mRNA sequence features that contribute to translational regulation in Arabidopsis

Abstract

DNA microarrays were used to evaluate the regulation of the proportion of individual mRNA species in polysomal complexes in leaves of Arabidopsis thaliana under control growth conditions and following a mild dehydration stress (DS). The analysis determined that the percentage of an individual gene transcript in polysomes (ribosome loading) ranged from over 95 to <5%. DS caused a decrease in ribosome loading from 82 to 72%, with maintained polysome association for over 60% of the mRNAs with an increased abundance. To identify sequence features responsible for translational regulation, ribosome loading values and features of full-length mRNA sequences were compared. mRNAs with extreme length or high GU content in the 5′-untranslated regions (5′-UTRs) were generally poorly translated. Under DS, mRNAs with both a high GC content in the 5′-UTR and long open reading frame showed a significant impairment in ribosome loading. Evaluation of initiation A+1UG codon context revealed distinctions in the frequency of adenine in nucleotides −10 to −1 (especially at −4 and −3) in mRNAs with different ribosome loading values. Notably, the mRNA features that contribute to translational regulation could not fully explain the variation in ribosome loading, indicating that additional factors contribute to translational regulation in Arabidopsis.

Plant L10 Ribosomal Proteins Have Different Roles during Development and Translation under Ultraviolet-B Stress

“…Only the RPL10B transcript in the RPL10 family has a 5#TOP sequence (Supplemental Table S4); however, the role of the 5#TOP motif in the regulation of translation has not been demonstrated in plants. The analysis of the features in mRNA sequences responsible for translational regulation in Arabidopsis showed important determinants in the 5# UTR, although probably other unknown mRNA sequence motifs also contribute to differential mRNA translation in plants (Kawaguchi and Bailey-Serres, 2005). Furthermore, it is well known that the amount of mRNA does not necessarily correlate with the abundance of the protein present in plant cells (Kawaguchi et al, 2004;Branco-Price et al, 2008, Mustroph et al, 2009.…”

“…The comparison of total and polysomal mRNA populations showed a significant decrease in polysomal abundance without a concomitant decrease in transcript levels. Transcripts for RPL10A to RPL10C, along with other mRNAs encoding for components of the machinery for the synthesis of cytosolic proteins, show minor changes in transcript accumulation but are decreased in polysomes after hypoxia; this indicates that ribosome biogenesis is restricted under the energy crisis caused by hypoxia and also other stresses such as mild dehydration and Suc starvation (Kawaguchi et al, 2004;Kawaguchi and Bailey-Serres, 2005;BrancoPrice et al, 2008). In conclusion, these observations indicate that RPL10 translation is highly regulated (Branco-Price et al, 2008).…”

A Short Period of Mannitol Stress but Not LiCl Stress Led to Global Translational Repression in Plants

“…2) Recent genome-scale analyses of translation have revealed that translational repression upon salinity stress and the other abiotic stresses can severely restrict gene expression and affect various mRNAs differently. [3][4][5] These findings suggest that global translational repression upon salinity stress is a major mechanism of gene expression control in the plant salinity stress response.…”

Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data

“…In addition, studies in plants have shown that variation in UTR length or structure lead to changes in mRNA accumulation as well as the association of mRNAs with ribosomes [15]. Of the ten oppositely differentially expressed loci identified in the light vs. dark study, five are predicted to have relatively major effects on the amino acid sequence of the encoded protein, including or excluding large proteins segments, while four have more moderate effects on protein structure, changing small protein-coding exons toward the ends of the genes ( Figure S1).…”

“…Then, we selected genes showing at least a twofold change in expression in the light or dark and further analyzed the distribution of log 2 fold change for the other oligo(s) for each gene locus, as shown in Table 1. Validation of expression patterns of candidate genes using RT-PCR For the first-strand cDNA synthesis, 100 ng of mRNAs from the same RNA samples used for the microarray experiments was reverse-transcribed in a total volume of 50 μl that contained 10 ng of oligo (dT) [12][13][14][15][16][17][18] primer, 2.5 mM dNTP, and 100 units of SuperScript™ III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) in reaction buffer supplied by the manufacturer. PCR reactions were performed in 50 μl volumes in solutions containing 1 μl aliquots of the respective cDNA reaction mixture, 0.2 μM of gene-specific primers, 10 mM dNTPs, one unit of Taq DNA polymerase (Invitrogen), and 10× Taq buffer supplied by the manufacturer.…”