Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis

Molecular Systems Biology

Volumn 8, Issue , 2012, Pages

  Wu, Shu Hsing ^a,b,c   Liu, Ming Jung ^a,b,c   Wu, Szu Hsien ^a,b,c   Chen, Ho Ming ^a,b  

^a INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

^b ACADEMIA SINICA   (Taiwan)

^c NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

photomorphogenesis; polysome; translation

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; RIBOSOME PROTEIN; TRANSCRIPTOME;

5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; GENE CONTROL; GENE EXPRESSION REGULATION; GENOME; HALF LIFE TIME; LIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOMORPHOGENESIS; PLANT DEVELOPMENT; PLANT GROWTH; POLYSOME; PRIORITY JOURNAL; REGULATORY MECHANISM; STEADY STATE; TRANSLATION REGULATION; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROARRAY ANALYSIS; MORPHOGENESIS; PHYSIOLOGY; PROTEIN SYNTHESIS; RADIATION EXPOSURE; RIBOSOME; SEEDLING; TRANSGENIC PLANT; VALIDATION STUDY;

ARABIDOPSIS;

ARABIDOPSIS; BASE SEQUENCE; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; LIGHT; MICROARRAY ANALYSIS; MODELS, BIOLOGICAL; MORPHOGENESIS; PLANTS, GENETICALLY MODIFIED; PROTEIN BIOSYNTHESIS; RIBOSOMES; SEEDLING; VALIDATION STUDIES AS TOPIC;

EID: 84862908082     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2011.97     Document Type: Article

References (62)

