Open Access Research article

The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant

Bayu Sisay Tiruneh1, Byung-Hoon Kim12, Daniel R Gallie3, Bijoyita Roy14 and Albrecht G von Arnim15*

Author Affiliations

1 Department of Biochemistry, Cellular and Molecular Biology, M407 Walters Life Sciences, The University of Tennessee, Knoxville, TN 37996-0840, USA

2 Department of Natural Science, Albany State University, Albany, GA 31705, USA

3 Department of Biochemistry, 3432 Boyce Hall, University of California, Riverside, CA 92521, USA

4 University of Massachussetts Medical School, Worcester, MA 01655-0122, USA

5 Genome Science and Technology Program, The University of Tennessee, Knoxville, TN 37996, USA

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BMC Biology 2013, 11:123  doi:10.1186/1741-7007-11-123

Published: 30 December 2013

Abstract

Background

Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different environmental stresses and genetic lesions in the translation apparatus. To identify additional features of the global landscape of translational control, we used microarray analysis of polysomal as well as non-polysomal mRNAs to examine the defects in translation in a poly(A) binding protein mutant, pab2 pab8, as well as in a mutant of a large ribosomal subunit protein, rpl24b/shortvalve1.

Results

The mutation of RPL24B stimulated the ribosome occupancy of mRNAs for nuclear encoded ribosomal proteins. Detailed analysis yielded new insights into the translational regulon containing the ribosomal protein mRNAs. First, the ribosome occupancy defects in the rpl24b mutant partially overlapped with those in a previously analyzed initiation factor mutant, eif3h. Second, a group of mRNAs with incomplete coding sequences appeared to be uncoupled from the regulon, since their dependence on RPL24B differed from regular mRNAs. Third, different sister paralogs of the ribosomal proteins differed in their translation state in the wild-type. Some sister paralogs also differed in their response to the rpl24b mutation. In contrast to rpl24b, the pab2 pab8 mutant revealed few gene specific translational defects, but a group of seed storage protein mRNAs were stimulated in their ribosome occupancy. In the course of this work, while optimizing the statistical analysis of ribosome occupancy data, we collected 12 biological replicates of translation states from wild-type seedlings. We defined 20% of mRNAs as having a high variance in their translation state. Many of these mRNAs were functionally associated with responses to the environment, suggesting that subtle variation in the environmental conditions is sensed by plants and transduced to affect the translational efficiency of hundreds of mRNAs.

Conclusions

These data represent the first genome-wide analysis of translation in a eukaryote defective in the large ribosomal subunit. RPL24 and eIF3h play similar but non-identical roles in eukaryotic translation. The data also shed light on the fine structure of the regulon of ribosomal protein mRNAs.

Keywords:
Translation state; Ribosome occupancy; RPL24; PABP; Regulon; Arabidopsis