Structural insights into nascent polypeptide-mediated translation regulation

• Applicant: Professor Dr. Daniel Nicodemus Wilson
• Subject Area: Structural Biology ; Biochemistry
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 548507277

During protein synthesis, the activity of the ribosome can be directly influenced by the nascent polypeptide chain that it is translating. Indeed, a number of nascent polypeptide contexts or motifs have been identified that are problematic for the ribosome to translate, including polyproline, polyacidic or polybasic stretches of amino acids. Additionally, genetic selection of nascent polypeptide sequences has led to the identification of a range of diverse sequence motifs that can arrest translation. In fact, many organisms have taken advantage of the ability of the nascent polypeptide chain to slow-down or even arrest translation for cellular function. This is exemplified by the diverse classes of arrest peptides that utilize translational stalling to regulate expression of downstream genes in both bacteria and eukaryotes. Despite intense research in the past decades, the mechanism of how arrest peptides can modulate and, in most cases, inactivate the ribosome is only in its infancy. Moreover, recent studies have revealed that bacteria have evolved a series of specialized factors that bind to the ribosome and facilitate relieve of stalled ribosomes and translation through problematic sequences, however, a structural basis for this activity is unknown. In this proposal, we plan to provide much needed mechanistic insight into how arrest peptides inactivate ribosome function and how specialized protein factors can relieve stalling at problematic polypeptide contexts. To do this, we will employ cryo-electron microscopy to determine structures of ribosomes stalled on a diverse array of novel arrest peptides, including arrest peptides that target elongating ribosomes as well as arrest peptides specifically targeting translation termination. In addition, we will determine structures of specialized protein factors in complex with ribosomes stalled on problematic nascent chain sequences, in order to visualize how these protein factors can promote translation and rescue the stalled ribosomes.

• DFG Programme: Research Grants