Staphylococcus aureus RNAIII is one of the main intracellular effectors of the quorum-sensing system. It is a multifunctional RNA that encodes a small peptide, and its noncoding parts act as antisense RNAs to regulate the translation and/or the stability of mRNAs encoding transcriptional regulators, major virulence factors, and cell wall metabolism enzymes. In this review, we explain how regulatory proteins and RNAIII are embedded in complex regulatory circuits to express virulence factors in a dynamic and timely manner in response to stress and environmental and metabolic changes.

Pathogenic bacteria must rapidly adapt to ever‐changing environmental signals resulting in metabolism remodeling. The carbon catabolite repression, mediated by the catabolite control protein A (CcpA), is used to express genes involved in utilization and metabolism of the preferred carbon source. Here, we have identified RsaI as a CcpA‐repressed small non‐coding RNA that is inhibited by high glucose concentrations. When glucose is consumed, RsaI represses translation initiation of mRNAs encoding a permease of glucose uptake and the FN3K enzyme that protects proteins against damage caused by high glucose concentrations. RsaI also binds to the 3′ untranslated region of icaR mRNA encoding the transcriptional repressor of exopolysaccharide production and to sRNAs induced by the uptake of glucose‐6 phosphate or nitric oxide. Furthermore, RsaI expression is accompanied by a decreased transcription of genes involved in carbon catabolism pathway and an activation of genes involved in energy production, fermentation, and nitric oxide detoxification. This multifaceted RNA can be considered as a metabolic signature when glucose becomes scarce and growth is arrested.

Cells adapt to environmental changes by efficiently adjusting gene expression programs. Staphylococcus aureus, an opportunistic pathogenic bacterium, switches between defensive and offensive modes in response to quorum sensing signal. We identified and studied the structural characteristics and dynamic properties of the core regulatory circuit governing this switch by deterministic and stochastic computational methods, as well as experimentally. This module, termed here Double Selector Switch (DSS), comprises the RNA regulator RNAIII and the transcription factor Rot, defining a double-layered switch involving both transcriptional and post-transcriptional regulations. It coordinates the inverse expression of two sets of target genes, immuno-modulators and exotoxins, expressed during the defensive and offensive modes, respectively. Our computational and experimental analyses show that the DSS guarantees fine-tuned coordination of the inverse expression of its two gene sets, tight regulation, and filtering of noisy signals. We also identified variants of this circuit in other bacterial systems, suggesting it is used as a molecular switch in various cellular contexts and offering its use as a template for an effective switching device in synthetic biology studies.

30Pathogenic bacteria must rapidly adapt to ever-changing environmental signals or nutrient 31 availability resulting in metabolism remodeling. The carbon catabolite repression represents 32 a global regulatory system, allowing the bacteria to express genes involved in carbon 33 utilization and metabolization of the preferred carbon source. In Staphylococcus aureus, 34 regulation of catabolite repressing genes is mediated by the carbon catabolite protein A 35 (CcpA). Here, we have identified a CcpA-dependent small non-coding RNA, RsaI that is 36 inhibited by high glucose concentrations. RsaI represses the translation of mRNAs encoding 37 a major permease of glucose uptake, the FN3K enzyme that protects proteins against 38 damages caused by high glucose concentrations, and IcaR, the transcriptional repressor of 39 exopolysaccharide production. Besides, RsaI regulates the activities of other sRNAs 40 responding to the uptake of glucose-6 phosphate or NO. Finally, RsaI inhibits the expression 41 of several enzymes involved in carbon catabolism pathway, and activates genes involved in 42 energy production, fermentation and NO detoxification when the glucose concentration 43 decreases. This multifunctional RNA provides a signature for a metabolic switch when 44 glucose is scarce and growth is arrested. 45 46 47 48All bacteria require a carbon source, providing energy for their growth, division, and for the 49 synthesis of all macromolecules. Besides, pathogenic bacteria during the infectious process 50 of the host, must cope with hostile conditions such as nutrient deficiency, temperature, 51 oxidative and osmotic shocks, and must overcome innate immune responses. For instance, 52Staphylococcus aureus uses carbohydrates to grow under high NO and anaerobiosis (Vitko 53 et al., 2016). To survive in these complex environments and to counteract the host defense, 54 S. aureus produces a plethora of virulence factors. The synthesis of these factors is fine-55 tuned by intricate interactions between multiple regulators involving both proteins and RNAs 56 (Novick, 2003). Additionally, biosynthetic intermediates, generated from the central 57 metabolism of S. aureus, have strong impacts on the synthesis of virulence factors. Besides, 58 several metabolite-sensing regulatory proteins (CcpA, CodY, Rex and RpiR) act as key 59 regulatory factors to coordinate the synthesis of genes involved in metabolic pathways, in 60 stress responses, and in pathogenesis (Somerville and Proctor, 2009; Richardson et al., 61 2015). Through the adaptation of the metabolism of the bacteria to specific host 62 microenvironment, these proteins contribute to S. aureus pathogenesis (Richardson et al., 63 2015). 64Among these proteins, the carbon catabolite protein A (CcpA) acts as a catabolite 65 regulator, allowing the bacteria to use the preferred carbon source (i.e., glucose) in a 66 hierarchical manner (Seidl et al., 2008a;Seidl et al., 2009). CcpA belongs to the LacI 67 repressor family and binds to a specific DNA sequence, called the cre ...

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