DB, Wollman FA (1994) The petD gene is transcribed by functionally redundant promoters in Chlamydomonas reinhardtii chloroplasts. Mol Cell Biol 14:6171-6179
45. Turmel M, Boulanger J, Lemieux C (1989) Two group-I introns with long internal open reading frames in the chloroplast psbA gene of Chlamydomonas moewusii. Nucleic Acids Res 10:3875-3887
46. Turmel M, Boudreau E, Boulanger J, Mercier JP, Otis C, Lemieux C (1991 a) Chloroplast DNA evolution and phylogenetic relationships in Chlamydomonas. In: The unity of evolutionary biology. Dioscorides Press, Oregon, USA, pp 816-827
47. Turmel M, Boulanger J, Schnare MN, Gray MW, Lemieux C (1991 b) Six group-I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos. J Mol Biol 218:293-311
48. Turmel M, Côté V, Otis C, Mercier JP, Gray MW, Lonergan KM, Lemieux C (1995) Evolutionary transfer of ORF-containing group-I introns between different subcellular compartments (chloroplast and mitochondria). Mol Biol Evol 12:533-45
49. Vaughn JC, Mason MT, Sper-Whitis GL, Kuhlman P, Palmer JD (1995) Fungal origin by horizontal transfer of a plant mitochondrial group-I intron in the chimeric coxl gene of Peperomia. J Mol Evol 41:563-572
50. Wallweber GJ, Mohr S, Rennard R, Caprara MG, Lambowitz AM (1997) Characterization of Neurospora mitochondrial group-I introns reveals different cyt-18 dependent and independent splicing strategies and an alternative 3' splice site for an intron ORF. RNA 3:114-131
51. Weeks KM, Cech TR (1995) Protein facilitation of group-I intron splicing by assembly of the catalytic core and the 5′ splice site domain. Cell 82:221-230