The goal we want to achieve is to identify the key features allowing the cross-talk between the ribonucleoprotein complexes (RNPs) and their targets. For this purpose, we determine atomic models of strategic components. They are often multi-domain proteins or multi-protein complexes driving post-transcriptional or post-translational modifications. We use a combination of established biophysical methods and X-ray crystallographic technique to obtain structural information on these macromolecular complexes.
Transcriptional Gene Silencing
We collaborate with the group of J. Paszkowski on the structural study of the Morpheus Molecule 1. The Arabidopsis thaliana Morpheus' Molecule 1 (MOM1) is a protein that regulates chromatin structure and gene expression without affecting DNA and histone methylation. An evolutionarily and functionally conserved domain of MOM1 maps to a region between about amino acids 1734-1815 (Caikovski et al., 2008 ). To begin to understand the function of this domain, we have determine its three-dimensional structure and perform additional biochemical experiments ( Nishimura et al., 2012 ). We are continuing our structural effort to further characterize the complex pathway regulated by the MOM1 protein.
RNA modifying enzymes
RNA editing machineries deaminate Cytidine or Adenosine residues within RNA sequences. Strikingly, this modification can occur highly specifically and totally unspecifically. Currently, more than 30’000 sites have been confirmed or predicted as targets for RNA editing enzymes and the list is still growing (Ramaswami et al., 2012 ). The functional consequences of these modifications are numerous and as diverse as RNA silencing, antibody diversity, alternative splicing or retroviruses protection. We are studying both the enzymes and the factors involved in RNA target selections.
tRNA modifications are numerous and their structural characterization is still incomplete. In recent years, an unexpected connection has been shown between tRNA modifying enzyme and DNA transcription (via for example the Elongator complex). Such connection has driven significant attention on these machineries. We are studying two particular modifications: The thiolation and the pseudouridylation.
RNA degradation is controlled by the poly(A) or the poly(U) tail length found at the 3'-end of mRNA. Several factors are recruited via these sequences and we have been studying the specificity driving the association of the Sm-like protein ring ( Thore et al., 2003a; Thore et al., 2003b). Recently, we focused our attention on the factor controlling the formation of the mRNA 3'-end tail, the poly(U) polymerase Cid1. We have obtained its atomic model and are continuing our studies toward a complete understanding of its enzymatic properties (Munoz et al., 2012).
Preventing mRNA degradation is the "yang" aspect of mRNA homeostasis. Numerous factors are essential in protecting or targeting given mRNAs. The laboratory has several projects aiming at unraveling the determinant behind these specific mRNA recognition events.
- Vitamin metabolisms (Prof. Teresa Fitzpatrick, web site ). Although vitamins are well characterized molecules, their production still lacks a complete structural picture. We have obtained numerous crystals of enzymes involved in key steps during vitamin synthesis. Our atomic models together with their biochemical characterization may allow us to fine tune the synthesis of these key metabolites.
- Growth control (Prof. Robbie Loewith). Cell size is a fundamental process controlled by the Target of Rapamycin complexes. These complexes contain 5-6 proteins and are extremely conserved within the eukaryotic kingdom. We have recently started their structural characterization using multiple approaches.