Chloroplast RNA Splicing

The Chlamydomonas Sourcebook 3-Vol set

Volumn 2, Issue , 2009, Pages 915-935

  Goldschmidt Clermont, Michel ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77957318465     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-370873-1.00034-4     Document Type: Chapter

References (86)

1. Asacra Y., Barkan A. Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns. Plant Physiol. 2006, 142:1656-1663.
2. Auchincloss A.H., Zerges W., Perron K., Girard-Bascou J., Rochaix J.D. Characterization of Tbc2, a nucleus-encoded factor specifically required for translation of the chloroplast psbC mRNA in Chlamydomonas reinhardtii. J. Cell Biol. 2002, 157:953-962.
3. Balczun C., Bunse A., Hahn D., Bennoun P., Nickelsen J., Kück U. Two adjacent nuclear genes are required for functional complementation of a chloroplast trans-splicing mutant from Chlamydomonas reinhardtii. Plant J. 2005, 43:636-648.
4. Balczun C., Bunse A., Schwarz C., Piotrowski M., Kück U. Chloroplast heat shock protein Cpn60 from Chlamydomonas reinhardtii exhibits a novel function as a group II intron-specific RNA-binding protein. FEBS Lett. 2006, 580:4527-4532.
5. Barkan A., Goldschmidt-Clermont M. Participation of nuclear genes in chloroplast gene expression. Biochimie 2000, 82:559-572.
6. Barkan A., Klipcan L., Ostersetzer O., Kawamura T., Asakura Y., Watkins K.P. The CRM domain: An RNA binding module derived from an ancient ribosome-associated protein. RNA 2007, 13:55-64.
7. Bonen L., Vogel J. The ins and outs of group II introns. Trends Genet. 2001, 17:322-331.
8. Boynton J.E., Harris E.H., Burkhart B.D., Lamerson P.M., Gillham N.W. Transmission of mitochondrial and chloroplast genomes in crosses of Chlamydomonas. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:2391-2395.
9. Bruick R.K., Mayfield S.P. Light-activated translation of chloroplast mRNAs. Trends Plant Sci. 1999, 4:190-195.
10. Bunse A.A., Nickelsen J., Kück U. Intron-specific RNA binding proteins in the chloroplast of the green alga Chlamydomonas reinhardtii. Biochim. Biophys. Acta. 2001, 1519:46-54.
11. Bussieres J., Lemieux C., Lee R.W., Turmel M. Optional elements in the chloroplast DNAs of Chlamydomonas eugametos and C. moewusii: Unidirectional gene conversion and co-conversion of adjacent markers in high-viability crossses. Curr. Genet. 1996, 30:356-365.
12. Chevalier B., Sussman D., Otis C., Noel A.J., Turmel M., Lemieux C., Stephens K., Monnat R.J., Stoddard B.L. Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry 2004, 43:14015-14026.
13. Choquet Y., Goldschmidt-Clermont M., Girard-Bascou J., Kück U., Bennoun P., Rochaix J.D. Mutant phenotypes support a trans-splicing mechanism for the expression of the tripartite psaA gene in the C. reinhardtii chloroplast. Cell 1988, 52:903-913.
14. Cote M.J., Turmel M. In vitro self-splicing reactions of chloroplast and mitochondrial group-I introns in Chlamydomonas eugametos and Chlamydomonas moewusii. Curr. Genet. 1995, 27:177-183.
15. Deshpande N.N., Hollingsworth M., Herrin D.L. The atpF group-II intron-containing gene from spinach chloroplasts is not spliced in transgenic Chlamydomonas chloroplasts. Curr. Genet. 1995, 28:122-127.
16. Deshpande N.N., Bao Y., Herrin D.L. Evidence for light/redox-regulated splicing of psbA pre-RNAs in Chlamydomonas chloroplasts. RNA 1997, 3:37-48.
17. Dujardin G., Herbert C. Aminoacyl tRNA synthetases involved in group I intron splicing. Ribosomal RNA and Group I Introns 1997, 179-198. R. G. Landes Company, Austin, TX. R. Green, R. Schroeder (Eds.).
18. 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, 10:3495-3501.
19. Dürrenberger F., Rochaix J.D. Characterization of the cleavage site and the recognition sequence of the I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii. Mol. Gen. Genet. 1993, 236:409-414.
20. Dürrenberger F., Thompson A.J., Herrin D.L., Rochaix J.D. Double strand break-induced recombination in Chlamydomonas reinhardtii chloroplasts. Nucleic Acids Res. 1996, 24:3323-3331.
