mRNA sequence features that contribute to translational regulation in Arabidopsis

Nucleic Acids Research

Volumn 33, Issue 3, 2005, Pages 955-965

  Kawaguchi, Riki ^a,b   Bailey Serres, Julia ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; MESSENGER RNA; NUCLEOTIDE; PLANT RNA;

5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; CODON; CONTROLLED STUDY; DEHYDRATION; DNA MICROARRAY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLANT GROWTH; PLANT LEAF; POLYSOME; PRIORITY JOURNAL; RIBOSOME; RNA SEQUENCE; RNA TRANSLATION; TRANSCRIPTION REGULATION; 3' UNTRANSLATED REGION; CHEMISTRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PROTEIN SYNTHESIS; REGULATORY RNA SEQUENCE; START CODON;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ARABIDOPSIS; CODON; CODON, INITIATOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; POLYRIBOSOMES; PROTEIN BIOSYNTHESIS; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RIBOSOMES; RNA, MESSENGER; RNA, PLANT;

EID: 13944270653     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki240     Document Type: Article

References (68)

1. Gutierrez,R.A., Ewing,R.M., Cherry,J.M. and Green,P.J. (2002) Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc. Natl Acad. Sci. USA, 99, 11513-11518.
2. Arava,Y., Wang,Y., Storey,J.D., Liu,C.L., Brown,P.O. and Herschlag,D. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 100, 3889-3894.
3. Carter,M.S., Kuhn,K.M. and Sarnow,P. (2000) Cellular internal ribosome entry site elements and the use of cDNA microarrays in their investigation. In Sonenberg,N., Hershey,J.W.B. and Mathews,M.B. (eds), Translational Control of Gene Expression. Cold Spring Harbor Laboratory Press, NY, pp. 615-635.
4. Diehn,M., Eisen,M.B., Botstein,D. and Brown,P.O. (2000) Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nature Genet., 25, 58-62.
5. Grolleau,A., Bowman,J., Pradet-Balade,B., Puravs,E., Hanash,S., Garcia-Sanz,J.A. and Beretta,L. (2002) Global and specific translational control by rapamycin in T cells uncovered by microarrays and proteomics. J. Biol. Chem., 277, 22175-22184.
6. Johannes,G., Carter,M.S., Eisen,M.B., Brown,P.O. and Sarnow,P. (1999) Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl Acad. Sci. USA, 9, 13118-13123.
7. Kawaguchi,R., Girke,T., Bray,E.A. and 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.
8. Kuhn,K.M., DeRisi,J.L., Brown,P.O. and Sarnow,P. (2001) Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol., 21, 916-927.
9. Pradet-Balade,B., Boulme,F., Beug,H., Mullner,E.W. and Garcia-Sanz,J.A. (2001) Translation control: Bridging the gap between genomics and proteomics? Trends Biochem. Sci., 26, 225-229.
10. Zong,Q., Schummer,M., Hood,L. and Morris,D.R. (1999) Messenger RNA translation state: The second dimension of high-throughput expression screening. Proc. Natl Acad. Sci. USA, 96, 10632-10636.
11. MacKay,V.L., Li,X., Flory,M.R., Turcott,E., Law,G.L., Serikawa,K.A., Xu,X.L., Lee,H., Goodlett,D.R., Aebersold,R., Zhao,L.P. and Morris,D.R. (2004) Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: Response of yeast to mating pheromone. Mol. Cell. Proteomics, 3, 478-489.
12. Serikawa,K.A., Xu,X.L., MacKay,V.L., Law,G.L., Zong,Q., Zhao,L.P., Bumgarner,R. and Morris,D.R. (2003) The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae. Mol. Cell. Proteomics, 2, 191-204.
13. Kozak,M. (1991) A short leader sequence impairs the fidelity of initiation by eukaryotic ribosomes. Gene Expr., 1, 111-115.
14. Kozak,M. (1994) Determinants of translational fidelity and efficiency in vertebrate mRNAs. Biochimie, 76, 815-821.
15. Gayen,A.K. and Peffley,D.M. (1995) The length of 5′-untranslated leader sequences influences distribution of 3-hydroxy-3-methylglutaryl-coenzyme A reductase mRNA in polysomes: effects of lovastatin, oxysterols, and mevalonate. Arch. Biochem. Biophys., 322, 475-485.
16. Kozak,M. (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene, 299, 1-34.
17. Kozak,M. (1989) Circumstances and mechanisms of inhibition of translation by secondary structure in eukaryotic mRNAs. Mol. Cell. Biol., 9, 5134-5142.
