Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome

Abstract

SummaryIn Escherichia coli the initial step in the processing or decay of many messenger and structural RNAs is mediated by the endonuclease RNase E, which forms the core of a large RNA-catalysis machine termed the degradosome. Previous experiments have identified a protein that globally modulates RNA abundance by binding to RNase E and regulating its endonucleolytic activity. Here we report the discovery of RraB, which interacts with a different site on RNase E and interferes with cleavage of a different set of transcripts. We show that expression of RraA or RraB in vivo is accompanied by dramatic, distinct, and inhibitorspecific changes in degradosome composition -and that these are in turn associated with alterations in RNA decay and global transcript abundance profiles that are dissimilar to the profile observed during simple RNase E deficiency. Our results reveal the existence of endonuclease binding proteins that modulate the remodelling of degradosome composition in bacteria and argue that such degradosome remodelling is a mechanism for the differential regulation of RNA cleavages in E. coli.

Preliminary crystallographic analysis of RraB fromEscherichia coli

“…In addition, RraB exhibits key differences in its mode of action and its effects on the transcript profile (Zhou et al, 2009). The previous study also revealed that amino acids 694-727 of RNase E were required for the binding of RraB (Gao et al, 2006), similar to the major degradosome components which bind to specific continuous regions within the C-terminal region of RNase E. This region partially overlaps a stretch of amino acids extending from positions 685 to 712 which is predicted to be important for binding of the enzyme to structured RNAs (Callaghan et al, 2004). In contrast to RraB, the binding region between RraA and RNase E could not be mapped to a single contiguous epitope, instead mapping to a long region from amino acids 585 to 1061 of RNase E.…”

“…The activity of RNAse E in E. coli is also controlled by the protein inhibitors RraA and RraB (regulators of RNAse activity A and B; Yeom et al, 2008). These two inhibitors can repress the endonucleolytic activity of RNAse E by connecting to the scaffold domains of the enzyme because the catalytic domain alone is not sufficient to bind the RNA substrates (Gao et al, 2006). RraA and RraB have a conserved function in RNA metabolism and modulation of RNA stability in bacteria, but share only a very low sequence identity with each other (14.2% over 138 amino acids).…”

mRNA degradation and maturation in prokaryotes: the global players

“…However, the CTH is important for the rapid degradation of many untranslated mRNA (98) and a microarray study shows that the assembled degradosome regulates the abundance of certain metabolic pathways in E. coli (99). The composition of the degradosome can be modified depending on conditions of growth or stress (100)(101)(102)(103). Functional and structural aspects of the E. coli degradosome have been extensively reviewed elsewhere (104).…”

Identification of Amino Acid Residues in the Catalytic Domain of RNase E Essential for Survival of Escherichia coli: Functional Analysis of DNase I Subdomain

“…For a recent review, see Carpousis (2007). RNase E has additionally been shown to be capable of interacting with poly(A) polymerase (Raynal and Carpousis 1999), ribosomal protein S1 (Kalapos et al 1997;Feng et al 2001), RNA-binding protein Hfq (Morita et al 2005), and the protein inhibitors of RNase E activity, RraA and RraB Gao et al 2006). However, the Nterminal half (amino acid residues 1-498) is sufficient for cell survival (Kido et al 1996;Ow et al 2000).…”