Cold shock protein 1 chaperones mRNAs during translation in Arabidopsis thaliana

SUMMARYRNA binding proteins (RBPs) function post-transcriptionally to ﬁne-tune gene regulation. Arabidopsis thali-ana has four Gly-rich, zinc ﬁnger-containing RBPs called cold shock proteins 1–4 (CSP1–CSP4), that possessan evolutionary conserved cold shock domain. Here, we determined that CSP1 associates with polyribo-somes (polysomes) via an RNA-mediated interaction. Both the abundance and polysomal co-fractionation ofCSP1 was enhanced in the cold (4°C), but did not inﬂuence global levels of polysomes, which were mini-mally perturbed by above freezing cold temperatures. Using a polyclonal antiserum, CSP1 was co-immuno-puriﬁed with several hundred transcripts from rosettes of plants cultivated at 23°C or transferred to 4°C for12 h. CSP1-associated mRNAs were characterized by G+C-rich 5′ untranslated regions and gene ontologiesrelated to cellular respiration, mRNA binding and translation. The majority of the CSP1-associated mRNAswere constitutively expressed and stable in the cold. CSP1 abundance was correlated with improved trans-lation of ribosomal protein mRNAs during cold stress and improved maintenance of homeostasis and trans-lation of mRNAs under water-deﬁcit stress. In summary, CSP1 selectively chaperones mRNAs, providingtranslational enhancement during stress.Keywords: translation, RNA binding protein, cold stress, drought stress, ribosomal protein.INTRODUCTIONAbiotic stresses, including low temperatures and waterdeﬁcit, pose a major limitation on plant growth and devel-opment. Some plants can acclimate to cold or freezingtemperatures; however, this usually requires reprogram-ming of gene expression to accumulate freezing protectiveproteins and metabolites (Zhu et al., 2007). Cold stress-induced transcription networks, such as those regulated bythe conserved CBF/DREB1 transcription factors, are wellcharacterized (Liu et al., 1998; Fowler and Thomashow,2002). Similarly, there is knowledge of transcription factor-based networks that reconﬁgure the transcriptome inresponse to water-deﬁcit stress (Yamaguchi-Shinozaki andShinozaki, 2006). However, gene regulation in response toenvironmental stimuli extends beyond the control oftranscription. Regulation at the post-transcriptional levelsduring abiotic stresses includes alternative splicing, miRNA-and siRNA-mediated RNA turnover, and translationalcontrol (Kawaguchi et al., 2004; Kawaguchi and Bailey-Serres,2005; Chinnusamy et al., 2007; Bailey-Serres et al., 2009;Filichkin et al., 2010; Zhu et al., 2011; Ambrosone et al.,2012; Park et al., 2012; Sunkar et al., 2012).The mechanisms that orchestrate gene regulation at thepost-transcriptional level involve hundreds of RNA-bindingproteins (RBPs), which interact with mRNA via RNA bind-ing domains (Bailey-Serres et al., 2009; Lorkovic, 2009).Among the plant RBPs is a small class of cold shock pro-teins (CSPs), containing a specialized DNA/RNA bindingdomain called a cold shock domain (CSD). This domain ofapproximately 70 amino acids includes two consensusRNA binding motifs, and is conserved across organisms(Graumann and Marahiel, 1998). Bacterial CSPs accumu-late to high levels in response to cold shock, and functionas RNA chaperones to destabilize nucleic acid secondarystructure (Sommerville, 1999). They serve to reduce tran-scription anti-termination, enhancing ribosome biogenesisand mRNA translation during conditions of limited proteinsynthesis (Phadtare and Severinov, 2010). CSPs have beenrecognized in representative dicots, monocots and mosses(Karlson et al., 2002; Karlson and Imai, 2003; Chaikam andKarlson, 2008). The Arabidopsis thaliana Columbia (Col-0)genome has four genes that encode a protein with anN-terminal CSD domain, multiple CCHC zinc ﬁngers and