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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
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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

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