Escherichia coliRNase R Has Dual Activities, Helicase and RNase

Abstract

In Escherichia coli, the cold shock response occurs when there is a temperature downshift from 37°C to 15°C, and this response is characterized by induction of several cold shock proteins, including the DEAD-box helicase CsdA, during the acclimation phase. CsdA is involved in a variety of cellular processes. Our previous studies showed that the helicase activity of CsdA is critical for its function in cold shock acclimation of cells and that the only proteins that were able to complement its function were another helicase, RhlE, an RNA chaperone, CspA, and a cold-inducible exoribonuclease, RNase R. Interestingly, other major 3-to-5 processing exoribonucleases of E. coli, such as polynucleotide phosphorylase and RNase II, cannot complement the cold shock function of CsdA. Here we carried out a domain analysis of RNase R and showed that this protein has two distinct activities, RNase and helicase, which are independent of each other and are due to different domains. Mutant RNase R proteins that lack the RNase activity but exhibit the helicase activity were able to complement the cold shock function of CsdA, suggesting that only the helicase activity of RNase R is essential for complementation of the cold shock function of CsdA. We also observed that in vivo deletion of the two cold shock domains resulted in a loss of the ability of RNase R to complement the cold shock function of CsdA. We further demonstrated that RNase R exhibits helicase activity in vitro independent of its RNase activity. Our results shed light on the unique properties of RNase R and how it is distinct from other exoribonucleases in E. coli.When exponentially growing cells of Escherichia coli are shifted from 37°C to a low temperature, such as 15°C, a cold shock response is elicited. This response is characterized by a transient arrest of cell growth termed the acclimation phase, followed by resumption of growth at the low temperature. During the acclimation phase there is severe inhibition of general protein synthesis. However, several cold shock proteins are induced during this phase, including CspA (19) and its homologues, such as CspB (26) CsdA is a DEAD-box protein that belongs to the large family of putative RNA helicases. Members of this family are conserved in organisms from bacteria to humans (29) and play important roles in many cellular processes, such as processing, transport, or degradation of RNA or ribosome biogenesis (for a review, see reference 21). CsdA has been identified as a multifunctional protein, and it has been proposed that this protein participates in a variety of processes, such as ribosome biogenesis, mRNA decay, translation initiation, and gene regulation. CsdA is essential at low temperatures, and deletion of its gene impairs growth when there is a cold shock (8, 24). On the other hand, it is dispensable at 37°C. Previously, we showed that the helicase activity of CsdA is pivotal in its role at low temperature (3). Our in vivo genetic screening of an E. coli strain revealed that another DEAD-box RNA helicase, RhlE...

Helicase Activity Plays a Crucial Role for RNase R Function in Vivo and for RNA Metabolism

“…In the absence of CsdA, PNPase would be unable to function properly, thereby leading to the same impaired growth as is observed for a PNP Ϫ strain. The single chromosomal copy of rnr is unable to provide sufficient activity to overcome the absence of PNPase activity, but RNase R can complement when overexpressed (10). This scenario would explain the earlier complementation data.…”

“…In contrast to most exoribonucleases, RNase R is particularly adept at degrading highly structured RNA molecules (2,(5)(6)(7), and defining the mechanism by which it carries out this process is highly important (8,9). Escherichia coli RNase R contains an intrinsic RNA helicase activity (10), and recent work from our laboratory characterized this helicase and defined its relation to overall nuclease activity (8,9). In the E. coli protein, we also identified Walker A and Walker B motifs that are responsible for ATP binding and consequent RNA helicase activity, and found that they are conserved in most mesophilic bacterial genera, but are absent from thermophilic bacteria (8), suggesting that the helicase is important for RNase R function.…”

Direct observation of processive exoribonuclease motion using optical tweezers

“…In particular, RNase R has been observed to unwind and degrade completely dsRNA substrates of nearly 20 bp (4,7,21). Recent singlemolecule FRET data indicate that both RNase R and its homolog, the Rrp44 subunit of the eukaryotic exosome (22,23), advance 3′-to-5′ along dsRNA in steps of approximately four base pairs through internal elastic coupling of their binding and catalytic sites (24).…”

“…Recent singlemolecule FRET data indicate that both RNase R and its homolog, the Rrp44 subunit of the eukaryotic exosome (22,23), advance 3′-to-5′ along dsRNA in steps of approximately four base pairs through internal elastic coupling of their binding and catalytic sites (24). RNase R mutants that lack the nuclease activity required for processive motion nonetheless may separate hybridized strands of RNA (21,25), presumably through an entirely different, distributive mechanism similar to that described for DEAD-box helicases under certain conditions (26). Although RNase R appears to have a minor preference for adenine (13), no significant sequence-dependent behavior has been reported for this enzyme.…”

Novel One-step Mechanism for tRNA 3′-End Maturation by the Exoribonuclease RNase R of Mycoplasma genitalium

“…This helps the separation of the doublestranded RNA region immediately outside of the channel and leads the resulting single-stranded RNA to the channel for degradation (13). E. coli RNase R also possesses a RNA helicase activity in its CsdA domain that contributes to the degradation of double-stranded RNA (23). M. genitalium RNase R is able to degrade highly structured rRNA; however, it is sensitive to the aminoacyl-acceptor stem of tRNA and to RNA 2Ј-O-methylation (Ref.…”