Transcript stability in the protein interaction network of Escherichia coli Sarath Chandra Janga* and M. Madan Babu Received 25th September 2008, Accepted 21st November 2008 First published as an Advance Article on the web 9th December 2008 DOI: 10.1039/b816845h Gene expression is a dynamic process which can be controlled by a number of mechanisms as genetic information flows from nucleic acids to proteins. The study of gene expression in the steady state, while informative, overlooks the underlying dynamics of the processes. Steady-state transcript levels are a result of both RNA synthesis and degradation, and as such, measurements of degradation rates can be used to determine their rates of synthesis as well as reveal regulation that occurs via changes in RNA stability. Messenger RNA degradation plays a central role in diverse cellular processes and is controlled primarily by the activity of the degradosome in prokaryotes. In this study, we use the currently available network of protein–protein interactions (PPIs) and mRNA half-lives in Escherichia coli to demonstrate that centrality of a protein in the PPI network is strongly correlated with its mRNA half-life. We find that interacting proteins tend to show similar half-lives, commonly referred to as assortative behavior in networks, which is frequently found in biological and social networks. While a major fraction of the interacting proteins show significantly lower differences in mRNA stabilities, a smaller but significant number of protein pairs tend to show higher differences than expected by chance. Higher differences in transcript stabilities often involved those that encode for transcription factors and enzymes, suggesting a feedback link at the post-translational level. We also note that although essential genes, which act as a proxy for in vivo centrality in PPI networks, are highly expressed compared to non-essential ones, they do not encode for more stable transcripts than non-essential genes. Our results provide a direct link between mRNA stability and centrality of a protein in PPI network indicating the importance of post-transcriptional mechanisms on nascent RNAs in the cell. Introduction RNAs can be classified by their stability in the cell. The best- known stable RNAs are the tRNAs and rRNAs. mRNAs are unstable, with half-lives in Escherichia coli ranging from 2 to 25 min (see Fig. 1A). In eukaryotic cells, mRNA turnover is slower, but the half-lives are usually shorter than the genera- tion time. The instability of mRNA is an important property permitting timely adjustments to changes in growth conditions or to genetically controlled programs of expression. Until recently, tRNAs and rRNAs were believed to be protected by their rapid folding and assembly into compact structures. This simplistic view seems unlikely because of the discovery of ribonucleolytic multienzyme complexes capable of unwinding and degrading structured RNA. Another widely held precon- ception was that the enzymes involved in the processing of stable RNA would be distinct from those involved in the degradation of mRNA. With the discovery in E. coli and Saccharomyces cerevisiae that ribonucleases involved in the processing of rRNA are also important in the degradation of mRNA, it is now clear that there is a close connection between processing and degradation. 1–4 mRNA instability is an intrinsic property that permits timely changes in gene expression by limiting the lifetime of a transcript and acts as a regulator for controlling the produc- tion of a protein product at the post-transcriptional level. It is becoming increasingly clear that in eubacteria like E. coli, RNase E, a single-strand-specific endonuclease is involved in the processing of rRNA and the degradation of mRNA. 5–7 A nucleolytic multienzyme complex now known as the RNA degradosome was discovered during the purification and characterization of RNase E. 8,9 Two other major components of this complex include a 3 0 exoribonuclease (polynucleotide phosphorylase, PNPase) and a DEAD-box RNA helicase (RNA helicase B, RhlB). RNase E is a large multidomain protein with N-terminal ribonucleolytic activity, an RNA- binding domain and a C-terminal ‘scaffold’ that binds PNPase, enolase and RhlB. The association of RNase E and PNPase in a complex provides a direct physical link for their co-operation in the degradation of mRNA. Other associated proteins, present in substoichiometric amounts, include poly- phosphate kinase (PPK), DnaK and GroEL. Interactions with other enzymes, such as E. coli poly(A) polymerase and the ribosomal protein S1, have also been described, although the role of enolase, PPK and other associated proteins in the degradation of mRNA is still unknown. 7 However, a ‘minimal’ degradosome containing RNase E, RhlB, PNPase and enolase can be reconstituted from purified components and has been proposed to comprise the degradosome complex. In E. coli, the degradation of mRNA is mediated by the combined action of endo- and exo-ribonucleases, RNase E and PNPase, respectively, which degrade RNA in a 3 0 –5 0 MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK CB2 0QH. E-mail: sarath@mrc-lmb.cam.ac.uk; Fax: +44 (0)1223 213556; Tel: +44 (0)1223 402479 154 | Mol. BioSyst., 2009, 5, 154–162 This journal is  c The Royal Society of Chemistry 2009 PAPER www.rsc.org/molecularbiosystems | Molecular BioSystems