Microarray analysis of mRNA translation state in Arabidopsis thaliana

The synthesis of proteins – translation – is one of the cellular processes that consume a great deal of energy. Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different stresses and environmental and growth signals. Similar assays have revealed how translation of specific mRNAs is perturbed by genetic mutations in eukaryotic translation initiation factors (eIFs). I performed genome-wide analyses of translation state in A. thaliana seedlings with mutant genotypes for a specific eIF (subunit h of eIF3) and the large ribosomal protein, L24 (RPL24B). Using data from prior microarray analysis of polysome-bound (polysomal, PL) and free or monosomal (non-polysomal, NP) mRNA pools, we identified a total of 155 and 388 mRNAs that are translationally regulated by mutation in rpl24b and eIF3h, respectively. These data bolster the conclusion that RPL24 and eIF3h play similar but nonidentical regulatory roles in eukaryotic translation. Moreover, by comparing 12 bona fide identical wild-type replicates, we found that 20% of mRNAs have unusually high stochastic variation in their translation state. These mRNAs tend to be functionally associated with responses to the environment. Finally, we performed a meta-analysis of translation data from this laboratory and in the public domain to compare changes in translation state under ten different environmental conditions and mutant genotypes. A large proportion of Arabidopsis mRNAs change their translation state in at least one experiment. We see evidence that a large number of mRNAs are translationally coregulated under a subset of environmental conditions. For example, many mRNAs encoding ribosomal proteins (RPs) and ribosome-associated proteins cluster together through rpl24b, eif3h, herbicide, diurnal cycle, darkness and hypoxia experiments providing new evidence that these mRNAs form a regulon of translational control. However, many of the generally coregulated mRNAs seem to break away from the pack under one or more specific environmental conditions. These data begin to uncover the complex landscape of translational control in Arabidopsis.