Polyadenylation in RNA Degradation Processes in Plants

Abstract

Although polyadenylation is best known for stabilizing eukaryotic mRNAs and promoting their translation, the primordial role of polyadenylation is to target RNAs for degradation by 3¢→5¢ exoribonucleases. This ancient mechanism is conserved among bacteria and eukaryotes, and in plants, polyadenylation-assisted RNA degradation operates in the nucleus, the chloroplast, and the mitochondrion. Polyadenylation-assisted RNA degradation contributes to maturation, turnover, and quality control of a variety of transcripts, the nature of which varies in the different genetic compartments of the plant cell. Moreover, polyadenylation-assisted RNA degradation rapidly removes a large variety of novel transcripts of unknown function that are produced by extensive transcription of extragenic regions, in particular from nuclear and mitochondrial genomes. In this chapter, we review the current knowledge of polyadenylation-assisted RNA degradation in plants, highlighting the different impact of this RNA degradation pathway on the expression of nuclear, plastidial, or mitochondrial genomes.

A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis

“…PAPs and/or PNPase are the enzymes responsible for polyadenylation in plastids of plants and green algae [21,22]. PNPase function was demonstrated in polyadenylation and degradation not only of mRNAs, but also tRNAs and rRNAs [20,23,34]. We failed to identify homologs of the enzymes involved in polyA-degradation pathway in the currently available E. gracilis EST data, but this may be due to an inherent incompleteness of any EST survey based on limited Sanger sequencing of cDNA libraries.…”

“…EgB polyA, cDNA from E. gracilis strain bacillaris synthesized using the oligo(dT) primer; EgB total, cDNA from E. gracilis strain bacillaris synthesized using random hexanucleotide primers; EgZ polyA, cDNA from E. gracilis strain Z synthesized using the oligo(dT) primer; EgZ total, cDNA from E. gracilis strain Z synthesized using random hexanucleotide primers. a signal for exonucleolytic degradation in primary plastids of the green lineage [20][21][22]. Indeed, only incomplete sequences of E. gracilis plastid genes are found in the EST database, suggesting that they may correspond to degradation intermediates.…”

“…Polyadenylation-facilitated RNA degradation in plastids in those species, where it was studied in detail, proceeds in three steps: (i) endonucleolytic cleavage, (ii) polyadenylation of fragments and (iii) exonucleolytic degradation of polyadenylated fragments [20][21][22]24]. The polyA tails can be homopolymeric, composed solely of adenosines, or heteropolymeric composed of all four nucleotides, but with adenosines being the most abundant ones.…”

“…It has been documented in metazoan mitochondria, where it is particularly important for some transcripts by restoring their termination codons [19]. On the other hand, polyadenylation of transcripts in primary plastids has been shown to serve as a signal for degradation [20][21][22]. As a result, polyadenylated transcripts are much more abundant in the cytosol and mitochondria than in plastids [23].…”

Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa

“…In eukaryotic cells, aberrant rRNA biogenesis activates RNA quality control in the nucleus, which triggers higher polyadenylation of certain rRNA intermediates and by-products catalyzed by the Trf/Air/Mtr4 polyadenylation complex (TRAMP; Jia et al, Lange et al, 2014). These intermediates are degraded sequentially by the nuclear exosome complex (LaCava et al, 2005;Houseley et al, 2006;Doma and Parker, 2007;Lange et al, 2009;Losh and van Hoof, 2015;Thoms et al, 2015). Dysfunction of ribosomal biogenesis (Gallagher et al, 2004;Ferreira-Cerca et al, 2005Tafforeau et al, 2013) results in severe developmental defects in higher plants (Byrne, 2009;Fujikura et al, 2009;Horiguchi et al, 2011;Weis et al, 2015aWeis et al, , 2015b and serious genetic diseases in mammals (Choesmel et al, 2007;Narla and Ebert, 2010;McCann and Baserga, 2013;Sondalle and Baserga, 2014;Bai et al, 2016).…”