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Ganske A, Busch LM, Hentschker C, Reder A, Michalik S, Surmann K, Völker U, Mäder U. Exploring the targetome of IsrR, an iron-regulated sRNA controlling the synthesis of iron-containing proteins in Staphylococcus aureus. Front Microbiol 2024; 15:1439352. [PMID: 39035440 PMCID: PMC11257911 DOI: 10.3389/fmicb.2024.1439352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
Staphylococcus aureus is a common colonizer of the skin and nares of healthy individuals, but also a major cause of severe human infections. During interaction with the host, pathogenic bacteria must adapt to a variety of adverse conditions including nutrient deprivation. In particular, they encounter severe iron limitation in the mammalian host through iron sequestration by haptoglobin and iron-binding proteins, a phenomenon called "nutritional immunity." In most bacteria, including S. aureus, the ferric uptake regulator (Fur) is the key regulator of iron homeostasis, which primarily acts as a transcriptional repressor of genes encoding iron acquisition systems. Moreover, Fur can control the expression of trans-acting small regulatory RNAs that play an important role in the cellular iron-sparing response involving major changes in cellular metabolism under iron-limiting conditions. In S. aureus, the sRNA IsrR is controlled by Fur, and most of its predicted targets are iron-containing proteins and other proteins related to iron metabolism and iron-dependent pathways. To characterize the IsrR targetome on a genome-wide scale, we combined proteomics-based identification of potential IsrR targets using S. aureus strains either lacking or constitutively expressing IsrR with an in silico target prediction approach, thereby suggesting 21 IsrR targets, of which 19 were negatively affected by IsrR based on the observed protein patterns. These included several Fe-S cluster- and heme-containing proteins, such as TCA cycle enzymes and catalase encoded by katA. IsrR affects multiple metabolic pathways connected to the TCA cycle as well as the oxidative stress response of S. aureus and links the iron limitation response to metabolic remodeling. In contrast to the majority of target mRNAs, the IsrR-katA mRNA interaction is predicted upstream of the ribosome binding site, and further experiments including mRNA half-life measurements demonstrated that IsrR, in addition to inhibiting translation initiation, can downregulate target protein levels by affecting mRNA stability.
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Affiliation(s)
| | | | | | | | | | | | | | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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2
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Barrault M, Chabelskaya S, Coronel-Tellez RH, Toffano-Nioche C, Jacquet E, Bouloc P. Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity. Nucleic Acids Res 2024:gkae506. [PMID: 38869061 DOI: 10.1093/nar/gkae506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Pathogenic bacteria employ complex systems to cope with metal ion shortage conditions and propagate in the host. IsrR is a regulatory RNA (sRNA) whose activity is decisive for optimum Staphylococcus aureus fitness upon iron starvation and for full virulence. IsrR down-regulates several genes encoding iron-containing enzymes to spare iron for essential processes. Here, we report that IsrR regulates the tricarboxylic acid (TCA) cycle by controlling aconitase (CitB), an iron-sulfur cluster-containing enzyme, and its transcriptional regulator, CcpE. This IsrR-dependent dual-regulatory mechanism provides an RNA-driven feedforward loop, underscoring the tight control required to prevent aconitase expression. Beyond its canonical enzymatic role, aconitase becomes an RNA-binding protein with regulatory activity in iron-deprived conditions, a feature that is conserved in S. aureus. Aconitase not only negatively regulates its own expression, but also impacts the enzymes involved in both its substrate supply and product utilization. This moonlighting activity concurrently upregulates pyruvate carboxylase expression, allowing it to compensate for the TCA cycle deficiency associated with iron scarcity. These results highlight the cascade of complex posttranscriptional regulations controlling S. aureus central metabolism in response to iron deficiency.
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Affiliation(s)
- Maxime Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Svetlana Chabelskaya
- Université de Rennes 1, BRM (Bacterial regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Rodrigo H Coronel-Tellez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR2301, 91198 Gif-sur-Yvette, 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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3
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Warrier I, Perry A, Hubbell SM, Eichelman M, van Opijnen T, Meyer MM. RNA cis-regulators are important for Streptococcus pneumoniae in vivo success. PLoS Genet 2024; 20:e1011188. [PMID: 38442125 PMCID: PMC10942264 DOI: 10.1371/journal.pgen.1011188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/15/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms.
