A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas

Nucleic Acids Research

Volumn 34, Issue 1, 2006, Pages 262-274

  Merendino, Livia ^a,b   Perron, Karl ^a,c   Rahire, Michèle ^a   Howald, Isabelle ^a   Rochaix, Jean David ^a   Goldschmidt Clermont, Michel ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b UNIV GRENOBLE ALPES   (France)

^c CMU ^*  (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPLAST RNA; COMPLEMENTARY DNA; DNA FRAGMENT; MESSENGER RNA; OLIGONUCLEOTIDE; PROTEIN RAA1; RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; CELL FRACTIONATION; CHLAMYDOMONAS REINHARDTII; CHLOROPLAST GENETICS; CONTROLLED STUDY; DIPLOIDY; GENE DELETION; GENE EXPRESSION; GENE MAPPING; GENE MUTATION; GENETIC SCREENING; GENOTYPE; IMMUNOBLOTTING; INTRON; MOLECULAR CLONING; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; RNA TRANSCRIPTION; SEQUENCE ANALYSIS;

CHLAMYDOMONAS; CHLAMYDOMONAS REINHARDTII;

EID: 31544468450     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkj429     Document Type: Article

References (52)

1. Qin,P.Z. and Pyle,A.M. (1998) The architectural organization and mechanistic function of group II intron structural elements. Curr. Opin. Struct. Biol., 8, 301-308.
2. Bonen,L. and Vogel,J. (2001) The ins and outs of group II introns. Trends Genet., 17, 322-331.
3. Toro,N. (2003) Bacteria and Archaea Group II introns: Additional mobile genetic elements in the environment. Environ. Microbiol., 5, 143-151.
4. Villa,T., Pleiss,J.A. and Guthrie,C. (2002) Spliceosomal snRNAs: Mg(2+)-dependent chemistry at the catalytic core? Cell, 109, 149-152.
5. Kück,U., Choquet,Y., Schneider,M., Dron,M. and Bennoun,P. (1987) 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., 6, 2185-2195.
6. Choquet,Y., Goldschmidt-Clermont,M., Girard-Bascou,J., Kuck,U., Bennoun,P. and Rochaix,J.D. (1988) Mutant phenotypes support a trans-splicing mechanism for the expression of the tripartite psaA gene in the C.reinhardtii chloroplast. Cell, 52, 903-913.
7. Goldschmidt-Clermont,M., Choquet,Y., Girard-Bascou,J., Michel,F., Schirmer-Rahire,M. and Rochaix,J.D. (1991) A small chloroplast RNA may be required for trans-splicing in Chlamydomonas reinhardtii. Cell, 65, 135-143.
8. Schroeder,R., Grossberger,R., Pichler,A. and Waldsich,C. (2002) RNA folding in vivo. Curr. Opin. Struct. Biol., 12, 296-300.
9. Goldschmidt-Clermont,M., Girard-Bascou,J., Choquet,Y. and Rochaix,J.D. (1990) Trans-splicing mutants of Chlamydomonas reinhardtii. Mod. Gen. Genet., 223, 417-425.
10. Rivier,C., Goldschmidt-Clermont,M. and Rochaix,J.D. (2001) Identification of an RNA-protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J., 20, 1765-1773.
11. Perron,K., Goldschmidt-Clermont,M. and Rochaix,J.D. (1999) A factor related to pseudouridine synthases is required for chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J., 18, 6481-6490.
12. Balczun,C., Bunse,A., Hahn,D., Bennoun,P., Nickelsen,J. and Kuck,U. (2005) Two adjacent nuclear genes are required for functional complementation of a chloroplast trans-splicing mutant from Chlamydomonas reinhardtii. Plant J., 43, 636-648.
13. Harris,E.H. (1989) The Chlamydomonas sourcebook. A comprehensive guide to biology and laboratory use. Academic Press, Inc., San Diego, CA.
14. Debuchy,R., Purton,S. and Rochaix,J.D. (1989) The argininosuccinate lyase gene of Chlamydomonas reinhardtii: An important tool for nuclear transformation and for correlating the genetic and molecular maps of the ARG7 locus. EMBO J., 8, 2803-2809.
