Chapter 5 The Role of 3′–5′ Exoribonucleases in RNA Degradation

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).…”

“…Although strains of Escherichia coli remain viable with a loss of either enzyme, the elimination of both results in an accumulation of rRNA fragments and cell death (3). 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)(9)(10). After binding RNA, PNPase and RNase R processively digest the substrate in the 3′-to-5′ direction (11)(12)(13).…”

Transfer-messenger RNA-SmpB Protein Regulates Ribonuclease R Turnover by Promoting Binding of HslUV and Lon Proteases

“…Ribonucleases (RNases) play important roles in all aspects of RNA metabolism including maturation of RNA precursors, turnover of mRNA, and degradation of stable RNAs (1)(2)(3)(4)(5). One of these enzymes, RNase R, a processive, 3Ј to 5Ј Escherichia coli exoribonuclease (6, 7) is unusual in that, by itself, it is able to digest structured RNAs (8).…”

Investigating the 3' RNA Phosphodiesterase and 3'-5' Exoribonuclease Activities of APE1.

“…They usually do not recognize specific RNA targets but degrade any RNA that is single-stranded (Gerlt et al 1993). However, even if a 3'overhang (linear stretch) is provided to initiate degradation and exoribonucleases are able to bind RNA, they may detach upon approaching stem-loops (Ibrahim et al 2008;Andrade et al 2009). To date, only RNase R is able to overcome highly folded structures on its own (Andrade et al 2009).…”