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Affiliation(s)
- Indu Warrier
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ariana Perry
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Sara M. Hubbell
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Matthew Eichelman
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Boston Children’s Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michelle M. Meyer
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
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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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5
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Abstract
Bacterial small RNAs (sRNAs) contribute to a variety of regulatory mechanisms that modulate a wide range of pathways, including metabolism, virulence, and antibiotic resistance. We investigated the involvement of sRNAs in rifampicin resistance in the opportunistic pathogen Staphylococcus aureus. Using a competition assay with an sRNA mutant library, we identified 6S RNA as being required for protection against low concentrations of rifampicin, an RNA polymerase (RNAP) inhibitor. This effect applied to rifabutin and fidaxomicin, two other RNAP-targeting antibiotics. 6S RNA is highly conserved in bacteria, and its absence in two other major pathogens, Salmonella enterica and Clostridioides difficile, also impaired susceptibility to RNAP inhibitors. In S. aureus, 6S RNA is produced from an autonomous gene and accumulates in stationary phase. In contrast to what was reported for Escherichia coli, S. aureus 6S RNA does not appear to play a critical role in the transition from exponential to stationary phase but affects σB-regulated expression in prolonged stationary phase. Nevertheless, its protective effect against rifampicin is independent of alternative sigma factor σB activity. Our results suggest that 6S RNA helps maintain RNAP-σA integrity in S. aureus, which could in turn help bacteria withstand low concentrations of RNAP inhibitors.
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Le Huyen KB, Gonzalez CD, Pascreau G, Bordeau V, Cattoir V, Liu W, Bouloc P, Felden B, Chabelskaya S. A small regulatory RNA alters Staphylococcus aureus virulence by titrating RNAIII activity. Nucleic Acids Res 2021; 49:10644-10656. [PMID: 34554192 PMCID: PMC8501977 DOI: 10.1093/nar/gkab782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 01/17/2023] Open
Abstract
Staphylococcus aureus is an opportunistic human and animal pathogen with an arsenal of virulence factors that are tightly regulated during bacterial infection. The latter is achieved through a sophisticated network of regulatory proteins and regulatory RNAs. Here, we describe the involvement of a novel prophage-carried small regulatory S. aureus RNA, SprY, in the control of virulence genes. An MS2-affinity purification assay reveals that SprY forms a complex in vivo with RNAIII, a major regulator of S. aureus virulence genes. SprY binds to the 13th stem-loop of RNAIII, a key functional region involved in the repression of multiple mRNA targets. mRNAs encoding the repressor of toxins Rot and the extracellular complement binding protein Ecb are among the targets whose expression is increased by SprY binding to RNAIII. Moreover, SprY decreases S. aureus hemolytic activity and virulence. Our results indicate that SprY titrates RNAIII activity by targeting a specific stem loop. Thus, we demonstrate that a prophage-encoded sRNA reduces the pathogenicity of S. aureus through RNA sponge activity.
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Affiliation(s)
- Kim Boi Le Huyen
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | | | - Gaëtan Pascreau
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Valérie Bordeau
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Vincent Cattoir
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Wenfeng Liu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Brice Felden
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Svetlana Chabelskaya
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
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Monk IR, Stinear TP. From cloning to mutant in 5 days: rapid allelic exchange in Staphylococcus aureus. Access Microbiol 2021; 3:000193. [PMID: 34151146 PMCID: PMC8209637 DOI: 10.1099/acmi.0.000193] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/11/2020] [Indexed: 12/02/2022] Open
Abstract
In the last 10 years, the barriers preventing the uptake of foreign DNA by clinical Staphylococcus aureus isolates have been identified and powerful mutagenesis techniques such as allelic exchange are now possible in most genotypes. However, these targeted approaches can still be cumbersome, and the construction of unmarked deletions/point mutations may take many weeks or months. Here, we introduce a streamlined allelic exchange protocol using IMxxB Escherichia coli and the plasmid pIMAY-Z. With this optimized approach, a site-specific mutation can be introduced into S. aureus in 5 days, from the start of cloning to isolation of genomic DNA for confirmatory whole-genome sequencing. This streamlined protocol considerably reduces the time required to introduce a specific, unmarked mutation in S. aureus and should dramatically improve the scalability of gene-function studies.
