Abstract
The control of translation in the course of gene expression regulation plays a crucial role in plants’ cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein products in eukaryotic cells, including plants, requires thorough investigation of the regulatory mechanisms of translation. A wide and amazingly complex network of mechanisms decoding the plant genome into proteome challenges researchers to design new methods for genome-wide analysis of translational control, develop computational algorithms detecting regulatory mRNA contexts, and to establish rules underlying differential translation. The aims of this review are to (i) describe the experimental approaches for investigation of differential translation in plants on a genome-wide scale; (ii) summarize the current data on computational algorithms for detection of specific structure–function features and key determinants in plant mRNAs and their correlation with translation efficiency; (iii) highlight the methods for experimental verification of existed and theoretically predicted features within plant mRNAs important for their differential translation; and finally (iv) to discuss the perspectives of discovering the specific structural features of plant mRNA that mediate differential translation control by the combination of computational and experimental approaches.
Highlights
The genomic information in plants, similar to other eukaryotes, is implemented via a successive series of biological processes, including transcription and translation as the key events
This review focuses on the experimental methods for genome-wide analysis of translational control, computational algorithms to search and analyze various regulatory contexts within mRNAs, and approaches for subsequent experimental verification of their correlation with mRNA translation in plants
A comparative testing of all types of reporter constructs has shown that removal of the initiation codon from conserved peptide uORFs (CPuORFs) considerably increases the reporter gene expression; the frameshift mutations in CPuORFs efficiently increase the reporter gene expression, to a lower degree as compared with the removal of initiation codon; while the simultaneous presence of frameshift mutations and absence of the initiation codon have almost no effect on the reporter gene expression. These results clearly demonstrate that (i) the peptide sequences are partially responsible for strong repressive effects of these CPuORFs on the main open reading frames (ORFs) expression; (ii) repression of the main ORF expression depends on CPuORF translation; and (iii) these CPuORFs induce ribosomal arrest and thereby considerably inhibit expression of the main ORF [62]
Summary
The genomic information in plants, similar to other eukaryotes, is implemented via a successive series of biological processes, including transcription and translation as the key events. For example, RNA-Seq and DNA microarrays, have given insight into many key mechanisms involved in transcription regulation in plants: the first stage of gene expression and the easiest to study in terms of experimental methodology. The observed fluctuations in the levels of a transcript do not always lead to changes in the levels of the corresponding protein [1]. This suggests an intricate nature of the mechanisms providing the decoding of a genome, which involve differential transcription, and differential translation
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