Gemma C Atkinson

Home     |    Tools     |    Publications     |     Lab Members     |     Blog     |     Tartu Institute of Technology     |    CV on ETIS

 
 

The focus of my research is the evolution of protein function and structure. I’m interested in how evolutionary analyses can be combined with experimental research to reconstruct functional evolution of proteins, and to generate testable hypotheses about unknown aspects of protein function.


I’m interested in the evolutionary dynamics of those proteins involved in the most ancient cellular processes: translation of messenger RNA into protein sequences (translation). Proteins involved in translation and its regulation are often ancient and highly conserved through evolution, although they are by no means immune to intriguing evolutionary phenomena such as lateral transfer and convergent evolution. The methods I use to study these proteins are purely in silico, involving sensitive sequence searching of genomes, multiple sequence alignments, phylogenetic reconstruction, consensus sequence and evolutionary rate analysis.


My current position began with the evolution of the stringent response machinery. The stringent response is onset during amino acid limitation, and results in the down-regulation of the translational machinery and upregulation of amino acid biosynthesis machinery. The classical stringent response protein is RelA, which senses the presence of uncharged tRNA on the ribosome and in response releases the alarmone ppGpp. RelA is just one member of a multiprotein, multidomain family found in various branches of the tree of life. These are referred to as RSHs (RelA/SpoT homologs). Through sensitive sequence searching and phylogenetic analyses, we have classified the RSHs from over 1000 genomes from archaea, bacteria and eukaryotes into 30 subgroups. Most of these RSHs were previously unknown, including homologs in archaea, previously not thought to synthesise or hydrolyse ppGpp.


My other favourite proteins belong to the ancient family of translational GTPases (trGTPases). The trGTPases form a diverse protein superfamily involved in a wide variety of functions throughout the cell and across the tree of life. They include the well known elongation factors EF-Tu/EF1A and EF-G/EF2. The core components of the superfamily originated before the last universal common ancestor (LUCA) and occur in some form in all living organisms. These core components have given rise to over 20 protein subfamilies with diverse functions, including major roles in all four stages of protein synthesis. 


For more information on the research that interests me, check out my blog proteinevolution.fieldofscience.com


I’m on the lookout for MSc and BSc students! If you’re interested in doing a project with me, check out this page and drop me an email with your CV.



 

Research interests

Researcher and PI within the group of Tanel Tenson

Institute of Technology

Tartu University

Tartu, Estonia


Email Me

Collaborators

Vasili Hauryliuk, University of Tartu

Daniel Wilson, Gene Centre, Munich

Piotr Kamenski, Moscow State University

Alexander (Shura) Mankin, University of Illinois at Chicago

Birte Vester, University of Southern Denmark


RSS feed of my blog