21. Eberhard S., Drapier D., Wollman F.A. Searching limiting steps in the expression of chloroplast-encoded proteins: Relations between gene copy number, transcription, transcript abundance and translation rate in the chloroplast of Chlamydomonas reinhardtii. Plant J. 2002, 31:149-160.
22. Erickson J.M., Rahire M., Rochaix J.D. Chlamydomonas reinhardtii gene for the 32 000mol.wt. protein of photosystem II contains four large introns and is located entirely within the chloroplast inverted repeat. EMBO J. 1984, 3:2753-2762.
23. Glanz S., Bunse A., Wimbert A., Balczun C., Kück U. A nucleosome assembly protein-like polypeptide binds to chloroplast group II intron RNA in Chlamydomonas reinhardtii. Nucleic Acids Res. 2006, 34:5337-5351.
24. Goldschmidt-Clermont M., Girard-Bascou J., Choquet Y., Rochaix J.D. Trans-splicing mutants of Chlamydomonas reinhardtii. Mol. Gen. Genet. 1990, 223:417-425.
25. Goldschmidt-Clermont M., Choquet Y., Girard-Bascou J., Michel F., Schirmer-Rahire M., Rochaix J.D. A small chloroplast RNA may be required for trans-splicing in Chlamydomonas reinhardtii. Cell 1991, 65:135-143.
26. Hahn D., Nickelsen J., Hackert A., Kück U. A single nuclear locus is involved in both chloroplast RNA trans-splicing and 3' end processing. Plant J. 1998, 15:575-581.
27. Haugen P., Simon D.M., Bhattacharya D. The natural history of group I introns. Trends Genet. 2005, 21:111-119.
28. Hausner G., Olson R., Simon D., Johnson I., Sanders E.R., Karol K.G., McCourt R.M., Zimmerly S. Origin and evolution of the chloroplast trnK (matK) intron: A model for evolution of group II intron RNA structures. Mol. Biol. Evol. 2006, 23:380-391.
29. Herbert C.J., Labouesse M., Dujardin G., Slonimski P.P. The NAM2 proteins from S. cerevisiae and S. douglasii are mitochondrial leucyl-tRNA synthetases, and are involved in mRNA splicing. EMBO J. 1988, 7:473-483.
30. Herdenberger F., Holländer V., Kück U. Correct in vivo RNA splicing of a mitochondrial intron in algal chloroplasts. Nucleic Acids Res. 1994, 22:2869-2875.
31. Herrin D.L., Nickelsen J. Chloroplast RNA processing and stability. Photosynth. Res. 2004, 82:301-314.
32. Herrin D.L., Schmidt G.W. Trans-splicing of transcripts for the chloroplast psaA1 gene. In vivo requirement for nuclear gene products. J. Biol. Chem. 1988, 263:14601-14604.
33. Herrin D.L., Chen Y.F., Schmidt G.W. RNA splicing in Chlamydomonas chloroplasts. Self-splicing of 23 S preRNA. J. Biol. Chem. 1990, 265:21134-21140.
34. Herrin D.L., Bao Y., Thompson A.J., Chen Y.F. Self-splicing of the Chlamydomonas chloroplast psbA introns. Plant Cell 1991, 3:1095-1107.
35. Herrin D., Kuo T.C., Goldschmidt-Clermont M. RNA splicing in the chloroplast. The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas 1998, 183-195. Kluwer Academic Publishers, Dordrecht, The Netherlands. J.-D. Rochaix, M. Goldschmidt-Clermont, S. Merchant (Eds.).
36. Holländer V., Kück U. Group II intron splicing in chloroplasts: Identification of mutations determining intron stability and fate of exon RNA. Nucleic Acids Res. 1999, 27:2345-2353.
37. Holloway S.P., Herrin D.L. Processing of a composite large subunit rRNA. Studies with Chlamydomonas mutants deficient in maturation of the 23S-like rRNA. Plant Cell 1998, 10:1193-1206.
38. Holloway S.P., Deshpande N.N., Herrin D.L. The catalytic group-I introns of the psbA gene of Chlamydomonas reinhardtii: Core structures, ORFs and evolutionary implications. Curr. Genet. 1999, 36:69-78.
39. Houghland J.L., Piccirilli J.A., Forconi M., Jihee L., Herschlag D. How the group I intron works: A case study of RNA structure and function. The RNA World 2006, 133-205. Laboratory Press, Cold Spring Harbor. 3rd ed. R.F. Gesteland, T.R. Cech, J.F. Atkins (Eds.).
40. Jenkins B.D., Barkan A. Recruitment of a peptidyl-tRNA hydrolase as a facilitator of group II intron splicing in chloroplasts. EMBO J. 2001, 20:872-879.
41. Jenkins B.D., Kulhanek D.J., Barkan A. Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors. Plant Cell 1997, 9:283-296.