15. Kindle,K.L. (1990) High-frequency nuclear transformation of Chlamydomonas reinhardtii. Proc. Natl Acad. Sci. USA, 87, 1228-1232.
16. Shimogawara,K., Fujiwara,S., Grossman,A. and Usuda,H. (1998) High-efficiency transformation of Chlamydomonas reinhardtii by electroporation. Genetics, 148, 1821-1828.
17. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning. A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
18. Purton,S. and Rochaix,J.D. (1994) Complementation of a Chlamydomonas reinhardtii mutant using a genomic cosmid library. Plant Mol. Biol., 24, 533-537.
19. Zhang,H., Herman,P.L. and Weeks,D.P. (1994) Gene isolation through genomic complementation using an indexed library of Chlamydomonas reinhardtii DNA. Plant Mol. Biol., 24, 663-672.
20. Sizova,I., Fuhrmann,M. and Hegemann,P. (2001) A Streptomyces rimosus aphVIII gene coding for a new type phosphotransferase provides stable antibiotic resistance to Chlamydomonas reinhardtii. Gene, 277, 221-229.
21. Goldschmidt-Clermont,M. and Rahire,M. (1986) Sequence, evolution and differential expression of the two genes encoding variant small subunits of ribulose bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii. J. Mol. Biol., 191, 421-432.
22. Silflow,C.D., LaVoie,M., Tam,L.W., Tousey,S., Sanders,M., Wu,W., Borodovsky,M. and Lefebvre,P.A. (2001) The Vfl1 Protein in Chlamydomonas localizes in a rotationally asymmetric pattern at the distal ends of the basal bodies. J. Cell. Biol., 153, 63-74.
23. Merendino,L., Falciatore,A. and Rochaix,J.D. (2003) Expression and RNA-binding properties of the chloroplast ribosomal protein S1 from Chlamydomonas reinhardtii. Plant Mol. Biol., 53, 371-382.
24. Schloss,J.A. (1990) A Chlamydomonas gene encodes a G protein beta subunit-like polypeptide. Mol. Gen. Genet., 221, 443-452.
25. Silflow,C. (1998) Organization of the nuclear genome. In Rochaix,J.D., Goldschmidt-Clermont,M. and Merchant,S (1998) The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas. Kluwer Academic Publishers, Dordrecht, The Netherlands, Vol. 7, pp. 25-40.
26. Emanuelsson,O., Nielsen,H. and von Heijne,G. (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci., 8, 978-984.
27. Small,I., Peeters,N., Legeai,F. and Lurin,C. (2004) Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics, 4, 1581-1590.
28. Garnier,J., Gibrat,J.F. and Robson,B. (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol., 266, 540-553.
29. Hahn,D., Nickelsen,J., Hackert,A. and Kuck,U. (1998) A single nuclear locus is involved in both chloroplast RNA trans-splicing and 3′ end processing. Plant J., 15, 575-581.
30. Baginsky,S., Siddique,A. and Gruissem,W. (2004) Proteome analysis of tobacco bright yellow-2 (BY-2) cell culture plastids as a model for undifferentiated heterotrophic plastids. J. Proteome Res., 3, 1128-1137.
31. Auchincloss,A.H., Zerges,W., Perron,K., Girard-Bascou,J. and Rochaix,J.D. (2002) Characterization of Tbc2, a nucleus-encoded factor specifically required for translation of the chloroplast psbC mRNA in Chlamydomonas reinhardtii. J. Cell. Biol., 157, 953-962.
32. Perron,K., Goldschmidt-Clermont,M. and Rochaix,J.D. (2004) A multiprotein complex involved in chloroplast group II intron splicing. RNA, 10, 704-710.
33. Yamazaki,H., Tasaka,M. and Shikanai,T. (2004) PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis. Plant J., 38, 152-163.
