Exonucleases and endonucleases involved in polyadenylation‐ assisted RNA decay

Abstract

RNA polyadenylation occurs in most forms of life, excluding a small number of biological systems. This posttranscriptional modification undertakes two roles, both of which influence the stability of the polyadenylated transcript. One is associated with the mature 3' ends of nucleus-encoded mRNAs in eukaryotic cells and is important for nuclear exit, translatability, and longevity. The second form of RNA polyadenylation assumes an almost opposite role; it is termed 'transient' and serves to mediate the degradation of RNA. Poly(A)-assisted RNA decay pathways were once thought to occur only in prokaryotes/organelles but are now known to be a common phenomenon, present in bacteria, organelles, archaea, and the nucleus and cytoplasm of eukaryotic cells, regardless of the fact that in some of these systems, stable polyadenylation exists as well. This article will summarize the current knowledge of polyadenylation and degradation factors involved in poly(A)-assisted RNA decay in the domains of life, focusing mainly on that which occurs in prokaryotes and organelles. In addition, it will offer an evolutionary view of the development of RNA polyadenylation and degradation and the cellular machinery that is involved.

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

“…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.…”

“…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].…”

“…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.…”

“…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. The enzymes performing polyadenylation are polynucleotide phosphorylase (PNPase) and several polyA polymerases (PAPs) [21,22].…”

Cell Type-Dependent RNA Recombination Frequency in the Japanese Encephalitis Virus

“…Since transfected RNA fragments were degraded in both C6/36 cells and BHK-21 cells, RNase cleavage may be actually involved in viral RNA degradation to form small RNAs [41]. However, degradation of transfected RNA fragments in C6/36 cells was partially ameliorated by treatment with PAP, suggesting that viral RNAs are not completely degraded by the RNase cleavage pathway [42]. Perhaps RNA interference (RNAi) plays an important role in the related events [43].…”