Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression

Plant Physiology

Volumn 138, Issue 2, 2005, Pages 624-635

  Zanetti, María Eugenia ^a   Chang, Ing Feng ^a   Gong, Fangcheng ^b   Galbraith, David W ^b   Bailey Serres, Julia ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; DNA; GENETIC ENGINEERING; IMMUNOLOGY; PHYSIOLOGY; RNA;

BIOLOGICAL REPLICATES; PLANT CELLS; POLYSOMES; TOTAL CELLULAR RNA;

PLANTS (BOTANY);

CELLS; GENETIC ENGINEERING; NUCLEIC ACIDS; PHYSIOLOGY; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAULIFLOWER MOSAIC VIRUS;

ARABIDOPSIS PROTEIN; MESSENGER RNA; PLANT RNA;

AFFINITY CHROMATOGRAPHY; ARABIDOPSIS; ARTICLE; CELL FRACTIONATION; CHEMISTRY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; IMMUNOCHEMISTRY; ISOLATION AND PURIFICATION; METHODOLOGY; POLYSOME; PROTEIN BINDING;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL FRACTIONATION; CHROMATOGRAPHY, AFFINITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; IMMUNOCHEMISTRY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYRIBOSOMES; PROTEIN BINDING; RNA, MESSENGER; RNA, PLANT;

EID: 26944438704     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.105.059477     Document Type: Review

References (56)

1. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 100: 3889-3894
2. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920
3. Barakat A, Szick-Miranda K, Chang IF, Guyot R, Blanc G, Cooke R, Delseny M, Bailey-Serres J (2001) The organization of cytoplamic ribosomal protein genes in the Arabidopsis genome. Plant Physiol 127: 398-415
4. Bassler J, Grandi P, Gadal O, Lessmann T, Petfalski E, Tollervey D, Lechner J, Hurt E (2001) Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol Cell 8: 517-529
5. Baugh LR, Hill AA, Brown EL, Hunter CP (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29: E29
6. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN (2003) A gene expression map of the Arabidopsis root. Science 302: 1956-1960
7. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al (2001) Minimum information about a microarray experiment (MIAME): toward standards for microarray data. Nat Genet 29: 365-371
8. Chang IF, Szick-Miranda K, Pan S, Bailey-Serres J (2005) Proteomic characterization of evolutionary conserved and variable proteins of Arabidopsis cytosolic ribosomes. Plant Physiol 137: 848-862
9. Chiu W, Niwa Y, Zeng W, Hirano T, Kobayashi H, Sheen J (1996) Engineered GFP as a vital reporter in plants. Curr Biol 6: 325-330
10. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743
11. Deyholos MK, Galbraith DW (2001) High-density DNA microarrays for gene expression analysis. Cytometry 43: 229-238
12. Fennoy SL, Bailey-Serres J (1995) Posttranscriptional regulation of gene expression in oxygen-deprived roots of maize. Plant J 7: 287-295
13. Galbraith DW (2003) Global analysis of cell type-specific gene expression. Comp Funct Genom 4: 208-215
14. Galbraith DW, Elumalai R, Gong FC (2004) Integrative flow cytometric and microarray approaches for use in transcriptional profiling. Methods Mol Biol 263: 259-280
15. Gutierrez RA, MacIntosh GC, Green PJ (1999) Current perspectives on mRNA stability in plants: multiples levels and mechanisms of control. Trends Plant Sci 4: 429-438
16. Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19: 1720-1730
17. Hajdukiewicz P, Svab Z, Maliga P (1994) The small, versatile pPZP family of Agrobacterium binary vectors for plant transformation. Plant Mol Biol 25: 989-994
18. Harnpicharnchai P, Jakovljevic J, Horsey E, Miles T, Roman J, Rout M, Meagher D, Imai B, Guo Y, Brame C, et al (2001) Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell 8: 505-515
19. Hellmann H, Estelle M (2002) Plant development: regulation by protein degradation. Science 297: 793-797
20. Hoffmann B, Mosch HU, Sattlegger E, Barthelmess IB, Hinnebusch A, Braus GH (1999) The WD protein Cpc2p is required for repression of Gcn4 protein activity in yeast in the absence of amino-acid starvation. Mol Microbiol 31: 807-822
21. Inada T, Winstall E, Tarun SZ, Yates JR, Schieltz D, Sachs AB (2002) One step affinity purification of yeast ribosome and its associated proteins and mRNAs. RNA 8: 948-958
22. Jeeninga RE, Venema J, Raue HA (1996) Rat RPL23a ribosomal protein efficiently competes with Saccharomyces cerevisiae L25 homologue for assembly into 60 S subunit. J Mol Biol 263: 643-656
23. Jefferson RA (1989) The GUS reporter gene system. Nature 342: 837-838
24. Jones JDG, Shlumukov L, Carland F, English J, Scofield S, Bishop G, Harrison K (1992) Effective vectors for transformation, expression of heterologous genes, and assaying transposon excision in transgenic plants. Transgenic Res 1: 285-297
25. Jones MA, Grierson CS (2003) A simple method for obtaining cell-specific cDNA from small numbers of growing root-hair cells in Arabidopsis thaliana. J Exp Bot 54: 1373-1378
26. Ju J, Huang C, Minskoff SA, Mayotte JE, Taillon BE, Simons JF (2003) Simultaneous gene expression analysis of steady-state and actively translated mRNA populations from osteosarcoma MG-63 cells in response to IL-1 via an open expression analysis platform. Nucleic Acids Res 31: 5157-5166
27. Kawaguchi R, Bailey-Serres J (2002) Regulation of translational initiation in plants. Curr Opin Plant Biol 5: 460-465
28. Kawaguchi R, Bailey-Serres J (2005) mRNA sequence features responsible for translational regulation in Arabidopsis. Nucleic Acids Res 33: 955-965
29. Kawaguchi R, Girke T, Bray EA, Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J 38: 823-839
30. Kerk NM, Ceserani T, Tausta SL, Sussex IM, Nelson TM (2003) Laser capture microdissection of cells from plant tissues. Plant Physiol 132: 27-35
31. Kuhn KM, DeRissi JL, Brown PO, Sarnow P (2001) Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a non fermentable carbon source. Mol Cell Biol 21: 916-927
32. Kumar KU, Srivastava SP, Kaufman RJ (1999) Double-stranded RNA-activated protein kinase (PKR) is negatively regulated by 60S ribosomal subunit protein L18. Mol Cell Biol 19: 1116-1125
33. Meyerowitz EM (1987) In situ hybridization to RNA in plant tissue. Plant Mol Biol Rep 5: 242-250
34. Nilsson J, Sengupta J, Frank J, Nissen P (2004) Regulation of eukaryotic translation by the RACK1 protein: a platform for signaling molecules on the ribosome. EMBO Rep 5: 1137-1141
35. Park HS, Himmelbach A, Browning KS, Hohn T, Ryabova LA (2001) A viral reinitiation factor interacts with the host translational machinery Cell 106: 723-733
36. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence data based using mass spectrometry data. Electrophoresis 20: 3551-3567
37. Preiss T, Baron-Benhamou J, Ansorge W, Hentze M (2003) Homodirectional changes in transcriptome and mRNA translation induced by rapamycin and heat shock. Nat Struct Biol 10: 1039-1047
38. Preiss T, Hentze M (2003) Starting the protein synthesis machine: eukaryotic translation initiation. Bioessays 10: 1201-1211
39. Rohila JS, Chen M, Cerny R, Fromm ME (2004) Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J 38: 172-181
40. Ron D, Chen CH, Caldwell J, Jamieson L, Orr E, Mochly-Rosen D (1994) Cloning of an intracellular receptor for protein kinase C: a homolog of the β subunit of G proteins. Proc Natl Acad Sci USA 91: 839-843
41. Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed gene in Caenorhabditis elegans. Nature 418: 975-979
42. Sambrook J, Fritish F, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, Ed 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
43. Schafer T, Strauss D, Petfalski E, Tollervey D, Hurt E (2003) The path form nucleolar 90S to cytoplasmic 40S pre-ribosomes. EMBO J 22: 1370-1380
44. Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae tRNA-ribosome and subunit-subunit interactions. Cell 107: 373-386
45. Szick-Miranda K, Bailey-Serres J (2001) Regulated heterogeneity in 12-kDa P-protein phosphorylation and composition of ribosomes in maize (Zea mays L.). J Biol Chem 276: 10921-10928
46. Tenenbaum SA, Carson CC, Lager PJ, Keene JD (2000) Identifying subsets in messenger ribonucleoprotein complexes by cDNA arrays. Proc Natl Acad Sci USA 97: 14085-14090
47. Tenenbaum SA, Lager PJ, Carson CC, Keene JD (2002) Ribonomics: identifying subset in mRNP complexes using antibodies to RNA-binding proteins and genomics array. Methods 26: 191-198
48. Turck F, Kozma SC, Thomas G, Nagy F (1998) A heat-sensitive Arabidopsis thaliana kinase substitutes for human p70s6k function in vivo. Mol Cell Biol 18: 2038-2044
49. Tzamarias D, Roussou I, Thireos G (1989) Coupling of GCN4 mRNA translational activation with decreased rates of polypeptide chain initiation. Cell 57: 947-954
50. van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 87: 1663-1667
51. Verschoor A, Srivastava S, Grassucci R, Frank J (1996) Native 3D structure of eukaryotic 80S ribosome: morphological homology with the E. coli 70S ribosome. J Cell Biol 133: 495-505
52. Wang Q, Guo L, Sjolund R, Shih MC (1997) Immunolocalization of GAPDH in Arabidopsis thaliana. Protoplasma 198: 155-162
53. Williams AJ, Werner-Fraczek J, Chang IF, Bailey-Serres J (2003) Regulated phosphorylation of 40S ribosomal protein S6 in root tips of maize. Plant Physiol 132: 2086-2097
54. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8: 625-637
55. Zhao H, Hastie T, Whitfield ML, Borresen-Dale AL, Jeffrey SS (2002) Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. BMC Genomics 3: 31
56. Zong Q, Schummer M, Hood L, Morris DR (1999) Messenger mRNA translation state: the second dimension of high-throughput expression screening. Proc Natl Acad Sci USA 96: 10632-10636