1. Agresti A (1992) A survey of exact inference for contingency tables. Stat Sci 7: 131-177
2. Alexa A, Rahnenfuhrer J, Lengauer T (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607 (Pubitemid 43985293)
3. 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 (Pubitemid 36418127)
4. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36
5. Bailey-Serres J, Sorenson R, Juntawong P (2009) Getting the message across: cytoplasmic ribonucleoprotein complexes. Trends Plant Sci 14: 443-453
6. Beyer A, Hollunder J, Nasheuer HP, Wilhelm T (2004) Posttranscriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 3: 1083-1092 (Pubitemid 40012101)
7. Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J (2008) Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J 56: 743-755
8. Branco-Price C, Kawaguchi R, Ferreira RB, Bailey-Serres J (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot 96: 647-660 (Pubitemid 41298054)
9. Casal JJ, Yanovsky MJ (2005) Regulation of gene expression by light. Int J Dev Biol 49: 501-511 (Pubitemid 41615605)
10. Chang CS, Li YH, Chen LT, Chen WC, Hsieh WP, Shin J, Jane WN, Chou SJ, Choi G, Hu JM, Somerville S, Wu SH (2008) LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. Plant J 54: 205-219 (Pubitemid 351503113)
11. Chang CS, Maloof JN, Wu SH (2011) COP1-Mediated Degradation of BBX22/LZF1 Optimizes Seedling Development in Arabidopsis. Plant Physiol 156: 228-239
12. Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N (1998) Arabidopsis bZIP protein HY5 directly interacts with lightresponsive promoters in mediating light control of gene expression. Plant Cell 10: 673-683 (Pubitemid 28542177)
13. Chory J (2010) Light signal transduction: an infinite spectrum of possibilities. Plant J 61: 982-991
14. Davies E, Abe S (1995) Methods for isolation and analysis of polyribosomes. Methods Cell Biol 50: 209-222
15. Davis JC (1986) Statistics and Data Analysis in Geology. New York: John Wiley & Sons
16. Dickey LF, Petracek ME, Nguyen TT, Hansen ER, ThompsonWF(1998) Light regulation of Fed-1 mRNA requires an element in the 50 untranslated region and correlates with differential polyribosome association. Plant Cell 10: 475-484 (Pubitemid 28553960)
17. Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210 (Pubitemid 34679544)
18. Gu S, Jin L, Zhang F, Sarnow P, Kay MA (2009) Biological basis for restriction of microRNA targets to the 30 untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16: 144-150
19. Helliwell CA,Webster CI, Gray JC (1997) Light-regulated expression of the pea plastocyanin gene is mediated by elements within the transcribed region of the gene. Plant J 12: 499-506 (Pubitemid 27434029)
20. Henriques R, Jang IC, Chua NH (2009) Regulated proteolysis in lightrelated signaling pathways. Curr Opin Plant Biol 12: 49-56
21. Hu W, Sweet TJ, Chamnongpol S, Baker KE, Coller J (2009) Cotranslational mRNA decay in Saccharomyces cerevisiae. Nature 461: 225-229
22. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223
23. Jiao Y, Meyerowitz EM (2010) Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol 6: 419
24. Kahvejian A, Roy G, Sonenberg N (2001) The mRNA closed-loop model: the function of PABP and PABP-interacting proteins in mRNA translation. Cold Spring Harb Symp Quant Biol 66: 293-300 (Pubitemid 36097936)
25. Kami C, Lorrain S, Hornitschek P, Fankhauser C (2010) Light-regulated plant growth and development. Curr Top Dev Biol 91: 29-66
26. Karniol B, Chamovitz DA (2000) The COP9 signalosome: from light signaling to general developmental regulation and back. Curr Opin Plant Biol 3: 387-393
27. Kawaguchi R, Bailey-Serres J (2002) Regulation of translational initiation in plants. Curr Opin Plant Biol 5: 460-465 (Pubitemid 34961410)
28. 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 (Pubitemid 38693461)
29. Kim BH, Cai X, Vaughn JN, von Arnim AG (2007) On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biol 8: R60
30. Kim JY, Song HR, Taylor BL, Carre IA (2003) Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY. EMBO J 22: 935-944 (Pubitemid 36227795)
31. Kim TH, Kim BH, Yahalom A, Chamovitz DA, von Arnim AG (2004) Translational regulation via 50 mRNA leader sequences revealed by mutational analysis of the Arabidopsis translation initiation factor subunit eIF3h. Plant Cell 16: 3341-3356 (Pubitemid 41096010)
32. Lackner DH, Bahler J (2008) Translational control of gene expression from transcripts to transcriptomes. Int Rev Cell Mol Biol 271: 199-251
33. Lackner DH, Beilharz TH, Marguerat S, Mata J, Watt S, Schubert F, Preiss T, Bahler J (2007) A network of multiple regulatory layers shapes gene expression in fission yeast. Mol Cell 26: 145-155 (Pubitemid 46550937)
34. Lin JF, Wu SH (2004) Molecular events in senescing Arabidopsis leaves. Plant J 39: 612-628