42. Johanningmeier U., Heiss S. Construction of a Chlamydomonas reinhardtii mutant with an intronless psbA gene. Plant Mol. Biol. 1993, 22:91-99.
43. Kim H.H., Corina L.E., Suh J.K., Herrin D.L. Expression, purification, and biochemical characterization of the intron-encoded endonuclease, I-CreII. Protein Expr. Purif. 2005, 44:162-172.
44. Kuchka M.R., Goldschmidt-Clermont M., van Dillewijn J., Rochaix J.D. Mutation at the Chlamydomonas nuclear NAC2 locus specifically affects stability of the chloroplast psbD transcript encoding polypeptide D2 of PS II. Cell 1989, 58:869-876.
45. Kück U., Choquet Y., Schneider M., Dron M., Bennoun P. Structural and transcription analysis of the two homolgous genes for the P700 chlorophyll a-apoprotein in Chlamydomonas reinhardtii: Evidence for in vivo trans-splicing. EMBO J. 1987, 6:2185-2195.
46. Kuo T.C., Odom O.W., Herrin D.L. Unusual metal specificity and structure of the group I ribozyme from Chlamydomonas reinhardtii 23S rRNA. FEBS J. 2006, 273:2631-2634.
47. Kurokawa S., Yamasaki T., Komatsu T., Watanabe K.I., Ohama T. Degenerated recognition property of a mitochondrial homing enzyme in the unicellular green alga Chlamydomonas smithii. Plant Mol. Biol. 2006, 62:141-150.
48. Lambowitz A.M., Perlman P.S. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 1990, 15:440-444.
49. Lambowitz A.M., Zimmerly S. Mobile group II introns. Annu. Rev. Genet. 2004, 38:1-35.
50. Lee J., Herrin D.L. Mutagenesis of a light-regulated psbA intron reveals the importance of efficient splicing for photosynthetic growth. Nucleic Acids Res. 2003, 31:4361-4372.
51. Lemieux C., Lee R.W. Nonreciprocal recombination between alleles of the chloroplast 23S rRNA gene in interspecific Chlamydomonas crosses. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:4166-4170.
52. Lemieux B., Turmel M., Lemieux C. Unidirectional gene conversions in the chloroplast of Chlamydomonas interspecific hybrids. Mol. Gen. Genet. 1988, 212:48-55.
53. Li F., Herrin D.L. FUGOID: Functional genomics of organellar introns database. Nucleic Acids Res. 2002, 30:385-386.
54. Li F., Holloway S.P., Lee J., Herrin D.L. Nuclear genes that promote splicing of group I introns in the chloroplast 23S rRNA and psbA genes in Chlamydomonas reinhardtii. Plant J. 2002, 32:467-480.
55. Lurin C., Andres C., Aubourg S., Bellaoui M., Bitton F., Bruyere C., Caboche M., Debast C., Gualberto J., Hoffmann B., Lecharny A., Le Ret M., Martin-Magniette M.L., Mireau H., Peeters N., Renou J.P., Szurek B., Taconnat L., Small I. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 2004, 16:2089-2103.
56. Merendino L., Perron K., Rahire M., Howald I., Rochaix J.D., Goldschmidt-Clermont M. A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas. Nucleic Acids Res. 2006, 34:262-274.
57. Minagawa J., Crofts A. A robust protocol for site-directed mutagenesis of the D1 protein in Chlamydomonas reinhardtii. Photosynth. Res. 1994, 42:121-131.
58. Nedelcu A.M., Lee R.W. A degenerate group II intron in the intronless mitochondrial genome of Chlamydomonas reinhardtii: Evolutionary implications. Mol. Biol. Evol. 1998, 15:918-922.
59. Odom O.W., Holloway S.P., Deshpande N.N., Lee J., Herrin D.L. Mobile self-splicing group I introns from the psbA gene of Chlamydomonas reinhardtii: Highly efficient homing of an exogenous intron containing its own promoter. Mol. Cell. Biol. 2001, 21:3472-3481.
60. Odom O.W., Shenkenberg D.L., Garcia J.A., Herrin D.L. A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: In vitro self-splicing and genetic evidence for maturase activity. RNA 2004, 10:1097-1107.
61. Ostheimer G.J., Williams-Carrier R., Belcher S., Osborne E., Gierke J., Barkan A. Group II intron splicing factors derived by diversification of an ancient RNA-binding domain. EMBO J. 2003, 22:3919-3929.
62. Paukstelis P.J., Coon R., Madabusi L., Nowakowski J., Monzingo A., Robertus J., Lambowitz A.M. A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface. Mol. Cell 2005, 17:417-428.
