Corler, E. | Search bioRxiv

bioRxiv2026

Ribo-seq reveals IsrR-mediated translational repression of SAOUHSC_02924 (gabT) during iron limitation in Staphylococcus aureus

Iron is essential for bacterial growth but can be toxic in excess. To maintain iron homeostasis, bacteria employ regulatory mechanisms, including small RNAs (sRNAs). In Staphylococcus aureus, we identified the sRNA IsrR as a critical mediator of the iron-sparing response, enabling bacterial fitness in iron-limited environments such as those encountered during host infection. Here, we use ribosome profiling (Ribo-seq) to define the translational regulatory network of IsrR under iron-limited conditions. Our analysis identifies multiple genes under IsrR control, including SAOUHSC_02924 (gabT), which encodes a putative 4-aminobutyrate aminotransferase. Given that IsrR downregulates iron-dependent TCA cycle enzymes, we propose that repression of gabT prevents the accumulation of TCA cycle precursors under iron depletion, thereby avoiding metabolic imbalances. These findings expand the role of IsrR in metabolic reprogramming and highlight its contribution to S. aureus survival in iron-restricted host niches.

microbiology↗

bioRxiv2025

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis

Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, little is still known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from Arabidopsis lyrata and characterized the evolution of translated regions genome-wide across the Arabidopsis genus. Synteny analysis revealed 163 actively translated regions in A. lyrata whose coding potential (Open Reading Frames, ORFs or Coding DNA sequences, CDSs) has emerged de novo within the Arabidopsis genus. Most of these de novo translated regions were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved protein-coding genes, and their GC content increased with phylogenetic conservation. Twenty-one of them belonged to previously annotated CDSs, and are therefore promising putative de novo genes, while most were located in intergenic regions and are thus newly discovered. Our results demonstrate the abundance of translation events outside of conserved CDSs, and their role as starting material for the emergence of novel genes in plants. Significance statementA central open question in genome evolution is how novel protein-coding genes arise from noncoding nucleotide DNA sequences and eventually contribute to the stable repertoires of "canonical" genes. Here, we focused specifically on the early stages of this important evolutionary process, whereby previously non-coding intergenic nucleotide sequences eventually acquire open reading frames carrying signatures of active translation. This phenomenon has been crucially under-studied so far, especially in plants. By combining ribosome profiling data and a careful genome comparison strategy among closely related Arabidopsis species, our results demonstrate the pervasive translation and de novo origin of a large number of small intergenic ORFs and illustrate their role as starting material for the emergence of novel genes in plants. Key-words: de novo genes, Arabidopsis, pervasive translation, intergenic ORFs, ribosome profiling

genomics↗