35. Matsuura H, Ishibashi Y, Shinmyo A, Kanaya S, Kato K (2010) Genome-wide analyses of early translational responses to elevated temperature and high salinity in Arabidopsis thaliana. Plant Cell Physiol 51: 448-462
36. McKim SM, Durnford DG (2006) Translational regulation of lightharvesting complex expression during photoacclimation to high-light in Chlamydomonas reinhardtii. Plant Physiol Biochem 44: 857-865 (Pubitemid 44920455)
37. Melamed D, Arava Y (2007) Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays. Methods Enzymol 431: 177-201
38. Melamed D, Pnueli L, Arava Y (2008) Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA 14: 1337-1351 (Pubitemid 351872191)
39. Molina C, Grotewold E (2005) Genome wide analysis of Arabidopsis core promoters. BMC Genomics 6: 25
40. Mussgnug JH, Wobbe L, Elles I, Claus C, Hamilton M, Fink A, Kahmann U, Kapazoglou A, Mullineaux CW, Hippler M, Nickelsen J, Nixon PJ, Kruse O (2005) NAB1 is an RNA binding protein involved in the light-regulated differential expression of the light-harvesting antenna of Chlamydomonas reinhardtii. Plant Cell 17: 3409-3421
41. Mustroph A, Zanetti ME, Jang CJ, Holtan HE, Repetti PP, GalbraithDW, Girke T, Bailey-Serres J (2009) Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci USA 106: 18843-18848
42. Narsai R, Howell KA, Millar AH, O'Toole N, Small I, Whelan J (2007) Genome-wide analysis of mRNAdecay rates and their determinants in Arabidopsis thaliana. Plant Cell 19: 3418-3436
43. Nicolai M, Roncato MA, Canoy AS, Rouquie D, Sarda X, Freyssinet G, Robaglia C (2006) Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol 141: 663-673 (Pubitemid 43974559)
44. Parker R, Sheth U (2007) P bodies and the control of mRNA translation and degradation. Mol Cell 25: 635-646 (Pubitemid 46341926)
45. Petracek ME, Dickey LF, Huber SC, Thompson WF (1997) Lightregulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis. Plant Cell 9: 2291-2300 (Pubitemid 28174063)
46. Piques M, Schulze WX, Hohne M, Usadel B, Gibon Y, Rohwer J, Stitt M (2009) Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol 5: 314
47. Pomeranz MC, Hah C, Lin PC, Kang SG, Finer JJ, Blackshear PJ, Jang JC (2010) The Arabidopsis tandem zinc finger protein AtTZF1 traffics between the nucleus and cytoplasmic foci and binds both DNA and RNA. Plant Physiol 152: 151-165
48. Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, Von Arnim AG (2010) The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames. RNA 16: 748-761
49. Schwechheimer C, Deng XW (2000) The COP/DET/FUS proteinsregulators of eukaryotic growth and development. Semin Cell Dev Biol 11: 495-503 (Pubitemid 32118755)
50. Shama S, Meyuhas O (1996) The translational cis-regulatory element of mammalian ribosomal protein mRNAs is recognized by the plant translational apparatus. Eur J Biochem 236: 383-388 (Pubitemid 26098819)
51. Sherameti I, Nakamura M, Yamamoto YY, Pfannschmidt T, Obokata J, Oelmuller R (2002) Polyribosome loading of spinach mRNAs for photosystem I subunits is controlled by photosynthetic electron transport. Plant J 32: 631-639 (Pubitemid 36010870)
52. Sormani R, Delannoy E, Lageix S, Bitton F, Lanet E, Saez-Vasquez J, Deragon JM, Renou JP, Robaglia C (2011) Sublethal cadmium intoxication in Arabidopsis thaliana impacts translation at multiple levels. Plant Cell Physiol 52: 436-447
53. Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E (2005) Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol 138: 757-766 (Pubitemid 43793156)
54. Tepperman JM, Hudson ME, Khanna R, Zhu T, Chang SH, Wang X, Quail PH (2004) Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-lightregulated gene expression during seedling de-etiolation. Plant J 38: 725-739 (Pubitemid 38693453)
55. Tepperman JM, Zhu T, Chang HS, Wang X, Quail PH (2001) Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci USA 98: 9437-9442 (Pubitemid 32743935)
56. Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE (2004) Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics 3: 960-969 (Pubitemid 40361231)
57. Tremousaygue D, Manevski A, Bardet C, Lescure N, Lescure B (1999) Plant interstitial telomere motifs participate in the control of gene expression in root meristems. Plant J 20: 553-561
58. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121 (Pubitemid 32397092)
59. Vogel C, Abreu Rde S, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO (2010) Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol 6: 400
60. Wang H, Deng XW (2002) Phytochrome signaling mechanism. In The Arabidopsis Book, Somerville CR, Meyerowitz EM (eds), Rockville, MD: American Society of Plant Biologists
61. Wu JF, Wang Y, Wu SH (2008) Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering. Plant Physiol 148: 948-959 (Pubitemid 352847551)
62. Yahalom A, Kim TH, Roy B, Singer R, von Arnim AG, Chamovitz DA (2008) Arabidopsis eIF3e is regulated by the COP9 signalosome and has an impact on development and protein translation. Plant J 53: 300-311