Figure 1: An example of cooperative, highly specific RNA recognition by two general but distinct RNA binding proteins, Sex-lethal and UNR, regulating the translation of msl-2 mRNA during Drosophila dosage compensation (Hennig et al., 2014).
Figure 2: Different modes of RNA binding by RNA binding proteins, where single RBDs, having low specificity can bind to multiple sites on the mRNA transcript (a). Affinity and specificity increases upon cooperative binding of multiple RBDs within a single RBP (b), conformational selection or fly-casting (c), or cooperative interaction between multiple but distinct RBPs.
The Hennig group employs integrated structural biology (nuclear magnetic resonance (NMR) spectroscopy, X-ray, small-angle scattering and cryo-electron microscopy) to investigate the molecular mechanisms underlying translation regulation and ribonucleoprotein complex assembly.
Previous and current research
Recognition of mRNA by RNA-binding proteins (RBPs) plays essential roles during all stages of gene expression, including splicing, translation, degradation and transport. Also, biogenesis of non-coding RNAs depends on RNA–protein interactions. It is not yet understood – spatially or temporally – how RBPs specify for their cognate RNA sequences on untranslated regions (UTRs). Single RBPs often have low sequence specificity, especially if they feature only one RNA binding domain. Specificity and affinity increases if RBPs harbour more RNA binding domains. Recently, we have shown that multiple but distinct RBPs act cooperatively to specify for their right target RNA (Figure 1), adding another recognition mechanism to the list of demonstrated protein–RNA interactions (Figure 2).
The atlas of RBPs has been extended to protein domains so far not known to bind RNAs. One of them, the NHL repeat domain, features in several members of the eukaryotic tripartite motif (TRIM) protein family. Members of this family featuring this domain are intricately involved in stem and progenitor cell development via interaction with the miRNA-induced silencing complex (miRISC) and are associated with different types of cancer. Biochemically, TRIM proteins are known to act as E3 ligases within ubiquitin signalling. Our research aims to understand the link between ubiquitylation and mRNA translation/degradation mediated by this multidomain protein family in a structural and functional way.
Given the intrinsically flexible regions in multidomain proteins and transient protein–protein interactions with other RBPs and proteins of the ubiquitin system, NMR spectroscopy is well-suited to the study of TRIM proteins and protein–RNA interactions. However, the size limitations of NMR are disadvantageous, making it necessary to combine sparse NMR data with small-angle scattering and X-ray crystallography.
Future projects and goals
Our future efforts will focus on TRIM proteins and other protein–RNA regulatory networks, and will encompass the following main tasks and goals:
- Investigating the structural basis for RNA recognition by the C-terminal NHL domain of different TRIM proteins.
- Investigating the structural basis for E2–E3 recognition within the ubiquitin system, between the N-terminal domains of TRIM proteins and protein interaction partners.
- Linking the complexes formed at the C-terminal and N-terminal domains, and getting a detailed picture of how TRIM proteins regulate stem cell development.
- Transfering the knowledge to other TRIM proteins involved in immunity.
- Developing and improving methods for integrated structural biology.