Specialized Ribosomes: A New Frontier in Gene Regulation
EMSL Project ID
49011
Abstract
A longstanding view in molecular biology is that all the ribosomes in a cell function identically. Our recent preliminary data, and those of others, challenge this dogma, and instead support the existence of a "ribosome code", whereby ribosomes with distinct compositions translate specific mRNAs. Understanding the ribosome code would greatly impact our understanding of gene regulation, and our ability to make proteins for biotechnology, such as for biomass degradation to achieve more efficient biofuel production. In this collaborative work, we will capitalize on our preliminary findings in Neurospora crassa showing that changes occur in the composition of the ribosome over the course of the day under control of the circadian clock. We will utilize the state of the art mass spectroscopy facilities at EMSL, which are not available at Texas A&M University, to do a much more precise determination of how the clock affects the type, quantity, and modifications of ribosomal proteins and accessory proteins that interact with ribosomes. To determine which mRNAs are translated by ribosomes with a specific rprotein composition, we will generate mutants that misexpress specific rproteins or accessory proteins, or express rproteins with altered posttranslational modification sites identified in our preliminary data and in Aim 1. We will then carry out genome-wide mapping of ribosome binding to mRNAs (ribosome profiling) in WT cells and in selected mutants to determine how ribosome composition affects the choice of which mRNAs get translated. The ribosome profiling will be coupled with RNA-seq from the same samples to control for any changes in mRNA levels in the mutant cells. The resulting ribosome profiling and RNA-seq libraries will be sequenced in collaboration with the JGI, and the data will be analyzed at Texas A&M to determine how changes in ribosome composition alter the specificity of mRNA translation. Our results will yield insight into new ways to alter protein expression, improve biofuel production, and will have a major impact on our understanding of fundamental mechanisms of gene expression.
Project Details
Project type
FICUS Research
Start Date
2015-10-01
End Date
2017-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)