18. Klaff,P., Riesner,D. and Steger,G. (1996) RNA structure and the regulation of gene expression. Plant Mol. Biol., 32, 89-106.
19. Rogozin,I.B., Kochetov,A.V., Kondrashov,F.A., Koonin,E.V. and Milanesi,L. (2001) Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinformatics, 17, 890-900.
20. Kawaguchi,R. and Bailey-Serres,J. (2002) Regulation of translational initiation in plants. Curr. Opin. Plant Biol., 5, 460-465.
21. Vilela,C. and McCarthy,J.E. (2003) Regulation of fungal gene expression via short open reading frames in the mRNA 5′ untranslated region. Mol. Microbiol., 49, 859-867.
22. Joshi,C.P., Zhou,H., Huang,X. and Chiang,V.L. (1997) Context sequences of translation initiation codon in plants. Plant Mol. Biol., 35 993-1001.
23. Preiss,T., Baron-Benhamou,J., Ansorge,W. and Hentze,M.W. (2003) Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nature Struct. Biol. 10, 1039-1047.
24. Kawaguchi,R., Bray,E.A. and Bailey-Serres,J. (2003) Water-deficit-induced translational control in Nicotiana tabacum. Plant Cell Environ., 26, 221-229.
25. Zhu,J., Spencer,E.D. and Kaspar,R.L. (2003) Differential translation of TOP mRNAs in rapamycin-treated human B lymphocytes. Biochim. Biophys. Acta., 1628, 50-55.
26. Caminci,P., Waki,K., Shiraki,T., Konno,H., Shibata,K., Itoh,M., Aizawa,K., Arakawa,T., Ishii,Y., Sasaki,D. et al. (2003) Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Res., 13, 1273-1289.
27. Haas,B.J., Volfovsky,N., Town,C.D., Troukhan,M., Alexandrov,N., Feldmann,K.A., Flavell,R.B., White,O. and Salzberg,S.L. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol., 3, 1-12.
28. Seki,M., Narusaka,M., Kamiya,A., Ishida,J., Satou,M., Sakurai,T., Nakajima,M., Enju,A., Akiyama,K, Oono,Y. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science, 296, 141-145.
29. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
30. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
31. Suzuki,Y., Yoshitomo-Nakagawa,K., Maruyama,K., Suyama,A. and Sugano,S. (2000) Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library. Gene, 200, 149-156.
32. Mazumder,B., Seshadri,V. and Fox,P.L. (2003) Translational control by the 3′-UTR: The ends specify the means. Trends Biochem. Sci., 28, 91-98.
33. Kozak,M. (1980) Evaluation of the "scanning model" for initiation of protein synthesis in eucaryotes. Cell, 22, 7-8.
34. Preiss,T. and Hentze,M.W. (2003) Starting the protein synthesis machine: eukaryotic translation initiation. BioEssays, 25, 1201-1211.
35. Zuker,M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.
36. Gallie,D.R., Ling,J., Niepel,M., Morley,S.J. and Pain,V.M. (2000) The role of 5′-leader length, secondary structure and PABP concentration on cap and poly(A) tail function during translation in Xenopus oocytes. Nucleic Acids Res., 28, 2943-2953.
37. Peri,S. and Pandey,A. (2001) A reassessment of the translation initiation codon in vertebrates. Trends Genet., 17, 685-687.
38. Joshi,C.P. (1987) An inspection of the domain between putative TATA box and translational start site in 79 plant genes. Nucleic Acids Res. 16, 6643-6653.
39. Gallie,D.R. (2002) Protein-protein interactions required during translation. Plant Mol. Biol., 50, 949-970.
40. Bailey-Serres,J. (1999) Selective translation of cytoplasmic mRNAs in plants. Trends Plant Sci., 4, 142-148.
41. Flexas,J. and Medrano,H. (2002) Drought-inhibition of photosynthesis in C3 plants: Stomatal and non-stomatal limitations revisited. Ann. Bot. 89, 183-189.
42. Gimenez,C., Mitchell,V.J. and Lawlor,D.W. (1992) Regulation of photosynthetic rate of low sunflower hybrids under water stress. Plant Physiol., 98, 516-524.
43. Lukaszewicz,M., Feuermannl,M., Jerouville,B., Stas,A. and Boutry,M. (2000) In vivo evaluation of the context sequence of the translation initiation codon in plants. Plant Sci., 154, 89-98.
44. Taylor,J.L., Jones,J.D.G., Sandler,S., Mueller,G.M., Bedbrook,J. and Dunsmuir,P. (1987) Optimizing the expression of chimeric genes in plant cells. Mol. Gen. Genet., 210, 572-577.
