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Coronel-Tellez RH, Pospiech M, Barrault M, Liu W, Bordeau V, Vasnier C, Felden B, Sargueil B, Bouloc P. sRNA-controlled iron sparing response in Staphylococci. Nucleic Acids Res 2022; 50:8529-8546. [PMID: 35904807 PMCID: PMC9410917 DOI: 10.1093/nar/gkac648] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/14/2022] Open
Abstract
Staphylococcus aureus, a human opportunist pathogen, adjusts its metabolism to cope with iron deprivation within the host. We investigated the potential role of small non-coding RNAs (sRNAs) in dictating this process. A single sRNA, named here IsrR, emerged from a competition assay with tagged-mutant libraries as being required during iron starvation. IsrR is iron-repressed and predicted to target mRNAs expressing iron-containing enzymes. Among them, we demonstrated that IsrR down-regulates the translation of mRNAs of enzymes that catalyze anaerobic nitrate respiration. The IsrR sequence reveals three single-stranded C-rich regions (CRRs). Mutational and structural analysis indicated a differential contribution of these CRRs according to targets. We also report that IsrR is required for full lethality of S. aureus in a mouse septicemia model, underscoring its role as a major contributor to the iron-sparing response for bacterial survival during infection. IsrR is conserved among staphylococci, but it is not ortholog to the proteobacterial sRNA RyhB, nor to other characterized sRNAs down-regulating mRNAs of iron-containing enzymes. Remarkably, these distinct sRNAs regulate common targets, illustrating that RNA-based regulation provides optimal evolutionary solutions to improve bacterial fitness when iron is scarce.
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Affiliation(s)
- Rodrigo H Coronel-Tellez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198, Gif-sur-Yvette, France
| | - Mateusz Pospiech
- CNRS UMR 8038, CitCoM, Université Paris Cité 75006, Paris, France
| | - Maxime Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198, Gif-sur-Yvette, France
| | - Wenfeng Liu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198, Gif-sur-Yvette, France
| | - Valérie Bordeau
- Université de Rennes 1, BRM (Bacterial regulatory RNAs and Medicine) UMR_S 1230 35000, Rennes, France
| | | | - Brice Felden
- Université de Rennes 1, BRM (Bacterial regulatory RNAs and Medicine) UMR_S 1230 35000, Rennes, France
| | - Bruno Sargueil
- CNRS UMR 8038, CitCoM, Université Paris Cité 75006, Paris, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198, Gif-sur-Yvette, France
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De Bisschop G, Allouche D, Frezza E, Masquida B, Ponty Y, Will S, Sargueil B. Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. Noncoding RNA 2021; 7:71. [PMID: 34842779 PMCID: PMC8628965 DOI: 10.3390/ncrna7040071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
As more sequencing data accumulate and novel puzzling genetic regulations are discovered, the need for accurate automated modeling of RNA structure increases. RNA structure modeling from chemical probing experiments has made tremendous progress, however accurately predicting large RNA structures is still challenging for several reasons: RNA are inherently flexible and often adopt many energetically similar structures, which are not reliably distinguished by the available, incomplete thermodynamic model. Moreover, computationally, the problem is aggravated by the relevance of pseudoknots and non-canonical base pairs, which are hardly predicted efficiently. To identify nucleotides involved in pseudoknots and non-canonical interactions, we scrutinized the SHAPE reactivity of each nucleotide of the 188 nt long lariat-capping ribozyme under multiple conditions. Reactivities analyzed in the light of the X-ray structure were shown to report accurately the nucleotide status. Those that seemed paradoxical were rationalized by the nucleotide behavior along molecular dynamic simulations. We show that valuable information on intricate interactions can be deduced from probing with different reagents, and in the presence or absence of Mg2+. Furthermore, probing at increasing temperature was remarkably efficient at pointing to non-canonical interactions and pseudoknot pairings. The possibilities of following such strategies to inform structure modeling software are discussed.
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Affiliation(s)
- Grégoire De Bisschop
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Delphine Allouche
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut Necker-Enfants Malades (INEM), Inserm U1151, 156 rue de Vaugirard, CEDEX 15, 75015 Paris, France
| | - Elisa Frezza
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
| | - Benoît Masquida
- Université de Strasbourg, CNRS UMR7156 GMGM, 67084 Strasbourg, France;
| | - Yann Ponty
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Sebastian Will
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Bruno Sargueil
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
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