Cold Triggered Paralog Rearrangements Indicate Potential Ribosome Specialization in Arabidopsis thaliana

ABSTRACT: Plant ribosomes are heterogeneous due to genome duplications that resulted in several paralog genes encoding each ribosomal protein (RP). The mainstream view suggests that heterogeneity provides sufficient ribosomes throughout the Arabidopsis lifespan without any functional implications. Nevertheless, genome duplications are known to produce sub- and neofunctionalization of initially redundant genes. Functional divergence of RP paralogs can be considered ribosome specialization if the diversified functions of these paralogs remain within the context of protein translation, especially if RP divergence should contribute to a preferential or ultimately even rigorous selection of transcripts to be translated by a RP-defined ribosome subpopulation. Here we provide evidence that cold acclimation triggers a reprogramming in structural RPs at the transcriptome and proteome level. The reprogramming alters the abundance of RPs or RP paralogs in non-translational 60S large subunits (LSUs) and translational polysome fractions, a phenomenon known as substoichiometry. Cold triggered substoichiometry of ribosomal complexes differ once Arabidopsis REIL-like mediated late maturation step for the LSU is impaired. Interestingly, remodeling of ribosomes after a cold stimulus appears to be significantly constrained to specific spatial regions of the ribosome. The regions that are significantly changed during cold acclimation as judged by transcriptome or proteome data include the polypeptide exit tunnel and the P-Stalk. Both substructures of the ribosome represent plausible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. This work represents a step forward towards understanding heterogeneity and potential specialization of plant ribosomal complexes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Rosette

SUBMITTER: Michal Gorka  

LAB HEAD: Joachim Kopka

PROVIDER: PXD016292 | Pride | 2021-06-28

REPOSITORIES: Pride