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The regulation of mRNP dynamics in gene expression

Eukaryotic gene expression is a fundamental cellular activity that is critical for cellular identity, function, and physiology. During gene expression, a messenger RNA (mRNA) is generated by transcription and undergoes a number of different steps, including splicing and nuclear processing, nucleocytoplasmic export and localization, translation, and decay. These steps result in dynamic changes to the RNA sequence, structure, and the cohort of proteins bound to the mRNA. Furthermore, these changes need to occur with the proper timing and in the correct sequence to avoid aberrant expression. Therefore elaborate regulation of mRNP dynamics is required for proper gene expression.

At virtually every step in gene expression, members of a highly conserved protein family called the DEAD-box proteins are required for facilitating mRNP transitions by acting either as RNA helicases or as ribonucleoprotein (RNP) remodeling enzymes. Furthermore, by regulating their activity, the potential exists to control mRNAs in different subsets and in response to different conditions. Thus we hypothesize that the DEAD-box proteins exert overarching control of mRNP dynamics in gene expression.

The DEAD-box protein Ded1 has long been known to function in translation regulation (Figure 2 below); however, its molecular mechanism remains unclear, as does its regulation. DDX3, the human ortholog of DDX3, has increasingly been linked to disease. Alteration of DDX3 has been observed in several cancers, including a high mutation rate in the brain cancer, medulloblastoma. Mutations in DDX3 can also cause DDX3 Syndrome, a developmental disorder and are associated with autism spectrum disorders. Furthermore, as with several RNA helicases, DDX3 has roles in the replication of several viruses, including HIV and hepatitis B and C.

Our research in the Bolger lab has dual goals: 1. addressing fundamental biological questions, and 2. utilizing this knowledge to advance human health. The Bolger laboratory primarily uses the budding yeast Saccharomyces cerevisiae as a model system, and takes advantage of the combination of genetics, biochemistry, and cell biology allowed by yeast work. Current projects in the lab include:

How does Ded1 mediate the translational response to cellular stress? We and others have described a role for Ded1 during cellular stresses such as lack of nutrients, extreme temperatures, or oxidative stress. In particular, we have shown that Ded1 contributes to both the general repression of translation in stress as well as subsequent upregulation after the stress has been removed. Our current model is that Ded1 causes dissociation of its binding partner eIF4G from translation complexes, leading to degradation of both eIF4G and Ded1 (Figure 5 below). We are currently studying how this process occurs as well as connections between Ded1, translation, and the cell cycle.

How do DDX3/Ded1 mutations contribute to medulloblastoma progression? Several studies have found frequent mutations in DDX3 in medulloblastoma, but it is unclear how the large number of identified missense mutations affect the function of the protein. We have shown what translation defects are common amongst these mutations and are currently expanding this work to examine possible defects in stress.

How is control of translation by Ded1 regulated? Ded1 is reported to have critical roles in pre-initiation complex assembly, facilitating start site scanning by the 40S subunit, and a role in translation repression and stress granule formation. How these different functions are coordinated in vivo is unknown. We hypothesize that this regulation is through Ded1’s known binding partners, which include the multi-functional DBP cofactor Gle1, the translation factor eIF4G, and oligomerization of Ded1 itself.

Our long-term goal in fundamental biology is to uncover the regulation of mRNP dynamics, focusing on the in vivo roles, molecular targets, and regulation of DEAD-box proteins. Our research will not only greatly increase our understanding of how these factors function in translation but will elucidate potential mechanisms for control of gene expression. Given that the cellular functions of these factors are not well-characterized, understanding of their physiological functions is critical to examining their roles in cancer, aging, and other diseases. Furthermore, some of our work directly targets the understanding of medulloblastoma. Our work may thus open up new avenues for therapies, either for cancer or for the other pathologies related to this research.

For further reading, check out the Publications page.