The RNA degradosome: life in the fast lane of adaptive molecular evolution

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In Escherichia coli, the multi-enzyme RNA degradosome contributes to the global, posttranscriptional regulation of gene expression. The degradosome components are recognized through natively unstructured ‘microdomains’ comprising as few as 15–40 amino acids. Consequently, the degradosome might experience a comparatively smaller number of evolutionary constraints, because there is little requirement to maintain a folded state for the interaction sites. New regulatory properties of the degradosome could arise with relative rapidity, because partners that modify its function could be recruited by quickly evolving microdomains. The unusual combination of the centrality of RNA degradation in gene expression and the generality of natively unstructured microdomains in recognition can fortuitously confer a capacity for efficacious adaptive change to degradosome-like assemblies in eubacteria.

Introduction

Most mRNA molecules are destroyed shortly after they are synthesized. Despite the apparent wastefulness, this and other ‘futile’ cycles could in fact confer the considerable selective benefits of ensuring fidelity and enabling rapid responses to environmental change. Furthermore, any mechanism that affects transcript turnover can provide a means of controlling gene expression, often in complex ways. In Salmonella enterica, for example, the exoribonuclease polynucleotide phosphorylase (PNPase) is a global regulator of virulence and persistence, which means that mutations in PNPase affect the capacity of this organism to infect tissues [1].

It seems likely that transcript turnover can operate at different levels of a regulatory hierarchy, and thus can link different centres in networks of genetic control and metabolism. Such extra layers of connectivity in regulatory control could facilitate the coordination of different metabolic pathways that might not otherwise communicate, thereby minimizing any wasteful effort or optimizing the robustness of networks during environmental changes. Thus, control of transcript turnover can, in principle, provide an essential mechanism of posttranscriptional regulation of gene expression.

In all three domains of life – eubacteria, archaea and eukaryotae – the machinery of RNA degradation often takes the form of multicomponent assemblies, and these complexes, or their individual components, can target specific gene products or affect the relative composition of different transcripts through differential decay rates [2]. From the perspective of regulatory control networks, RNA degradative machines effectively function as trans-acting regulators of gene expression, similar to the classical transcription factors that control rates of mRNA synthesis, except that RNA degradative machines affect rates of degradation.

In the well-studied eubacterium Escherichia coli, a multi-enzyme complex known as the ‘RNA degradosome’ can drive the energy-dependent turnover of mRNA and can trim some RNA species into their active forms [2]. Transcript analyses indicate that the degradosome has a broad role in gene regulation 3, 4, and mutants in which degradosome assembly is disrupted have a slow-growth phenotype [5] and altered metabolic profiles (Vidya Chandran, PhD thesis, University of Cambridge, 2006). Although disruption of the degradosome affects the levels of many transcripts, some are affected strongly, suggesting that these transcripts might contain a structural or sequence signal for recognition. Many of these transcripts encode enzymes of glycolysis and other processes of cellular energetics [3].

Surprisingly, the E. coli RNA degradosome is built on a region of RNase E that shows high sequence variation among closely related bacteria. Also somewhat surprisingly, the available evidence indicates that other degradosome-like assemblies show apparently wide compositional variation across the phyla. These observations seem paradoxical, given the role of the degradosome in the regulatory repertoire of E. coli. Here we explore the organization of the E. coli degradosome, its putative phylogenetic variation and the hypothesis that it might represent a special case of molecular evolution, and thereby discuss the wider implications.

Section snippets

Composition of the E. coli RNA degradosome

The E. coli degradosome comprises the following principal enzymes: the essential endoribonuclease RNase E, which initiates the turnover of many, if not most, mRNA molecules; the ATP-dependent RNA helicase RhlB, which unwinds and translocates RNA substrates; the glycolytic enzyme enolase; and the phosphorolytic exoribonuclease PNPase 2, 6, 7, 8 (Figure 1a). The physical association of the nucleases and the helicase in the degradosome facilitates the coordination and cooperation of their

Component structures and a subassembly of the degradosome

Recently, the crystal structure of the N-terminal half of E. coli RNase E (amino acids 1–529), which encompasses the catalytic function, has been solved [27]. The structure reveals a homotetramer in which the quaternary organization is a dimer of dimers 27, 28 (Figure 2a). The structure also accounts for the conservation of key residues of the catalytic site, the hydrophobic core and the protomer–protomer interfaces, and delimits the boundaries of this globular portion of the molecule.

Outside

Molecular diversity of RNase E and the radiation of degradosomes

In RNase E homologues that are similar to the E. coli enzyme, the segments corresponding to microdomains, including the two microdomains that are probably RNA-binding sites (RBD and AR2), are comparatively well conserved. These RNase E homologues (Figure 1a, type A) are colour-coded as the red branch in the phylogenetic tree (Figure 3). Organisms of this branch include Gram-negative species that are pathogens of animals and plants such as Salmonella typhimurium, Yersinia pestis, Yersinia

Synopsis and synthesis

The idea that the degradosome has an essential functional role seems at odds with the observed sequence variation outside the conserved catalytic core among RNase E homologues and the compositional variation of the putative RNase E-mediated assemblies among closely related proteobacterial species. However, the preservation of long open reading frames of the variable, noncatalytic portion of RNase E, which often encode >500 amino acids, suggests that there is significant selective pressure to

Concluding remarks

Molecular recognition mediated by microdomains is not unique to the E. coli degradosome because other regulatory complexes, such as the signalling and transcription machinery, are also assembled through microdomains. These other regulatory assemblies are predicted to have molecular evolution characteristics similar to those proposed for the degradosome [48]. Examples in eukaryotes abound in the recognition complexes formed by transmembrane receptors involved in signalling systems and by

Acknowledgements

We thank our many colleagues with whom we have worked over the years on various aspects of the RNA degradosome: Carol Robinson, Pol Ilag, Leonora Poljak, Günter Grossmann, Loretta Murphy, Kenny McDowall, Jon Stead, Yulia Redko, Jukka Aurrika, Karin Kühnel, Anastasia Callaghan and Martyn Symmons. We thank Jaime Garcia Mena, Nick Crump and Jeremy Tame for comments on the manuscript. B.F.L. is supported by the Wellcome Trust. M.A.D. is a Damon Runyon Fellow supported by the Damon Runyon Cancer

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