Hostname: page-component-848d4c4894-nmvwc Total loading time: 0 Render date: 2024-07-01T12:10:21.126Z Has data issue: false hasContentIssue false
  • English
  • Français

Analysis of plant mRNA upstream open reading frames

Published online by Cambridge University Press:  12 February 2007

Jin Yong-Feng ,
Jin Hui-Qing ,
Zhou Ping  and
Bian Teng-Fei
Jin Yong-Feng*
Affiliation:
Institute of Biochemistry, Zhejiang University, Hangzhou 310029, China
Jin Hui-Qing
Affiliation:
Institute of Biochemistry, Zhejiang University, Hangzhou 310029, China
Zhou Ping
Affiliation:
Institute of Vegetables, Zhejiang Agriculture Academy, Hangzhou 310021, China
Bian Teng-Fei
Affiliation:
Institute of Biochemistry, Zhejiang University, Hangzhou 310029, China
*
*Corresponding author: Email: jinyf@zju.edu.cn
Get access Rights & Permissions [Opens in a new window]

Abstract

Upstream open reading frames (uORFs) in 5′-untranslated regions (5′-UTRs) of eukaryotic mRNAs play an important role in translation efficiency. Computational analysis of the upstream ATG (uATG) and uORFs of 5′-UTRs of plant mRNAs, adopted from the nucleotide sequence databank, was carried out. Statistical analysis revealed that up to 18% of 5′-UTRs contain uATG, which is much higher than the earlier estimate. Among them, about 50% of the genes have one uATG and nearly 20% of them have two uATGs. About 85% of uORFs are non-overlapping. Thirty per cent of uORF peptides comprise 1–5 aa, and about 80% of uORFs fall in the range of below 20 aa. Sequences flanking the uATG codon differ strikingly from the functional initiation codon and the uATG triplet is more frequently located in a non-optimal context. Consensus sequences of the ATG codon context of mRNA with and without uATG are similar, whereas the ATG codon context of mRNA without uATG is more frequently located in an optimal context than is mRNA with uATG. Most mRNAs with uATGs are possibly related to regulatory functions. In addition, most mRNA uORFs have no similarity between plant species whereas sequences of a few uORFs are highly conserved. For example, mRNA uORFs encoding S-adenosyl-l-methionine decarboxylase (AdoMetDC) share 75–100% homology between plant species, which is much more conserved than AdoMetDC protein.

Keywords

upstream ATG codonupstream open reading frameplantsstatistical analysis
Type
Research Article
Information
Chinese Journal of Agricultural Biotechnology , Volume 2 , Issue 1 , April 2005 , pp. 59 - 66
Copyright
Copyright © China Agricultural University and Cambridge University Press 2005

