Preparation and Proteomic Analysis of Chloroplast Ribosomes

Methods in Molecular Biology

Volumn 775, Issue , 2011, Pages 241-264

  Yamaguchi, Kenichi ^a  

^a NAGASAKI UNIVERSITY   (Japan)

Author keywords

Arabidopsis thaliana; Chlamydomonas reinhardtii; Chloroplast ribosome; Plastid ribosomal protein; Proteomics; Sucrose density gradient ultracentrifugation

Indexed keywords

RIBOSOME PROTEIN; SUCROSE;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CELL FRACTIONATION; CHEMISTRY; CHLAMYDOMONAS; CHLOROPLAST; CYTOLOGY; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEOMICS; RIBOSOME; RIBOSOME SUBUNIT; TIME;

AMINO ACID SEQUENCE; ARABIDOPSIS; CELL FRACTIONATION; CHLAMYDOMONAS; CHLOROPLASTS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MOLECULAR SEQUENCE DATA; PROTEOMICS; RIBOSOMAL PROTEINS; RIBOSOME SUBUNITS; RIBOSOMES; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SUCROSE; TIME FACTORS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CHLAMYDOMONAS; CHLAMYDOMONAS REINHARDTII; EMBRYOPHYTA; SPINACIA OLERACEA;

EID: 80054717705     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-237-3_13     Document Type: Chapter

References (50)

