Abstract
Regulation of gene expression through processing and turnover of RNA is a key mechanism that allows bacteria to rapidly adapt to changing environmental conditions. Consequently, RNA degrading enzymes (ribonucleases; RNases) such as the endoribonuclease RNase E, frequently play critical roles in pathogenic bacterial virulence and are potential antibacterial targets. RNase E consists of a highly conserved catalytic domain and a variable non-catalytic domain that functions as the structural scaffold for the multienzyme degradosome complex. Despite conservation of the catalytic domain, a recent study identified differences in the response of RNase E homologues from different species to the same inhibitory compound(s). While RNase E from Escherichia coli has been well-characterised, far less is known about RNase E homologues from other bacterial species. In this study, we structurally and biochemically characterise the RNase E catalytic domains from four pathogenic bacteria: Yersinia pestis, Francisella tularensis, Burkholderia pseudomallei and Acinetobacter baumannii, with a view to exploiting RNase E as an antibacterial target. Bioinformatics, small-angle x-ray scattering and biochemical RNA cleavage assays reveal globally similar structural and catalytic properties. Surprisingly, subtle species-specific differences in both structure and substrate specificity were also identified that may be important for the development of effective antibacterial drugs targeting RNase E.
Highlights
Microorganisms must have the ability to rapidly adapt to environmental changes
In order to compare the protein sequences of the RNase E homologues from the gammaproteobacteria E. coli, Y. pestis, F. tularensis, and A. baumannii and betaproteobacteria B. pseudomallei a multiple sequence alignment of the five full-length proteins was generated and trimmed to the boundaries of the EcRNase E N-terminal domain (NTD) (Fig. 1)
As expected, based on their phylogeny, YpRNase, FtRNase E, AbRNase and BpRNase E all belong to the Type I class of RNase Es with catalytic domains of a similar length to EcRNase E NTD located at the N-terminus of the protein
Summary
Microorganisms must have the ability to rapidly adapt to environmental changes. Characterising the properties of the RNase E catalytic domain from a variety of species may be critical for the development of effective antibacterial drugs targeting RNase E. We have characterised the structural and biochemical properties of the catalytic domain of the RNase E homologue from four bacterial pathogens, chosen because of their importance in both the health and defence sectors. The substrate specificity was compared to that of EcRNase E using biochemical assays These studies have revealed subtle species-specific differences in the properties of previously uncharacterised RNase E catalytic domains from pathogenic species that may prove to be important for the development of effective antibacterial compounds targeting RNase E
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