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Ben-Zvi, Tamar; Pushkarev, Alina; Seri, Hemda; Elgrably-Weiss, Maya; Papenfort, Kai; Altuvia, Shoshy (2019): mRNA dynamics and alternative conformations adopted under low and high arginine concentrations control polyamine biosynthesis in Salmonella.
In: PLOS Genetics 15(2), e1007646
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Abstract

Putrescine belongs to the large group of polyamines, an essential class of metabolites that exists throughout all kingdoms of life. The Salmonella speF gene encodes an inducible ornithine decarboxylase that produces putrescine from ornithine. Putrescine can be also synthesized from arginine in a parallel metabolic pathway. Here, we show that speF expression is controlled at multiple levels through regulatory elements contained in a long leader sequence. At the heart of this regulation is a short open reading frame, orf34, which is required for speF production. Translation of orf34 interferes with Rho-dependent transcription termination and helps to unfold an inhibitory RNA structure sequestering speF ribosome-binding site. Two consecutive arginine codons in the conserved domain of orf34 provide a third level of speF regulation. Uninterrupted translation of orf34 under conditions of high arginine allows the formation of a speF mRNA structure that is degraded by RNase G, whereas ribosome pausing at the consecutive arginine codons in the absence of arginine enables the formation of an alternative structure that is resistant to RNase G. Thus, the rate of ribosome progression during translation of the upstream ORF influences the dynamics of speF mRNA folding and putrescine production. The identification of orf34 and its regulatory functions provides evidence for the evolutionary conservation of ornithine decarboxylase regulatory elements and putrescine production. Author summary Polyamines are widely distributed in nature, they bind nucleic acids and proteins and although their exact mechanism of action is not clear, their effect on fundamental cellular functions is well documented. The canonical biosynthesis pathway of polyamines is conserved and begins with speF encoding ornithine decarboxylase, an inducible enzyme that produces putrescine from ornithine. Putrescine can also be produced from arginine in an alternative metabolic pathway. Here, we show that the rate of ribosome progression during translation of a short ORF (ORF34) upstream of speF influences the dynamics of speF mRNA folding and thus putrescine production. Uninterrupted translation of orf34 carrying two consecutive arginine codons, under conditions of high arginine, results in the formation of a speF mRNA structure that is degraded by RNase G, whereas ribosomes slow-down at the consecutive arginine codons in the absence of arginine enables the formation of an alternative structure that is unsusceptible to RNase G and thus results in putrescine production. The study of Salmonella speF regulation provides evidence that, despite variations in the mechanistic details, RNA-based regulation of putrescine biosynthesis and ornithine decarboxylase is conserved from bacteria to mammals.