1. Subramanian, A. R., Stahl, D., and Prombona, A. (1991) Ribosomal proteins, ribosomes, and translation in plastids. In, The Molecular Biology of Plastids (Bogorad, L. and Vasil, I. K., eds.) Academic Press, New York, USA, pp. 191–215.
2. Bourque, D. P., Hagiladi, A., and Naylor, A. W. (1973) A method for extracting intact chloroplast and cytoplasmic ribosomal RNA from leaves. Biochem. Biophys. Res. Commun. 51, 993–999.
3. Subramanian, A. R. (1993) Molecular genetics of chloroplast ribosomal proteins. Trends Biochem. Sci. 18, 177–181.
4. Eberhard, S., Drapier, D., and Wollman, F. A. (2002) 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. 31, 149–160.
5. Barkan, A., and Goldschmidt-Clermont, M. (2000) Participation of nuclear genes in chloroplast gene expression. Biochimie 82, 559–572.
6. Malnoë, P., Mayfield, S. P., and Rochaix, J. D. (1988) Comparative analysis of the biogenesis of photosystem II in the wild-type and Y-1 mutant of Chlamydomonas reinhardtii. J. Cell Biol. 106, 609–616.
7. Bruick, R. K., and Mayfield, S. P. (1999) Light-activated translation of chloroplast mRNAs. Trends Plant Sci. 4, 190–195.
8. Somanchi, A., and Mayfield, S. P. (2001) Regulation of chloroplast translation. In, Advances in Photosynthesis and Respiration (Aro, E.-M. and Andersson, B., eds.) Kluwer Academic Publishers, Dordrecht, Netherlands, pp. 137–151.
9. Lyttleton, J. W. (1962) Isolation of ribosomes from spinach chloroplasts. Exp. Cell Res. 26, 312–317.
10. Ris, H., and Plaut, W. (1962) Ultrastructure of DNA-containing areas in the chloroplast of Chlamydomonas. J. Cell Biol. 13, 383–391.
11. Harris, E. H., Boynton, J. E., and Gillham, N. W. (1994) Chloroplast ribosomes and protein synthesis. Microbiol. Rev. 58, 700–754.
12. Beligni, M. V., Yamaguchi, K., and Mayfield, S. P. (2004) The translational apparatus of Chlamydomonas reinhardtii chloroplast. Photosynth. Res. 82, 315–325.
13. nd edn. (Stern D. B., ed.) Academic Press, New York, USA, pp. 967–1025.
14. Yamaguchi, K., von Knoblauch, K., and Subramanian, A. R. (2000) The plastid ribosomal proteins: Identification of all the proteins in the 30S subunit of an organelle ribosome (chloroplast). J. Biol. Chem. 275, 28455–28465.
15. Yamaguchi, K., and Subramanian, A. R. (2000) The plastid ribosomal proteins: Identification of all the proteins in the 50S subunit of an organelle ribosome (chloroplast). J. Biol. Chem. 275, 28466–28482.
16. Yamaguchi, K., and Subramanian, A. R. (2003) Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit. Eur. J. Biochem. 270, 190–205.
17. rd, and Mayfield, S. P. (2002) Proteomic characterization of the small subunit of Chlamydomonas
18. rd, and Mayfield, S. P. (2003) Proteomic characterization of the Chlamydomonas reinhardtii chloroplast ribosome: identification of proteins unique to the 70S ribosome. J. Biol. Chem. 278, 33774–33785.
19. Sharma, M. R., Wilson, D. N., Datta, P. P., Barat, C., Schluenzen, F., Fucini, P., and Agrawal, R. K. (2007) Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins. Proc. Natl. Acad. Sci. USA 104, 19315–19320.
20. Manuell, A. L., Quispe, J., and Mayfield, S. P. (2007) Structure of the chloroplast ribosome: novel domains for translation regulation. PLoS Biol. 5, e209.
21. Sharma, M. R, Dönhöfer, A., Barat, C., Marquez, V., Datta, P. P, Fucini, P., Wilson, D. N., and Agrawal, R. K. (2010) PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G). J. Biol. Chem. 285, 4006–4014.
22. Beligni, M. V., Yamaguchi, K., and Mayfield, S. P. (2004) Chloroplast elongation factor Ts pro-protein is an evolutionarily conserved fusion with the S1 domain-containing plastid-specific ribosomal protein-7. Plant Cell 16, 3357–3369.
23. Giavalisco, P., Wilson, D., Kreitler, T., Lehrach, H., Klose, J., Gobom, J., and Fucini, P. (2005) High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome. Plant Mol. Biol. 57, 577–591.
24. Chang, I. F., Szick-Miranda, K., Pan, S., and Bailey-Serres, J. (2005) Proteomic characterization of evolutionarily conserved and variable proteins of Arabidopsis cytosolic ribosomes. Plant Physiol. 137, 848–862.
25. Carroll, A. J., Heazlewood, J. L., Ito, J., and Millar, A. H. (2008) Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification. Mol. Cell. Proteomics 7, 347–369.
26. Posno, M., van Noot, M., Debise, R., and Groot, G. (1989) Isolation, characterization, phosphorylation and site of synthesis of Spinacia chloroplast ribosomal proteins. Curr. Genet. 8, 147–154.
27. Guitton, C., Dorne, A. M, and Mache, R. (1984) In organello and in vitro phosphoryla- tion of chloroplast ribosomal proteins. Biochem. Biophys. Res. Commun. 121, 297–303.
28. Reiland, S., Messerli, G., Baerenfaller, K., Gerrits, B., Endler, A., Grossmann, J., Gruissem, W., and Baginsky, S. (2009) Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol. 150, 889–903.
29. Bourque, D. P., and Capel, M. S. (1982) Isolation and purification of tobacco chloroplast ribosomes. In, Methods in Chloroplast Molecular Biology (Edelman, M., Hallick, R. B., and Chua, N. H., eds.) Elsevier Biomedical Press, Amsterdam, Netherlands, pp. 617–628.
30. Hewlett, N. G., and Bourque, D. P. (1986) Improved preparative methods for isolation and purification of tobacco chloroplast ribosomes, ribosomal proteins, and rRNA. Methods Enzymol. 118, 201–212.
31. Spedding, G. (1990) Isolation and analysis of ribosomes from prokaryotes, eukaryotes, and organelles. In, Ribosomes and Protein Synthesis: A Practical Approach (Spedding, G., ed.) Oxford University Press, Oxford, UK, pp. 1–29.
32. Harris, E. H. (1989) The Chlamydomonas Sourcebook. Academic Press, San Diego, USA.
33. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.
34. Bourque, D. P., and Wildman, S. G. (1973) Evidence that nuclear genes code for several chloroplast ribosomal proteins. Biochem. Biophys. Res. Commun. 50, 532–537.
35. Chua, N. H., Blobel, G., Siekevitz, P., and Palade, G. E. (1973) Attachment of chloroplast polysomes to thylakoid membranes in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 70, 1554–1558.
36. Chua, N. H., Blobel, G., and Siekevitz, P. (1973) Isolation of cytoplasmic and chloroplast ribosomes and their dissociation into active subunits from Chlamydomonas reinhardtii. J. Cell. Biol. 57, 798–814.
37. Hardy, S. J., Kurland, C. G., Voynow, P., and Mora, G. (1969) The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins. Biochemistry 8, 2897–2905.
38. Afonina, E., Chichkova, N., Bogdanova, S., and Bogdanov, A. (1991) 30S ribosomal subunits with fragmented 16S RNA: a new approach for structure and function study of ribosomes. Biochimie 73, 777–787.
39. Chomczynski, P., and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidi-nium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156–159.
40. Subramanian, A. R. (1974) Sensitive separation procedure for Escherichia coli ribosomal proteins and the resolution of high-molecular-weight components. Eur. J. Biochem. 45, 541–546.
41. Mets, L. J., and Bogorad, L. (1974) Two-dimensional polyacrylamide gel electrophoresis: an improved method for ribosomal proteins. Anal. Biochem. 57, 200–210.
42. Wada, A. (1986) Analysis of Escherichia coli ribosomal proteins by an improved two dimensional gel electrophoresis. I. Detection of four new proteins. J. Biochem. 100, 1583–1594.
43. Kurland, C. G. (1966) The requirements for specific sRNA binding by ribosomes. J. Mol. Biol. 18, 90–108.
44. Juan, H. F., Chang, S. C., Huang, H. C., and Chen, S. T. (2005) A new application of microwave technology to proteomics. Proteomics 5, 840–842.
45. Sun, W., Gao, S., Wang, L., Chen, Y., Wu, S., Wang, X., Zheng, D., and Gao, Y. (2006) Microwave-assisted protein preparation and enzymatic digestion in proteomics. Mol. Cell. Proteomics 5, 769–776.
46. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567.
47. Manuell, A. L., Yamaguchi, K., Haynes, P. A., Milligan, R. A., and Mayfield, S. P. (2005) Composition and structure of the 80S ribosome from the green alga Chlamydomonas reinhardtii: 80S ribosomes are conserved in plants and animals. J. Mol. Biol. 351, 266–279.
48. Agrawal, R. K., Penczek, P., Grassucci, R. A., Burkhardt, N., Nierhaus, K. H., and Frank, J. (1999) Effect of buffer conditions on the position of tRNA on the 70S ribosome as visualized by cryoelectron microscopy. J. Biol. Chem. 274, 8723–8729.
49. Rolland, N., Janosi, L., Block, M. A., Shuda, M., Teyssier, E., Miège, C., Chéniclet, C., Carde, J. P., Kaji, A., and Joyard, J. (1999) Plant ribosome recycling factor homologue is a chloroplastic protein and is bactericidal in Escherichia coli carrying temperature-sensitive ribosome recycling factor. Proc. Natl. Acad. Sci. USA 96, 5464–5469.
50. Schmitz-Linneweber, C., Maier, R. M., Alcaraz, J. P., Cottet, A., Herrmann, R.G., and Mache, R. (2001) The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45, 307–315.