The ribosome was believed to function like a well-tuned molecular machine due its highly conserved role in catalyzing protein synthesis from messenger RNA (mRNA). Our preliminary data challenge this paradigm, and instead supports the existence of a ribosome code, whereby ribosomes with distinct compositions translate specific mRNAs. As such, the ribosome code would greatly impact our understanding of gene regulation, and our ability to make proteins for biotechnology, including for biomass degradation to achieve more efficient biofuel production. In this work, we will capitalize on our preliminary findings in Neurospora crassa showing that changes occur in 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 currently not available at Texas A&M University, to identify and quantitate ribosomal proteins from intact ribosomes, examine changes in modifications of the ribosomal proteins, and changes in accessory proteins that interact with ribosomes, from cells harvested at different times of the day. Once differences in ribosome composition are identified, we will carry out ribosome profiling in wild type and mutant cells that will allow us to exclusively generate a desired type of ribosome at Texas A&M University, and sequence the libraries in collaboration with the JGI, to determine the mechanisms by which ribosome heterogeneity alters the specificity of mRNA translation. This collaborative effort will open up unlimited possibilities for extending this work to investigate the influence of any desired growth condition on ribosome dynamics and protein production.