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Affiliation(s)
- Ian R. Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
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8
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Liu W, Boudry P, Bohn C, Bouloc P. Staphylococcus aureus pigmentation is not controlled by Hfq. BMC Res Notes 2020; 13:63. [PMID: 32033621 PMCID: PMC7007678 DOI: 10.1186/s13104-020-4934-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/01/2020] [Indexed: 02/04/2023] Open
Abstract
Objective The golden color of Staphylococcus aureus is due to the synthesis of carotenoid pigments. In Gram-negative bacteria, Hfq is a global posttranscriptional regulator, but its function in S. aureus remains obscure. The absence of Hfq in S. aureus was reported to correlate with production of carotenoid pigment leading to the conclusion that Hfq was a negative regulator of the yellow color. However, we reported the construction of hfq mutants in several S. aureus strains and never noticed any color change; we therefore revisited the question of Hfq implication in S. aureus pigmentation. Results The absence or accumulation of Hfq does not affect S. aureus pigmentation.
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Affiliation(s)
- Wenfeng Liu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pierre Boudry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Chantal Bohn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, 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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Wang Y, Jin M, Chen G, Cui X, Zhang Y, Li M, Liao Y, Zhang X, Qin G, Yan F, Abd El-Aty A, Wang J. Bio-barcode detection technology and its research applications: A review. J Adv Res 2019; 20:23-32. [PMID: 31193255 PMCID: PMC6522771 DOI: 10.1016/j.jare.2019.04.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
With the rapid development of nanotechnology, the bio-barcode assay (BCA), as a new diagnostic tool, has been gradually applied to the detection of protein and nucleic acid targets and small-molecule compounds. BCA has the advantages of high sensitivity, short detection time, simple operation, low cost, good repeatability and good linear relationship between detection results. However, bio-barcode technology is not yet fully formed as a complete detection system, and the detection process in all aspects and stages is unstable. Therefore, studying the optimal reaction conditions, optimizing the experimental steps, exploring the multi-residue detection of small-molecule substances, and preparing immuno-bio-barcode kits are important research directions for the standardization and commercialization of BCA. The main theme of this review was to describe the principle of BCA, provide a comparison of its application, and introduce the single-residue and multi-residue detection of macromolecules and single-residue detection of small molecules. We also compared it with other detection methods, summarized its feasibility and limitations, expecting that with further improvement and development, the technique can be more widely used in the field of stable small-molecule and multi-residue detection.
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Affiliation(s)
- Yuanshang Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Ge Chen
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Xueyan Cui
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Yudan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Mingjie Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Yun Liao
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Xiuyuan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Guoxin Qin
- Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, PR China
| | - Feiyan Yan
- Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, PR China
| | - A.M. Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
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10
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Riffaud C, Pinel-Marie ML, Pascreau G, Felden B. Functionality and cross-regulation of the four SprG/SprF type I toxin-antitoxin systems in Staphylococcus aureus. Nucleic Acids Res 2019; 47:1740-1758. [PMID: 30551143 PMCID: PMC6393307 DOI: 10.1093/nar/gky1256] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 01/21/2023] Open
Abstract
Toxin–antitoxin (TA) systems are ubiquitous among bacteria, frequently expressed in multiple copies, and important for functions such as antibiotic resistance and persistence. Type I TA systems are composed of a stable toxic peptide whose expression is repressed by an unstable RNA antitoxin. Here, we investigated the functionalities, regulation, and possible cross-talk between three core genome copies of the pathogenicity island-encoded ‘sprG1/sprF1’ type I TA system in the human pathogen Staphylococcus aureus. Except for SprG4, all RNA from these pairs, sprG2/sprF2, sprG3/sprF3, sprG4/sprF4, are expressed in the HG003 strain. SprG2 and SprG3 RNAs encode toxic peptides whose overexpression triggers bacteriostasis, which is counteracted at the RNA level by the overexpression of SprF2 and SprF3 antitoxins. Complex formation between each toxin and its cognate antitoxin involves their overlapping 3′ ends, and each SprF antitoxin specifically neutralizes the toxicity of its cognate SprG toxin without cross-talk. However, overexpression studies suggest cross-regulations occur at the RNA level between the SprG/SprF TA systems during growth. When subjected to H2O2-induced oxidative stress, almost all antitoxin levels dropped, while only SprG1 and SprF1 were reduced during phagocytosis-induced oxidative stress. SprG1, SprF1, SprF2, SprG3 and SprF3 levels also decrease during hyperosmotic stress. This suggests that novel SprG/SprF TA systems are involved in S. aureus persistence.
