Ribosomal modifications in aging and infection: A dual-purpose research model and translational pathway analysis for global health

Abstract

Ribosomes are molecular machines that drive protein translation, and their dysfunction is central to both communicable and non-communicable diseases. Though ribosomes have historically been viewed as a homogeneous population, there is increasing evidence that chemical modifications to the ribosomal RNA (rRNA)—especially 2’-O-methylations (Nm) and pseudouridylations (Ѱ)—can be placed to varying degrees at different nucleotide sites and thereby affect translation. For instance, in protozoan parasites, specific rRNA sites are modified in order to change gene expression within different host environments. Certain Nm and Ѱ have also been associated with longevity or age-related translational errors, but no systematic study has yet probed the connection between rRNA modification heterogeneity and chronological age. In this thesis, I performed RiboMethSeq and Bisulfite-induced deletion sequencing (BID-seq) on total RNA from aging Caenorhabditis elegans to systematically probe whether Nm and Ѱ vary with age. The sequencing pipelines revealed three different patterns of aging-dependent modification change: one increasing Ѱ on the mitochondrial ribosome; a cluster of four increasing Nm near the peptidyl transferase center; and a likely somatic tissue-specific Nm that changes stoichiometry in total RNA via germline depletion. This research also serves a secondary purpose of technique development, since I establish rRNA modification sequencing tools (i.e. analyzing conserved helices, measuring cleaved fragments, bioinformatic analyses) that could play a role in drug development against protozoan rRNA modifications. Here, I demonstrate a novel connection between rRNA modifications and aging, while also making a methodological contribution that illustrates how fundamental biological principles can be studied to advance research for health problems in both developed and developing countries.