Uridylation prevents 3' trimming of oligoadenylated mRNAs

Abstract

Degradation of mRNAs is usually initiated by deadenylation, the shortening of long poly(A) tails to oligo(A) tails of 12–15 As. Deadenylation leads to decapping and to subsequent 5′ to 3′ degradation by XRN proteins, or alternatively 3′ to 5′ degradation by the exosome. Decapping can also be induced by uridylation as shown for the non-polyadenylated histone mRNAs in humans and for several mRNAs in Schizosaccharomyces pombe and Aspergillus nidulans. Here we report a novel role for uridylation in preventing 3′ trimming of oligoadenylated mRNAs in Arabidopsis. We show that oligo(A)-tailed mRNAs are uridylated by the cytosolic UTP:RNA uridylyltransferase URT1 and that URT1 has no major impact on mRNA degradation rates. However, in absence of uridylation, oligo(A) tails are trimmed, indicating that uridylation protects oligoadenylated mRNAs from 3′ ribonucleolytic attacks. This conclusion is further supported by an increase in 3′ truncated transcripts detected in urt1 mutants. We propose that preventing 3′ trimming of oligo(A)-tailed mRNAs by uridylation participates in establishing the 5′ to 3′ directionality of mRNA degradation. Importantly, uridylation prevents 3′ shortening of mRNAs associated with polysomes, suggesting that a key biological function of uridylation is to confer 5′ to 3′ polarity in case of co-translational mRNA decay.

Oligoadenylation of 3′ decay intermediates promotes cytoplasmic mRNA degradation in Drosophila cells

“…Oligo(U) sequences have been found at the ends of mRNA poly(A) tails in S. pombe (Rissland and Norbury 2009;Malecki et al 2013), mammalian cells Lim et al 2014), and Arabidopsis (Sement et al 2013); short C/U tags have been found in Aspergillus (Morozov et al 2010(Morozov et al , 2012. In mammalian cells, mRNAs with short poly(A) tails are preferred as substrates of uridylation over mRNAs with long tails, and the modification destabilizes the RNAs .…”

“…In mammalian cells, mRNAs with short poly(A) tails are preferred as substrates of uridylation over mRNAs with long tails, and the modification destabilizes the RNAs . Evidence has been presented that oligouridylation favors cap hydrolysis (Shen and Goodman 2004;Rissland and Norbury 2009;Sement et al 2013), presumably via binding of the Lsm1-7 complex (Song and Kiledjian 2007). In S. pombe and in mammals, oligouridylation also seems to promote 3 ′ decay (Hoefig et al 2013;Malecki et al 2013;Slevin et al 2014), whereas the opposite may be true in Arabidopsis (Sement et al 2013).…”

“…Evidence has been presented that oligouridylation favors cap hydrolysis (Shen and Goodman 2004;Rissland and Norbury 2009;Sement et al 2013), presumably via binding of the Lsm1-7 complex (Song and Kiledjian 2007). In S. pombe and in mammals, oligouridylation also seems to promote 3 ′ decay (Hoefig et al 2013;Malecki et al 2013;Slevin et al 2014), whereas the opposite may be true in Arabidopsis (Sement et al 2013). Consistent with a role in 3 ′ decay, U residues are added not only to poly(A) tails but also to the upstream fragments generated by siRNAdirected mRNA cleavage in Arabidopsis and mouse cells (Shen and Goodman 2004) and to 3 ′ decay intermediates of mammalian histone mRNAs (Mullen and Marzluff 2008;Hoefig et al 2013;Slevin et al 2014).…”

Insights into the regulation of GPEET procyclin during differentiation from early to late procyclic forms of Trypanosoma brucei

“…Oligo-uridylated transcripts were also identified when a truncated primer was used, however, or a different linker and reverse primer (S.K., unpublished data), arguing against the oligo(U) tails being artifacts. Although we cannot completely rule out alternative explanations for our findings, it is worth mentioning that linker ligation/RT-PCR is the established methodology for detecting non-templated oligo(U) stretches in yeast, Arabidopsis and mammalian cells (for example, [44]). …”

“…Uridylation of both mRNAs and non-coding RNA species like U6 small nucleolar RNA, microRNAs and short interfering RNAs has been reported in various eukaryotes and was mainly implicated in controlling the stability and/or processing of these RNAs [55][56][57][58]. Moreover, it was proposed that cytoplasmic addition of U-tails to mRNAs might protect the 3 end from degradation, and thus participates in establishing a 5 to 3 polarity of mRNA decay [44,58]. It is tempting to speculate that oligo(U) tails of GPEET mRNA elicit a similar degradation mechanism in late procyclic forms.…”