AltORF-encoded microprotein recruits primary-ORF-encoded dehydrogenase to cell poles upon heat shock

Abstract

Alternative open reading frames (altORFs) initiating from in-frame or out-of-frame start sites within annotated protein-coding genes represent a largely unexplored source of protein-coding potential and remain poorly understood in terms of regulation, function, and impact on physiology. Here we investigate Escherichia coli GndA, encoded by an out-of-frame altORF within gnd, which encodes 6-phosphogluconate dehydrogenase. We observe that the GndA protein is induced by heat shock, consistent with the initial identification in a quantitative membrane proteomics screen, but is unstable, while the levels of the stable Gnd dehydrogenase are unchanged. Using translational fusion assays and in vivo RNA structure probing, we show that an internal complementary sequence upstream of gndA acts as a thermo-responsive secondary RNA structure controlling GndA translation. Mutagenesis of either gnd or gndA reduce heat shock survival of E. coli indicating both gene products are important for resistance. GndA fractionates with membranes consistent with in silico predictions that the protein forms an amphipathic -helix. In contrast, Gnd is predominantly cytoplasmic but shows GndA-dependent relocalization to cell poles upon heat shock. Together, our results demonstrate that an altORF-encoded microprotein is required for stress-dependent relocalization of its primary ORF partner, revealing a functional interplay between proteins encoded by overlapping ORFs in bacterial stress adaptation.