Characterising the cellular roles of bacterial stress response proteins through molecular evolution and NGS bioinformatics methods

Supervisor: Gemma C. Atkinson, Department of Molecular Biology, and Umeå Centre for Microbial Research Umeå University, Sweden

Background and description of work tasks:

When bacteria encounter stressful conditions they rewire their intracellular physiology to increase their chances of survival until the environment becomes favourable again. One of the ways they do this is by producing the “alarmone” nucleotides ppGpp and pppGpp (collectively referred to as (p)ppGpp) that alter the gene expression profile of the cell through interactions with multiple targets. (p)ppGpp is produced by enzymes of the RelA-SpoT Homologue (RSH) superfamily, the evolution of which we characterized in 2011 [1].

The current project concerns the part of the RSH superfamily comprised of Small Alarmone Synthetases (SASs). There are at least 12 different classes of SASs, which have evolved through gene duplication, horizontal gene transfer and differential loss, and multiple classes can be present in the same bacterium. It is not known why bacteria carry multiple SASs, and what is their in vivo function. Only recently have details come to light about SAS regulation; our collaborators in the Hauryliuk lab, with our involvement, discovered that the SAS RelQ from pathogen Entercoccus faecalis is regulated in vitro both by single stranded RNA, and its product pppGpp [2]. This raises questions of how general this regulation is among SASs, what sequence and structural regions are involved, and what are the RNA targets in living cells. We will address these questions through bioinformatic methods including comparative molecular evolutionary analyses and analyses of next generation sequencing (NGS) data of SAS-bound RNA fragments.

The aims of the project are to:

1) Characterise the diversity of SASs across the bacterial tree of life, refining and bringing up to date our previous classifications, taking advantage of the significant number of new genome sequences available.

2) Develop tools for phylogenetic profiling to predict aspects of function that can be tested experimentally.

3) Determine the sequence specificity of RNA binding through analyses of NGS data of SAS-bound RNA fragments.

The selected candidate will design and carry out analyses of genomic (NGS), RNA and protein sequences, and present the findings.

The position will initially be temporary, up to 6 months as a project assistant. Conversion to a PhD opportunity will be possible if the temporary project shows promise. Contact for further details about this.

For questions regarding the position contact Gemma Atkinson, [Email Address Removed]

The Atkinson lab is part of the Umeå Centre for Microbial Research (UCMR), an interdisciplinary research centre devoted to top quality research and novel applications in the field of microbiology.

You can find more information about us at http://www.ucmr.umu.se and http://www.molbiol.umu.se/english.