Dr. Edvardas Golovinas has joined the ranks of PhDs at Vilnius University Life Sciences Center. After defending his thesis "Structural and Biochemical Studies of an Argonaute and Its Associated Protein from Archaeoglobus fulgidus", he was awarded a PhD in biochemistry. Congratulations!
Academic consultants of this dissertation are Dr. Elena Manakova and Dr. Mindaugas Zaremba (both researchers represent Vilnius University Life Sciences Center (VU LSC)).
Dissertation Defence Panel is composed of Chairman Prof. Rolandas Meškys (VU LSC), and members Prof. Vilmantė Borutaitė (Lithuanian University of Health Sciences), Dr. Rūta Gerasimaitė (Max Planck Institute, Germany), Dr. Stephen Knox Jones, Jr. (VU LSC), Dr. Daan Swarts (Wageningen University, The Netherlands).
Introduction:
Argonaute (Ago) proteins can be found in all three domains of life: bacteria, archaea, and eukaryotes. The first-discovered and best-characterized of these are the eukaryotic Argonaute proteins (eAgos). Being the core of the RNA interference (RNAi) machinery, they employ short RNA guides to target RNA for gene expression regulation and host defence. The structural and mechanistic diversity of prokaryotic Agos (pAgos) is much greater, however, phylogenetic analysis showed that pAgos can be separated into three distinct clades: long-A, long-B, and short pAgos. The long pAgos resemble eAgos in that they comprise the main structural domains – N-terminal, MID, PIWI, and PAZ, including two linker domains L1 and L2. Short pAgos, on the other hand, lack the N-terminal part and only bear the MID and PIWI domains, usually associating with another protein, containing an effector and APAZ domains. The best-studied is the long-A clade, to which all characterized catalytically active pAgo nucleases belong, with studies on short pAgos gaining interest and momentum. Some long and short pAgos have been demonstrated to have defensive roles, protecting the host from invading phages and plasmids by invader degradation or abortive infection, or performing other functions, like chromosome decatenation. The long-B clade, on the other hand, is severely lacking in attention and, therefore, in findings and information, with only one pAgo well-described. One of the likely reasons for this is that all known long-B pAgos are catalytically inactive, having substitutions of key residues in the catalytic site of the PIWI nuclease domain, which may limit their potential use as nucleases in various tools, akin to CRISPR-Cas. Indeed, quite a few catalytically-active pAgos have been developed into proof-of-concept tools, with some of them using catalytically-dead mutants of those pAgos. In fact, the applicability of innately catalytically inactive short pAgo has also been demonstrated. Therefore, the usefulness of such catalytically inactive pAgos cannot be dismissed, as has been discussed previously. The possibility of advanced tool development necessitates a profound and comprehensive grasp of the mechanisms at hand, however. Therefore, it is of paramount importance to characterize such potential candidates and dispel any misconceptions and uncertainties, stemming from previous results or lack thereof, potentially unveiling some unexplored features and paths of research.