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Affiliation(s)
- Camille Riffaud
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Marie-Laure Pinel-Marie
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Gaëtan Pascreau
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Brice Felden
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
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11
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Mikheyeva IV, Thomas JM, Kolar SL, Corvaglia AR, Gaϊa N, Leo S, Francois P, Liu GY, Rawat M, Cheung AL. YpdA, a putative bacillithiol disulfide reductase, contributes to cellular redox homeostasis and virulence in Staphylococcus aureus. Mol Microbiol 2019; 111:1039-1056. [PMID: 30636083 DOI: 10.1111/mmi.14207] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2018] [Indexed: 11/28/2022]
Abstract
The intracellular redox environment of Staphylococcus aureus is mainly buffered by bacillithiol (BSH), a low molecular weight thiol. The identity of enzymes responsible for the recycling of oxidized bacillithiol disulfide (BSSB) to the reduced form (BSH) remains elusive. We examined YpdA, a putative bacillithiol reductase, for its role in maintaining intracellular redox homeostasis. The ypdA mutant showed increased levels of BSSB and a lower bacillithiol redox ratio vs. the isogenic parent, indicating a higher level of oxidative stress within the bacterial cytosol. We showed that YpdA consumed NAD(P)H; and YpdA protein levels were augmented in response to stress. Wild type strains overexpressing YpdA showed increased tolerance to oxidants and electrophilic agents. Importantly, YpdA overexpression in the parental strain caused an increase in BSH levels accompanied by a decrease in BSSB concentration in the presence of stress, resulting in an increase in bacillithiol redox ratio vs. the vector control. Additionally, the ypdA mutant exhibited decreased survival in human neutrophils (PMNs) as compared with the parent, while YpdA overexpression protected the resulting strain from oxidative stress in vitro and from killing by human neutrophils ex vivo. Taken together, these data present a new role for YpdA in S. aureus physiology and virulence through the bacillithiol system.
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Affiliation(s)
- Irina V Mikheyeva
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jason M Thomas
- Biology Department, California State University, Fresno, Fresno, CA 93740, USA
| | - Stacey L Kolar
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Nadia Gaϊa
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Stefano Leo
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Patrice Francois
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - George Y Liu
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Rawat
- Biology Department, California State University, Fresno, Fresno, CA 93740, USA
| | - Ambrose L Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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12
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Rochat T, Bohn C, Morvan C, Le Lam T, Razvi F, Pain A, Toffano-Nioche C, Ponien P, Jacq A, Jacquet E, Fey PD, Gautheret D, Bouloc P. The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus. Nucleic Acids Res 2018; 46:8803-8816. [PMID: 29986060 PMCID: PMC6158497 DOI: 10.1093/nar/gky584] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 05/28/2018] [Accepted: 06/29/2018] [Indexed: 01/31/2023] Open
Abstract
RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of ΔrsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.
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Affiliation(s)
- Tatiana Rochat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Chantal Bohn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Claire Morvan
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Thao Nguyen Le Lam
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Fareha Razvi
- University of Nebraska Medical Center, Department of Pathology and Microbiology, Omaha, NE, USA
| | - Adrien Pain
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Claire Toffano-Nioche
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Annick Jacq
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Paul D Fey
- University of Nebraska Medical Center, Department of Pathology and Microbiology, Omaha, NE, USA
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
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Liu W, Rochat T, Toffano-Nioche C, Le Lam TN, Bouloc P, Morvan C. Assessment of Bona Fide sRNAs in Staphylococcus aureus. Front Microbiol 2018. [PMID: 29515534 PMCID: PMC5826253 DOI: 10.3389/fmicb.2018.00228] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches.
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Affiliation(s)
- Wenfeng Liu
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tatiana Rochat
- VIM, Institut National de la Recherche Agronomique, Université Paris-Saclay, Institut National de la Recherche Agronomique Centre Jouy-en-Josas, Jouy-en-Josas, France
| | - Claire Toffano-Nioche
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thao Nguyen Le Lam
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Claire Morvan
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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