Molecular recognition in post-transcriptional regulation 2

The functioning of the human body and of complex organisms in general requires different proteins to be produced in different types of cells. This cell-type-specific protein production is achieved by precisely regulating the translation of the genetic code into proteins. The two steps in this process of translation are, first, the translation of the DNA-encoded information into RNA and, then, the translation of the RNA code into a protein molecule. Both processes are regulated by biological machines, which are composed of proteins and, in some cases, RNA molecules. We focus on the regulation of the RNA-to-protein step (or post-transcriptional regulation) and investigate how the protein RNA machines assemble in a solution environment and regulate gene expression. Our structural studies complement other techniques such as X-ray crystallography, which can be used to study molecules in a static crystalline state. Analysing the structures of the molecules that govern regulation of protein synthesis has a direct medical relevance, as this process lies at the basis of common genetic diseases, cancer and viral infections. We work on an important regulatory mechanism, called ARE mediated mRNA decay (AMD), that increase the synthesis of specific proteins in inflammation and healing processes. This mechanism, if permanently switched on, can lead to inflammatory arthritis and cancer. We want to understand how the switch works at the molecular level and design specific therapies to switch in off when required.||Using a similar technical approach we are also investigating a key regulatory protein from herpes virus. This project wants to facilitate the design of anti-herpes drugs to treat people infected with this virus, which forms a major threat to immunodepressed patients, increases the risk of organ transplantation and chemotherapy and reduces the life expectancy of AIDS sufferers. Molecular insight into the interaction of ICP27 with its functional binding partners needs to be obtained if we are, for example, to design or optimise compounds to lock protein and RNA in a non-functional conformation or to (de)stabilise protein RNA complexes.

Multifunctional eukaryotic regulatory proteins and their viral functional equivalents control gene expression by interacting with mRNAs in large macromolecular aggregates. Dissection of the molecular basis of post-transcriptional regulatory mechanisms has a direct medical relevance, as changes in the regulation of mRNA metabolism lie at the basis of common genetic diseases, cancer and viral infection. Current therapies for these diseases do not focus on the post-transcriptional steps of regulation but rather on the transcriptional ones, that are better understood. Our aim is to clarify the structure-function relation that is at the basis of mRNA recognition by post-transcriptional regulatory proteins and to suggest strategies to control this recognition. Adenine-uracil-rich element (ARE)-mediated mRNA decay (AMD) regulates the concentration of mRNAs that contain AREs within their 3 untranslated regions (3 UTRs) by promoting their degradation. Transient AMD shut-off up-regulates the stability of these mRNAs and is important for processes that require a fast response of the organism such as cellular growth, immune response, cardiovascular toning and external stress-mediated pathways. However, impaired AMD and the consequent pathological long-term increase in the stability of a subset of mRNAs have been related to several types of cancer (skin tumours, colorectal cancer, Hodgkins lymphoma, lung carcinoma and leukaemia) and auto-inflammatory diseases (Crohn-like inflammatory bowel disease and inflammatory arthritis). K-homology splicing regulator protein (KSRP) is an important player in AMD that interacts with several different AREs mediating the degradation of the corresponding mRNAs. Our work centers on the analysis of the structural and functional elements that contribute to KSRP-RNA interactions and to mRNA degradation. We are studying the structure and dynamics of the different domains of the protein and investigated their relationship to mRNA degradation. Using structural and functional information, we plan to dissect the details of the interaction with the RNA and help the design of a strategy for the tuning of KSRP activity. Herpes viridae induced infections are a major threat to immunodepressed patients, increasing the risk of transplants and chemotherapy and reducing the life expectancy of AIDS sufferers. Current herpes virus therapies (e.g. Acyclovir) aim to block the synthesis of new DNA, but resistance to these treatments is increasing. Successful viral replication is achieved through the tightly regulated expression of viral genes. A key component of the regulatory mechanism is ICP27, an essential HSV-1 RNA binding protein that regulates protein expression, both at the transcriptional and post-transcriptional level. We will study both ICP27 and the mechanism of post-transcriptional regulation acted upon by this protein, in particular 3 mRNA editing. Using the same strategy described above for the protein KSRP, we will obtain a better understanding of the regulatory cycle of the virus and define specific structural features amenable to structure-aided drug design.