Wim Versees

Transfer RNA (tRNA) molecules are pivotal in the translation of the genetic code into protein sequences. In this process, the recognition of the mRNA codon by the correct tRNA does not solely dependent on the primary sequence of the tRNA molecule. Rather, posttranscriptional nucleoside modification, particularly in the anticodon loop, can modify cognate codon recognition, stabilize the codon-anticodon wobble base pairing and/or affect aminoacylation properties. To date more than 100 different RNA modifications have been reported, the majority occurring in tRNA. Correspondingly it is estimated that in most common organisms about 1% of the genome is dedicated to encoding tRNA modification enzymes. Not surprisingly considering the central role of tRNA and its modifications in translation, mutations in some of these genes have been linked to human diseases. To gain insight in the mechanisms of action of the enzymes corresponding to these genes, detailed structural and biochemical/physical studies are required. 

 

Our research aims at elucidating the mechanism and 3-dimensional structure of tRNA modifying enzymes, both from prokaryotic and eukaryotic origin, with particular emphasis on those involved in wobble modification. As a first system we are focusing on the MnmE and GidA catalyzed carboxymethylaminomethylation of uridine at the wobble position of certain tRNA’s.

 

 

In most eubacteria, the protein GidA and the G-protein MnmE are implicated in catalyzing the addition of a carboxymethylaminomethyl (cmnm) group onto the C5 carbon of uridine at position 34 (U-34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. Recent studies with the E. coli proteins suggest that GidA and MnmE physically interact and form a functional a₂b₂ complex in which they directly cooperate in the modification reaction. GidA and MnmE are also conserved in eukaryotes, where they localize in mitochondria, and the orthologs of GidA and MnmE in S. cerevisiae and human are called Mto1 and MSS1 and Mto1 and GTPBP3 respectively. In humans malfunctioning of Mto1 and GTPBP3 has been implicated in several mitochondrial diseases such as non-syndromic deafness, MELAS and MERRF.

A study of the structure and function of the MnmE and GidA proteins was initiated in the group of Prof. Wittinghofer (MPI for Molecular Physiology, Dortmund Germany). The crystal structure of the G-domain containing protein MnmE from Thermotoga maritima has been solved. Very recently we were also able to solve the crystal structure of the GidA proteins from E. coli and Chlorobium tepidum. In collaboration with Alfred Wittinghofer the study of the structure, function and regulation of the MnmE/GidA complex is now being continued in our group.

 

 

1) Versées W., De Groeve S, Van Lijsebettens, M. (2010) Elongator, a conserved multitasking complex ? Mol Microbiol. 76 (5), 1065-9.

  

2) Meyer S., Wittinghofer A., Versées W. (2009) G-domain dimerization orchestrates the tRNA wobble modification reaction in the MnmE/GidA complex. J.Mol.Biol. 392(4), 910-22.

 

3) Meyer S., Scrima A., Versées W., Wittinghofer A. (2008) Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate. J Mol Biol. 380, 532-47.

 

4) Vandemeulebroucke A., De Vos S., Van Holsbeke E, Steyaert S, Versées W. (2008) A flexible loop as a functional element in the catalytic mechanism of nucleoside hydrolase from Trypanosoma vivax. J.Biol.Chem. 283(32), 22272-82.

 

5)  Versées W., Spaepen S., Wood MD., Leeper FJ., Vanderleyden S., Steyaert J. (2007) Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase. J.Biol.Chem. 282(48), 35269-78.