The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

Abstract

The structure and function of polynucleotide phosphorylase (PNPase) and the exosome, as well as their associated RNA-helicases proteins, are described in the light of recent studies. The picture raised is of an evolutionarily conserved RNA-degradation machine which exonucleolytically degrades RNA from 3¢ to 5¢. In prokaryotes and in eukaryotic organelles, a trimeric complex of PNPase forms a circular doughnutshaped structure, in which the phosphorolysis catalytic sites are buried inside the barrel-shaped complex, while the RNA binding domains create a pore where RNA enters, reminiscent of the protein degrading complex, the proteasome. In some archaea and in the eukaryotes, several different proteins form a similar circle-shaped complex, the exosome, that is responsible for 3¢ to 5¢ exonucleolytic degradation of RNA as part of the processing, quality control, and general RNA degradation process. Both PNPase in prokaryotes and the exosome in eukaryotes are found in association with protein complexes that notably include RNA helicase.

Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli

“…Surprisingly, mRNA stabilization is dependent on PNPase. Thus upon translational stress induced by S1 overexpression an enzyme thought to be principally involved in mRNA degradation (for review, see Lin-Chao et al 2007) seems to prevent mRNA decay.…”

Analysis of the human polynucleotide phosphorylase (PNPase) reveals differences in RNA binding and response to phosphate compared to its bacterial and chloroplast counterparts

“…These RNA-binding domains were characterized in other RNA-binding proteins. The domain structure of the bacterial and organellar PNPases is very well conserved in the exosomes of archaea and eukaryotic cells (Buttner et al 2006;Houseley et al 2006;Lin-Chao et al 2007). Indeed, the archaeal exosome is a phosphorolytic complex that is very similar to PNPase and, in systems in which it exists, is responsible for the degradation and polymerization of RNA, resembling the PNPase found in cyanobacteria (Portnoy et al 2005;Portnoy and Schuster 2006).…”

Direct observation of processive exoribonuclease motion using optical tweezers

“…To degrade RNA, both ribonucleases require an unstructured binding site of at least 7-10 nt at the 3′ end of the substrate (5-7), a sequence that often is supplied by posttranscriptional polyadenylation (8-10). After binding RNA, PNPase and RNase R processively digest the substrate in the 3′-to-5′ direction (11-13).PNPase consists of a trimer that degrades RNA at catalytic sites within a central channel (9,14). The enzyme is homologous to eukaryotic and archaeal exosomes and, like these hexameric proteins, possesses a core of six RNase PH domains arranged in a ringlike configuration (two per protomer) (6, 15).…”

“…PNPase consists of a trimer that degrades RNA at catalytic sites within a central channel (9,14). The enzyme is homologous to eukaryotic and archaeal exosomes and, like these hexameric proteins, possesses a core of six RNase PH domains arranged in a ringlike configuration (two per protomer) (6, 15).…”