mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases

Abstract

SummaryTranslation and decay of eukaryotic mRNAs is controlled by shortening of the poly(A) tail and release of the poly(A)-binding protein Pab1/PABP. The Ccr4-Not complex contains two exonucleases—Ccr4 and Caf1/Pop2—that mediate mRNA deadenylation. Here, using a fully reconstituted biochemical system with proteins from the fission yeast Schizosaccharomyces pombe, we show that Pab1 interacts with Ccr4-Not, stimulates deadenylation, and differentiates the roles of the nuclease enzymes. Surprisingly, Pab1 release relies on Ccr4 activity. In agreement with this, in vivo experiments in budding yeast show that Ccr4 is a general deadenylase that acts on all mRNAs. In contrast, Caf1 only trims poly(A) not bound by Pab1. As a consequence, Caf1 is a specialized deadenylase required for the selective deadenylation of transcripts with lower rates of translation elongation and reduced Pab1 occupancy. These findings reveal a coupling between the rates of translation and deadenylation that is dependent on Pab1 and Ccr4-Not.

The Dynamics of Cytoplasmic mRNA Metabolism

“…Despite the utility of our mathematical model, it did not capture some finer details of mRNA metabolism. For example, it was not designed to model the burst of deadenylation that typically accompanies loss of each terminal PABPC molecule (Webster et al, 2018). However, when considering the aggregate behavior of multiple mRNAs from the same gene, these bursts become blurred, with some molecules in the burst phase and others between bursts.…”

Role of the Citrus sinensis RNA deadenylase CsCAF1 in citrus canker resistance

“…It should also be noted that PthA4 binds poly(U) RNA and is structurally related to PUF (pumelo and FBF) proteins, which recognize U‐rich sequences at the 3′‐end of mRNAs and are known to interact with CAF1 and recruit the CCR4‐NOT complex to modulate mRNA stability and translation (Goldstrohm et al , ; Filipovska and Rackham, ; de Souza et al , ; Van Etten et al , ; Wang et al, ). Thus, given that the CCR4‐NOT complex is a macromolecular machine that connects transcription elongation to translation (Babbarwal et al , ; Gupta et al , ; Villanyi et al , ; Webster et al , ; Yi et al , ), it seems reasonable to suggest that PthA4 could modulate its activity to enhance transcription and translation of citrus canker susceptibility genes.…”

“…The miRNA‐mediated deadenylation, on the other hand, required CAF1 deadenylase activity and its interaction with poly(A)‐binding proteins (PABPs) (Behm‐Ansmant et al , ; Fabian et al , ; Flamand et al , ; Piao et al , ). Importantly, recent studies in yeast using reconstituted CCR4‐NOT complex have revealed that while CCR4 is a general deadenylase that degrades PABP1‐bound poly(A) tails, CAF1 is required for the selective deadenylation of transcripts not bound by PABP1 and with lower rates of translation elongation (Webster et al , ; Yi et al , ). Thus, as new evidence emerges, the CCR4‐NOT complex has been regarded as a macromolecular structure that not only connects transcription to translation, but also determines the translational capacity of the cell during transcription elongation (Babbarwal et al , ; Gupta et al , ; Villanyi et al , ; Webster et al , ; Yi et al , ).…”

Connections between 3′ end processing and DNA damage response: Ten years later

“…These mRNA 3′ end modifications confer stability and translational efficiency to the transcripts (Bentley, ; Jalkanen, Coleman, & Wilusz, ; Proudfoot, ; Y. Shi & Manley, ). Conversely, removal of the poly(A) tail by deadenylation can signal mRNA decay and/or translational repression of poly(A) + transcripts (Aström, Aström, & Virtanen, ; Mayya & Duchaine, ; Nicholson & Pasquinelli, ; Webster et al, ; Yi et al, ; X. Zhang, Kleiman, & Devany, ).These modifications in the 3′ end are controlled by cis ‐acting elements present in the mRNA and trans ‐acting regulatory factors, such as RNA binding proteins (RBPs) and RNAs with complementary base‐pairing, such as, but not restricted to, microRNAs (miRNAs). For better understanding of basic aspects of 3′ end formation and its regulation, we suggest the reading of comprehensive reviews that have covered this topic (Hollerer, Grund, Hentze, & Kulozik, ; Neve, Patel, Wang, Louey, & Furger, ; Y. Shi & Manley, ).…”

“…Shi & Manley, 2015). Conversely, removal of the poly(A) tail by deadenylation can signal mRNA decay and/or translational repression of poly(A) + transcripts (Aström, Aström, & Virtanen, 1991;Mayya & Duchaine, 2019;Nicholson & Pasquinelli, 2019;Webster et al, 2018;Yi et al, 2018;X. Zhang, Kleiman, & Devany, 2014).These modifications in the 3 0 end are controlled by cis-acting elements present in the mRNA and trans-acting regulatory factors, such as RNA binding proteins (RBPs) and RNAs with complementary base-pairing, such as, but not restricted to, microRNAs (miRNAs).…”