PhD position available in bioinformatics and bacterial stress responses
Umeå University, Medical Faculty
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 .
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 . 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.
You must hold a University degree equivalent to a European University Master degree in molecular biology at the time of the recruitment (240 ECTS). Qualified are also those who completed eight semesters of medical or dental program, including medical chemistry, cell and molecular biology, genetics, physiology, microbiology and independent work and those that have acquired substantially equivalent knowledge in Sweden or abroad.
You should have experience in bioinformatics and computer programming (e.g. Python, Perl), and an enthusiasm for molecular biology and evolution. You need to be fluent in spoken and written English.
You should be highly motivated and able to work productively in a team as well as independently. Excellent communication skills for interacting effectively with senior colleagues and peers are required.
Enrolment onto the PhD program
The position will initially be temporary, for 3-6 months as a project assistant. Conversion of the project to a PhD opportunity will be possible if the temporary position shows promise. Contact Gemma email@example.com for more information.
How to apply
You apply through our recruitment system. Your application must contain the following documents written in English or Swedish:
- A CV with information on education, a list of previous and current employments, and a list of publications.
- A cover letter describing research experience and interests, motivation for applying for the position
- Contact details of one to three references.
For questions regarding the position contact Gemma Atkinson, firstname.lastname@example.org
More about us
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.
- Atkinson GC, Tenson T, Hauryliuk V: The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS ONE 2011, 6(8):e23479.
- Beljantseva J, Kudrin P, Andresen L, Shingler V, Atkinson GC, Tenson T, Hauryliuk V: Negative allosteric regulation of Enterococcus faecalis small alarmone synthetase RelQ by single-stranded RNA. Proc Natl Acad Sci U S A 2017, 114(14):3726-3731.