63. Perron K., Goldschmidt-Clermont M., Rochaix J.D. A factor related to pseudouridine synthases is required for chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J. 1999, 18:6481-6490.
64. Perron K., Goldschmidt-Clermont M., Rochaix J.D. A multiprotein complex involved in chloroplast group II intron splicing. RNA 2004, 10:704-710.
65. Podar M., Chu V.T., Pyle A.M., Perlman P.S. Group II intron splicing in vivo by first-step hydrolysis. Nature 1998, 391:891-915.
66. Pyle A.M., Lambowitz A.M. Group II introns: Ribozymes that splice RNA and invade DNA. The RNA World 2006, 469-505. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. 3rd ed. R.F. Gesteland, T.R. Cech, J.F. Atkins (Eds.).
67. Rivier C. Characterisation of a factor involved in the trans-splicing of a chloroplast tri-partite group II intron from Chlamydomonas reinhardtii. Ph.D. Dissertation 2000, University of Geneva, Geneva, Switzerland.
68. Rivier C., Goldschmidt-Clermont M., Rochaix J.D. Identification of an RNA-protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J. 2001, 20:1765-1773.
69. Robart A.R., Zimmerly S. Group II intron retroelements: Function and diversity. Cytogenet. Genome Res. 2005, 110:589-597.
70. Rochaix J.D., Malnoë P. Anatomy of the chloroplast ribosomal DNA of Chlamydomonas reinhardii. Cell 1978, 15:661-670.
71. Rochaix J.D., Rahire M., Michel F. The chloroplast ribosomal intron of Chlamydomonas reinhardii codes for a polypeptide related to mitochondrial maturases. Nucleic Acids Res. 1985, 13:975-984.
72. Roitgrund C., Mets L.J. Localization of two novel chloroplast genome functions: trans-splicing of RNA and protochlorophyllide reduction. Curr. Genet. 1990, 17:147-153.
73. Schafer B., Merlos-Lange A.M., Anderl C., Welser F., Zimmer M., Wolf K. The mitochondrial genome of fission yeast: Inability of all introns to splice autocatalytically, and construction and characterization of an intronless genome. Mol. Gen. Genet. 1991, 225:158-167.
74. Schmitz-Linneweber C., Williams-Carrier R.E., Williams-Voelker P.M., Kroeger T.S., Vichas A., Barkan A. A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA. Plant Cell 2006, 18:2650-2663.
75. Seraphin B., Boulet A., Simon M., Faye G. Construction of a yeast strain devoid of mitochondrial introns and its use to screen nuclear genes involved in mitochondrial splicing. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:6810-6814.
76. Sharp P.A. Five easy pieces. Science 1991, 254:663.
77. Spiegel P.C., Chevalier B., Sussman D., Turmel M., Lemieux C., Stoddard B.L. The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure 2006, 14:869-880.
78. Thompson A.J., Herrin D.L. A chloroplast group I intron undergoes the first step of reverse splicing into host cytoplasmic 5.8 S rRNA. Implications for intron-mediated RNA recombination, intron transposition and 5.8 S rRNA structure. J. Mol. Biol. 1994, 236:455-468.
79. Thompson A.J., Yuan X., Kudlicki W., Herrin D.L. Cleavage and recognition pattern of a double-strand-specific endonuclease (I-creI) encoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii. Gene 1992, 119:247-251.
80. Till B., Schmitz-Linneweber C., Williams-Carrier R., Barkan A. CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. RNA 2001, 7:1227-1238.
81. Trebitsh T., Danon A. Translation of chloroplast psbA mRNA is regulated by signals initiated by both photosystems II and I. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:12289-12894.
82. Turmel M., Gutell R.R., Mercier J.P., Otis C., Lemieux C. Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa. Three internal transcribed spacers and 12 group I intron insertion sites. J. Mol. Biol. 1993, 232:446-467.
83. Turmel M., Mercier J.P., Cote M.J. Group I introns interrupt the chloroplast psaB and psbC and the mitochondrial rrnL gene in Chlamydomonas. Nucleic Acids Res. 1993, 21:5242-5250.
84. Turmel M., Choquet Y., Goldschmidt-Clermont M., Rochaix J.D., Otis C., Lemieux C. The trans-spliced intron 1 in the psaA gene of the Chlamydomonas chloroplast: A comparative analysis. Curr. Genet. 1995, 27:270-279.
85. Vogel J., Börner T. Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing. EMBO J. 2002, 21:3794-3803.
86. Zerges W., Rochaix J.D. Low density membranes are associated with RNA-binding proteins and thylakoids in the chloroplast of Chlamydomonas reinhardtii. J. Cell Biol. 1998, 140:101-110.