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Arrick, BA, Lee, AL, Grendell, RL and Derynck, R (1991) Inhibition of translation of transforming growth factor-beta 3 mRNA by its 5′ untranslated region. Molecular and Cellular Biology 11: 4306–4313.Google ScholarPubMed
Bih, FY, Wu, SS, Ratnayake, C, Walling, LL, Nothnagel, EA and Huang, AH (1999) The predominant protein on the surface of maize pollen is an endoxylanase synthesized by a tapetum mRNA with a long 5′ leader. Journal of Biological Chemistry 274: 22884–22894.CrossRefGoogle ScholarPubMed
Chang, KS, Lee, SH, Hwang, SB and Park, KY (2000) Characterization and translational regulation of the arginine decarboxylase gene in carnation (Dianthus caryophyllus L.). Plant Journal 24: 45–56.CrossRefGoogle ScholarPubMed
Chen, D and Patton, JT (2001) Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5′-RACE and primer extension. Biotechniques 30: 574–580.CrossRefGoogle Scholar
Curie, C and McCormick, S (1997) A strong inhibitor of gene expression in the 5’ untranslated region of the pollen-specific LAT59 gene to tomato. Plant Cell 9: 2025–2036.Google Scholar
Gallie, DR, Ling, J, Niepel, M, Morley, SJ and Pain, VM (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 Research 28: 2943–2953.CrossRefGoogle Scholar
Geballe, AP and Sachs, MS (2000) Translational control by upstream open reading frame. In: SonenbergN, N,, Hershey, JWB and Mathews, MB (editors) Translational Control of Gene Expression. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 595–614.Google Scholar
Hulzink, RJ, de Groot, PF, Croes, AF, Quaedvlieg, W, Twell, D, Wullems, GJ et al. , (2002) The 5'-untranslated region of the ntp303 gene strongly enhances translation during pollen tube growth, but not during pollen maturation. Plant Physiology 129: 342–353.CrossRefGoogle Scholar
Hulzink, RJ, Weerdesteyn, H, Croes, AF, Gerats, T, van Herpen, MM, van Helden, J (2003) In silico identification of putative regulatory sequence elements in the 5′-untranslated region of genes that are expressed during male gametogenesis. Plant Physiology 132: 75–83.CrossRefGoogle ScholarPubMed
Jin, XP, Turcott, E, Englehardt, S, Mize, G and Morris, DR (2003) The two upstream open reading frames of oncogene mdm2 have different translational regulatory properties. Journal of Biological Chemistry 278: 25716–25721.CrossRefGoogle ScholarPubMed
Joshi, CP (1987) An inspection of the domain between putative TATA box and translation start site in 79 plant genes. Nucleic Acids Research 15: 6643–6652.CrossRefGoogle ScholarPubMed
Kozak, M (1987a) An analysis of 5′ noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Research 15: 8125–8148.CrossRefGoogle ScholarPubMed
Kozak, M (1987b) At least 6 nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. Journal of Molecular Biology 196: 947–950.CrossRefGoogle Scholar
Kozak, M (2001) New ways of initiating translation in eukaryotes? Molecular and Cellular Biology 21: 1899–1907.CrossRefGoogle ScholarPubMed
Krummeck, G, Gottenof, T and Rodel, G (1991) AUG codons in the RNA leader sequences of the yeast PET genes CBS1 and SCO1 have no influence on translation efficiency. Current Genetics 20: 465–469.CrossRefGoogle ScholarPubMed
Lutcke, HA, Chow, KC, Mickel, FS, Moss, KA, Kern, HF and Scheele, GA (1987) Selection of AUG initiation codons differs in plants and animals. EMBO Journal 6: 43–48.CrossRefGoogle ScholarPubMed
Seki, M, Narusaka, M, Kamiya, A, Ishida, J, Satou, M, Sakurai, T et al. , (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296: 141–145.CrossRefGoogle ScholarPubMed
Vilela, C, Linz, B, Rodrigues-Pousada, C and McCarthy, JE (1998) The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability. Nucleic Acids Research 26: 1150–1159.CrossRefGoogle ScholarPubMed
Wang, L and Wessler, SR (1998) Inefficient reinitiation is responsible for upstream open reading frame-mediated translational repression of the maize R gene. Plant Cell 10: 1733–1746.Google ScholarPubMed
Wang, L and Wessler, SR (2001) Role of mRNA secondary structure in translational repression of the maize transcriptional activator Lc(1,2). Plant Physiology 125: 1380–1387.CrossRefGoogle Scholar
Wu, J and Miller, BL (1997) Aspergillus asexual reproduction and sexual reproduction are differentially affected by transcriptional and translational mechanisms regulating stunted gene expression. Molecular and Cellular Biology 17: 6191–6201.CrossRefGoogle ScholarPubMed
Yaman, I, Fernandez, J, Liu, H, Caprara, M, Komar, AA, Koromilas, AE et al. , (2003) The zipper model of translational control: a small upstream ORF is the switch that controls structural remodeling of an mRNA leader. Cell 113: 519–531.CrossRefGoogle ScholarPubMed