Molecular evolution of RSH proteins, lookouts and messengers of stress signals

A few days ago (the day before my 30th birthday actually), my most recent paper, along with Vasili Hauryliuk and Tanel Tenson, "The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life" was published with PloS ONE. Hurrah!

The RSH proteins comprise a superfamily of enzymes that synthesize and/or hydrolyze the alarmone ppGpp. ppGpp is a nucleotide that acts as an alarm signal, activating the “stringent” response in bacteria during starvation conditions and regulating various other aspects of cellular metabolism, often in response to stress. Vasya's blog has a wealth of information about the stringent response and the molecules involved.

Rel, RelA and SpoT are the classical, most well known “long” RSHs. The carry the ppGpp hydrolase, synthetase, TGS and ACT domain architecture. They have been found across diverse bacteria and plant chloroplasts. Additionally, dedicated single domain ppGpp-synthesizing and -hydrolyzing RSHs have also been discovered in disparate bacteria and animals respectively. However, until now there has been considerable confusion in terms of nomenclature, and no comprehensive phylogenetic and sequence analyses have previously been carried out to classify RSHs on a genomic scale.

To remedy the situation, I carried out high-throughput sensitive sequence searching of over 1000 genomes from across the tree of life, in conjunction with phylogenetic analyses, to identify and classify diverse RSHs in different organisms and unify the terminology for the field. We classify RSHs into 30 subgroups comprising three groups: long RSHs, small alarmone synthetases (SASs), and small alarmone hydrolases (SAHs). That's 19 more subgroups than were previously known. Those previously unidentified RSH subgroups, which are mostly found in bacteria, but sometimes in archaea and eukaryotes, can now be studied experimentally.

What I think is possibly the most interesting result came from comparative sequence analysis of long and small RSHs. I found exposed sites limited in conservation to the long RSHs that seem to be involved in transmitting regulatory signals. These signals may be transmitted via inter-domain interactions, or inter-molecular interactions either among individual RSH molecules or among long RSHs and other binding partners such as the ribosome. These sites in RelA can now be directly targeted with mutagenesis in order to text these predictions.

I have to say I'm disappointed with how the figures look in the PDF version of the paper. Lines are really not as crisp as my uploaded figures. Unfortunately the tables also don't look how they're supposed to due to them having being automatically formatted for the PLoS format. I wasn't given the opportunity to check them in a proofing stage either. Oh well, I'm just happy this story is now out there!

Gemma C. Atkinson, Tanel Tenson, & Vasili Hauryliuk (2011). The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life PLoS ONE, 6 (8)