34. Fisk,D.G., Walker,M.B. and Barkan,A. (1999) Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression. EMBO J., 18, 2621-2630.
35. Till,B., Schmitz-Linneweber,C., Williams-Carrier,R. and Barkan,A. (2001) CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. RNA, 7, 1227-1238.
36. Jenkins,B.D. and Barkan,A. (2001) Recruitment of a peptidyl-tRNA hydrolase as a facilitator of group II intron splicing in chloroplasts. EMBO J., 20, 872-879.
37. Zerges,W. (2000) Translation in chloroplasts. Biochimie, 82, 583-601.
38. Ostersetzer,O., Cooke,A.M., Watkins,K.P. and Barkan,A. (2005) CRS1: A chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains. Plant Cell, 17, 241-255.
39. Ostheimer,G.J., Williams-Carrier,R., Belcher,S., Osborne,E., Gierke,J. and Barkan,A. (2003) Group II intron splicing factors derived by diversification of an ancient RNA-binding domain. EMBO J., 22, 3919-3929.
40. Ostheimer,G.J., Hadjivasiliou,H., Kloer,D.P., Barkan,A. and Matthews,B.W. (2005) Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces. J. Mol. Biol., 345, 51-68.
41. Mohr,G. and Lambowitz,A.M. (2003) Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants. Nucleic Acids Res., 31, 647-652.
42. Liere,K. and Link,G. (1995) RNA-binding activity of the matK protein encoded by the chloroplast trnK intron from mustard (Sinapis alba L.). Nucleic Acids Res., 23, 917-921.
43. Nakamura,T., Ohta,M., Sugiura,M. and Sugita,M. (1999) Chloroplast ribonucleoproteins are associated with both mRNAs and intron-containing precursor tRNAs. FEES Lett., 460, 437-441.
44. Bunse,A.A., Nickelsen,J. and Kuck,U. (2001) Intron-specific RNA-binding proteins in the chloroplast of the green alga Chlamydomonas reinhardtii. Biochim. Biophys. Acta., 1519, 46-54.
45. Boudreau,E., Nickelsen,J., Lemaire,S.D., Ossenbuhl,F. and Rochaix,J.D. (2000) The Nac2 gene of Chlamydomonas encodes a chloroplast TPR-like protein involved in psbD mRNA stability. EMBO J., 19, 3366-3376.
46. Vaistij,F.E., Boudreau,E., Lemaire,S.D., Goldschmidt-Clermont,M. and Rochaix,J.D. (2000) Characterization of Mbb1, a nucleus-encoded tetratricopeptide-like repeat protein required for expression of the chloroplast psbB/psbT/psbH gene cluster in Chlamydomonas reinhardtii. Proc. Natl Acad. Sci. USA, 97, 14813-14818.
47. Lown,F.J., Watson,A.T. and Purton,S. (2001) Chlamydomonas nuclear mutants that fail to assemble respiratory or photosynthetic electron transfer complexes. Biochem. Soc. Trans., 29, 452-455.
48. Lurin,C., Andres,C., Aubourg,S., Bellaoui,M., Bitton,F., Bruyere,C., Caboche,M., Debast,C., Gualberto,J., Hoffmann,B. et al. (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell, 16, 2089-2103.
49. Felder,S., Meierhoff,K., Sane,A.P., Meurer,J., Driemel,C., Plucken,H., Klaff,P., Stein,B., Bechtold,N. and Westhoff,P. (2001) The nucleus-encoded HCF107 gene of Arabidopsis provides a link between intercistronic RNA processing and the accumulation of translation-competent psbH transcripts in chloroplasts. Plant Cell, 13, 2127-2141.
50. Das,A.K., Cohen,P.W. and Barford,D. (1998) The structure of the tetratricopeptide repeats of protein phosphatase 5: Implications for TPR-mediated protein-protein interactions. EMBO J., 17, 1192-1199.
51. Small,I.D. and Peeters,N. (2000) The PPR motif: A TPR-related motif prevalent in plant organellar proteins. Trends Biochem. Sci., 25, 46-47.
52. Wang,X., McLachlan,J., Zamore,P.D. and Hall,T.M. (2002) Modular recognition of RNA by a human pumilio-homology domain. Cell, 110, 501-512.