45. Guerineau,F., Lucy,A. and Mullineaux,P. (1992) Effect of two consensus sequences preceding the translational initiator codon on gene expression in plant protoplasts. Plant Mol. Biol., 18, 815-818.
46. Yoshida,S., Ito,M., Callis,J., Nishida,I. and Watanabe,A. (2002) A delayed leaf senescence mutant is defective in arginyl-tRNA:pRotein arginyltransferase, a component of the N-end rule pathway in Arabidopsis. Plant J., 32, 129-137.
47. Tanguay,R.L. and Gallie,D.R. (1996) Translational efficiency is regulated by the length of the 3′ untranslated region. Mol. Cell. Biol., 16, 146-156.
48. Derrigo,M., Cestelli,A., Savettieri,G. and Di Liegro,I. (2000) RNA-protein interactions in the control of stability and localization of messenger RNA. Int. J. Mol. Med., 5, 111-123.
49. Macdonald,P. (2001) Diversity in translational regulation. Curr. Opin. Cell Biol., 13, 326-331.
50. Bailey,T.L. and Elkan,C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 21-29.
51. Hu,Y.J. (2003) GPRM: A genetic programming approach to finding common RNA secondary structure elements. Nucleic Acids Res., 31, 3446-3449.
52. Gorodkin,J., Stricklin,S.L. and Stormo,G.D. (2001) Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res., 29, 2135-2144.
53. Wolffe,A.P. and Meric,F. (1996) Coupling transcription to translation: A novel site for the regulation of eukaryotic gene expression. Int. J. Biochem. Cell. Biol., 28, 247-257.
54. Hirose,Y. and Manley,J.L. (2000) RNA polymerase II and the integration of nuclear events. Genes Dev., 14, 1415-1429.
55. Mazan-Mamczarz,K., Galban,S., Lopez de Silanes,I., Martindale,J.L., Atasoy,U., Keene,J.D. and Gorospe,M. (2003) RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation. Proc. Natl Acad. Sci. USA, 100, 8354-8359.
56. Proudfoot,N.J., Furger,A. and Dye,M.J. (2002) Integrating mRNA processing with transcription. Cell, 108, 501-512.
57. Rosonina,E., Bakowski,M.A., McCracken,S. and Blencowe,B.J. (2003) Transcriptional activators control splicing and 3′-end cleavage levels. J. Biol. Chem., 278, 43034-43040.
58. Manley,J.L. (2002) Nuclear coupling: RNA processing reaches back to transcription. Nature Struct. Biol., 9, 790-791.
59. Wang,Y., Newton,D.C., Robb,G.B., Kau,C.L., Miller,T.L., Cheung,A.H., Hall,A.V., VanDamme,S., Wilcox,J.N. and Marsden,P.A. (1999) RNA diversity has profound effects on the translation of neuronal nitric oxide synthase. Proc. Natl Acad. Sci. USA, 96, 12150-12155.
60. Pozner,A., Goldenberg,D., Negreanu,V., Le,S.Y., Elroy-Stein,O., Levanon,D. and Groner,Y. (2000) Transcription-coupled translation control of AML1/RUNX1 is mediated by cap- and internal ribosome entry site-dependent mechanisms. Mol. Cell. Biol., 20, 2297-2307.
61. Tanaka,M., Ito,S. and Kiuchi,K. (2001) The 5′-untranslated region of the mouse glial cell line-derived neurotrophic factor gene regulates expression at both the transcriptional and translational levels. Brain Res. Mol. Brain Res., 91, 81-95.
62. Gayen,A.K. and Peffley,D.M. (1995) The length of 5′-untranslated leader sequences influences distribution of 3-hydroxy-3-methylglutaryl-coenzyme A reductase mRNA in polysomes: effects of lovastatin, oxysterols, and mevalonate. Arch. Biochem. Biophys., 322, 475-485.
63. Larsen,L.K., Amri,E.Z., Mandrup,S., Pacot,C. and Kristiansen,K. (2002) Genomic organization of the mouse peroxisome proliferator-activated receptor beta/delta gene: Alternative promoter usage and splicing yield transcripts exhibiting differential translational efficiency. Biochem. J., 366, 767-775.
64. Arora,S. and Chauhan,S.S. (2002) Identification and characterization of a novel human cathepsin L splice variant. Gene, 293, 123-131.
65. Mironov,A.A., Fickett,J.W. and Gelfand,M.S. (1999) Frequent alternative splicing of human genes. Genome Res., 9, 1288-1293.
66. Kozak,M. (2001) New ways of initiating translation in eukaryotes? Mol. Cell. Biol., 21, 1899-1907.
67. Li,J., Kinoshita,T., Pandey,S., Ng,C.K., Gygi,S.P., Shimazaki,K. and Assmann,S.M. (2002) Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase. Nature, 418, 793-797.
68. Hugouvieux,V., Kwak,J.M. and Schroeder,J.I. (2001) An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis. Cell, 106, 477-487.