Endogenously Encoded Ribosomal RNA Sequence Variation Within the Assemble Ribosome Can Regulate Stress Response Gene Expression and Phenotype

Prevailing dogma holds that ribosomes are uniform in composition and function. Single-molecule investigations of translation reveal, however, that the ribosome and translation factors visit metastable, transient intermediates that can be highly sensitive to even modest perturbations, including small-molecule drugs and single-nucleotide substitutions in ribosomal RNA (rRNA). These insights suggest the possibility that subtle changes in the ribosome's composition may have functional impacts. Recent evidence further implicates changes in the ribosome's core protein composition with gene-specific changes in translational efficiency. In this light, we set out to examine the potential physiological impacts of endogenously encoded sequence variations in the rRNA components of the assembled ribosome. Mammalian genomes encode hundreds of ribosomal DNA operons (rDNA) that exhibit extensive sequence variation with the rRNA components of the ribosome, which are both conserved and expressed in a tissue-specific fashion. Using E.coli as a genetically tractable model system, we now show that nutrient limitation-induced stress changes the relative expression of rDNA operons to alter the ribosomal RNA (rRNA) composition within the actively translating ribosome pool. The most upregulated operon encodes the unique 16S rRNA gene, rrsH, distinguished by conserved sequence variation within the small ribosomal subunit. rrsH-bearing ribosomes alter the levels of the RpoS sigma factor, the master regulator of the general stress response, to affect the expression of functionally coherent gene sets. These impacts are associated with phenotypic changes in antibiotic sensitivity, biofilm formation, and cell motility, and are regulated by ribosome-associated stress response proteins. Specific aspects of these phenotypic differences could be reconstituted in vitro using highly purified translation components. These findings establish that endogenously encoded, naturally occurring rRNA sequence variation can modulate ribosome function, central aspects of gene expression regulation, and cellular physiology.