Divergence of the expression and subcellular localization of CCR4-associated factor 1 (CAF1) deadenylase proteins in Oryza sativa

Abstract

Deadenylation, also called poly(A) tail shortening, is the first, rate-limiting step in the general cytoplasmic mRNA degradation in eukaryotic cells. The CCR4-NOT complex, containing the two key components carbon catabolite repressor 4 (CCR4) and CCR4-associated factor 1 (CAF1), is a major player in deadenylation. CAF1 belongs to the RNase D group in the DEDD superfamily, and is a protein conserved through evolution from yeast to humans and plants. Every higher plant, including Arabidopsis and rice, contains a CAF1 multigene family. In this study, we identified and cloned four OsCAF1 genes (OsCAF1A, OsCAF1B, OsCAF1G, and OsCAF1H) from rice. Four recombinant OsCAF1 proteins, rOsCAF1A, rOsCAF1B, rOsCAF1G, and rOsCAF1H, all exhibited 3'-5' exonuclease activity in vitro. Point mutations in the catalytic residues of each analyzed recombinant OsCAF1 proteins were shown to disrupt deadenylase activity. OsCAF1A and OsCAF1G mRNA were found to be abundant in the leaves of mature plants. Two types of OsCAF1B mRNA transcript were detected in an inverse expression pattern in various tissues. OsCAF1B was transient, induced by drought, cold, abscisic acid, and wounding treatments. OsCAF1H mRNA was not detected either under normal conditions or during most stress treatments, but only accumulated during heat stress. Four OsCAF1-reporter fusion proteins were localized in both the cytoplasm and nucleus. In addition, when green fluorescent protein fused with OsCAF1B, OsCAF1G, and OsCAF1H, respectively, fluorescent spots were observed in the nucleolus. OsCAF1B fluorescent fusion proteins were located in discrete cytoplasmic foci and fibers. We present evidences that OsCAF1B colocalizes with AtXRN4, a processing body marker, and AtKSS12, a microtubules maker, indicating that OsCAF1B is a component of the plant P-body and associate with microtubules. Our findings provide biochemical evidence that OsCAF1 proteins may be involved in the deadenylation in rice. The unique expression patterns of each OsCAF1 were observed in various tissues when undergoing abiotic stress treatments, implying that each CAF1 gene in rice plays a specific role in the development and stress response of a plant.

Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection

“…In addition to validating our GWAS mapping results, many of the identified RMC LTSS -QTL that occur near previously mapped seedling chilling tolerance QTL help narrow down the QTL region and provide further support of locations where chilling tolerance genes occur. Of particular interest are the previously mentioned OsWRKY76 and Os09g24440 near qLTSS9-2 , and qLTSS4-3 , as it is 280,000 bp away from OsCAF1B , a gene involved in RNA processing previously reported to be cold induced (Chou et al, 2014; Supplementary Table S3). …”

“…9 reported as “ Survival Rate after Natural Chilling Stress ” Locus 100 (Lv et al, 2016). Eight of the nine QTL had previously annotated cold ( OsCAF1B ; Chou et al, 2014) and other abiotic stress tolerance genes such as the ABA receptor OsPYL/RCAR5 (Kim et al, 2014) within 1.5 Mb of the QTL markers (Supplementary Table S3), which might associate, at least in part, with genes that have a positive effect on chilling acclimation. The type of chilling acclimation potential addressed here is associated with low temperature germination, which might be different from exposing young seedlings first to a mild chilling temperature followed by a harsh cold temperature treatment previously shown to have a positive effect for some accessions of both the INDICA and JAPONICA (Mao and Chen, 2012).…”

Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function

“…The EEP domain of OsCCR4s is sufficient for in vitro 39-59 exonuclease activity on poly(A), poly(U), and poly(C) substrates (Chou et al, 2017). Similarly, recombinant OsCAF1A, OsCAF1B, OsCAF1G, and OsCAF1H are 39-59 exonucleases, with at least OsCAF1B associating with XRN4 in PB-like foci (Chou et al, 2014). In yeast and mammals, CAF1 serves as a bridge between CCR4 and NOT1 via interactions between the N-terminal Leu-rich repeat of CCR4 and the MIF4G domain of NOT1.…”

DsCaf1 is involved in environmental stress response of Dunaliella salina

“…For example in Arabidopsis thaliana, PARN is essential for embryogenesis [6,7], response to abscisic acid and salicylic acid [8,9] as well as mitochondrion functions [10]. Caf1 is involved in the responses to both biotic and abiotic stresses in Capsicum annuum, Arabidopsis thaliana and Oryza sativa [11][12][13][14]. Very recently, CCR4 has been shown to affect the sucrose and starch metabolism in Arabidopsis thaliana [15].…”

“…5). Previously Caf1s in Capsicum annuum, Arabidopsis thaliana and Oryza sativa have been shown to respond to both biotic and abiotic signals [11][12][13][14]. Thus it seems that the stress responsive functions of Caf1 are well conserved in the plant kingdom including algae.…”