Binding interface between the Salmonella σ(S)/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl
| Autor: | Christina Sizun, Jacques Bellalou, Claudine Mayer, Véronique Monteil, Mireille Nowakowski, Fabienne Levi-Acobas, Françoise Norel, François Bontems, Paola Cavaliere |
|---|---|
| Přispěvatelé: | Systèmes macromoléculaires et Signalisation, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Production de Protéines Recombinantes (Plate-Forme) (PRPF), Université Paris Diderot - Paris 7 (UPD7), Microbiologie structurale - Structural Microbiology (Microb. Struc. (UMR_3528 / U-Pasteur_5)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French National Research Agency [grant ANR- 11-BSV3-009], the IR-RMN-THC (CNRS FR3050) for access to the 950 MHz spectrometer at Gif-sur-Yvette for preliminary experiments and by grants from the Institut Pasteur and the Centre National de la Recherche Scientifique. The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572, www.wenmr.eu), supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan, the Latin America GRID infrastructure via the Gisela project and the US Open Science Grid (OSG) are acknowledged for the use of web portals, computing and storage facilities., ANR-11-BSV3-0009,SIGMADAPT,Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement(2011), European Project: 261572,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-2,WENMR(2010), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie des Substances Naturelles ( ICSN ), Centre National de la Recherche Scientifique ( CNRS ), Production de Protéines Recombinantes (Plate-Forme) ( PRPF ), Université Paris Diderot - Paris 7 ( UPD7 ), Microbiologie structurale, ANR-11-BSV3-0009,SIGMADAPT,Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement ( 2011 ), European Project : 261572,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-2,WENMR ( 2010 ), Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), ANR-11-BSV3-0009, SIGMADAPT, Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement(2011), European Project : 261572, EC:FP7:INFRA, FP7-INFRASTRUCTURES-2010-2, WENMR(2010) |
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
MESH : Models
Chemical MESH: Pseudomonas aeruginosa/metabolism MESH : Molecular Sequence Data Protein Conformation MESH : Protein Subunits Plasma protein binding MESH: Amino Acid Sequence MESH: DNA-Directed RNA Polymerases/chemistry chemistry.chemical_compound Protein structure MESH: Protein Conformation MESH: Structure-Activity Relationship MESH : Sigma Factor/ultrastructure MESH: Bacterial Proteins/ultrastructure Salmonella Sigma factor [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology RNA polymerase MESH: Sigma Factor/metabolism MESH: DNA-Directed RNA Polymerases/metabolism MESH : Structure-Activity Relationship MESH : Protein Conformation Genetics Multidisciplinary MESH : Amino Acid Sequence MESH: Models Chemical food and beverages MESH : Protein Binding DNA-Directed RNA Polymerases MESH: Protein Subunits MESH : Bacterial Proteins/ultrastructure MESH: Amino Acid Substitution Molecular Docking Simulation [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology Biochemistry Pseudomonas aeruginosa MESH : Molecular Docking Simulation MESH: Bacterial Proteins/metabolism Protein Binding MESH: Bacterial Proteins/chemistry MESH : Salmonella/metabolism MESH : Pseudomonas aeruginosa/metabolism MESH : Sigma Factor/chemistry Protein subunit Molecular Sequence Data MESH : DNA-Directed RNA Polymerases/chemistry Sigma Factor Biology Article Structure-Activity Relationship MESH: DNA-Directed RNA Polymerases/ultrastructure MESH : DNA-Directed RNA Polymerases/ultrastructure MESH : Amino Acid Substitution Bacterial Proteins Species Specificity [SDV.BBM] Life Sciences [q-bio]/Biochemistry Molecular Biology MESH: Molecular Docking Simulation MESH: Sigma Factor/chemistry MESH : Species Specificity MESH : Bacterial Proteins/chemistry MESH: Protein Binding MESH: Species Specificity [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Amino Acid Sequence MESH : DNA-Directed RNA Polymerases/metabolism Binding site Gene [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology Binding Sites MESH: Molecular Sequence Data fungi MESH : Sigma Factor/metabolism Protein Subunits Amino Acid Substitution Models Chemical chemistry MESH: Binding Sites MESH : Bacterial Proteins/metabolism MESH: Salmonella/metabolism rpoS MESH : Binding Sites MESH: Sigma Factor/ultrastructure |
| Zdroj: | Scientific Reports Scientific Reports, 2015, 5, pp.13564. ⟨10.1038/srep13564⟩ Scientific Reports, Nature Publishing Group, 2015, 5, pp.13564. ⟨10.1038/srep13564⟩ Scientific Reports, Nature Publishing Group, 2015, 5, pp.13564. 〈10.1038/srep13564〉 HAL-Pasteur Hyper Article en Ligne OpenAIRE INRIA a CCSD electronic archive server Europe PubMed Central Hal-Diderot |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/srep13564⟩ |
| Popis: | International audience; In many Gram-negative bacteria, including Salmonella enterica serovar Typhimurium (S. Typhimurium), the sigma factor RpoS/σ S accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σ S binding to the Crl protein increases σ S activity by favouring its association to E. Taking advantage of evolution of the σ S sequence in bacterial species that do not contain a crl gene, like Pseudomonas aeruginosa, we identified and assigned a critical arginine residue in σ S to the S. Typhimurium σ S-Crl binding interface. We solved the solution structure of S. Typhimurium Crl by NMR and used it for NMR binding assays with σ S and to generate in silico models of the σ S-Crl complex constrained by mutational analysis. The σ S-Crl models suggest that the identified arginine in σ S interacts with an aspartate of Crl that is required for σ S binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σ S-Crl complex. In bacteria, a primary housekeeping sigma factor and one or more alternative σ factors associate with the catalytically active RNA polymerase (RNAP) core enzyme (α 2β β 'ω , E), to form the holoenzyme Eσ , and direct transcription initiation of specific subsets of genes 1,2. In many Gram-negative bacteria, σ S /RpoS is produced during late exponential phase, or in response to stress, to modify global gene transcription and to allow stationary phase survival and general stress resistance 3–5. In the wide host-range pathogen S. Typhimurium, σ S is not only required for general stress resistance, but also for virulence, biofilm formation and development of the red dry and rough (rdar) morphotype, a colony morphology caused by the production of amyloid fibers (curli) and cellulose 6–8. The efficiency of formation of the housekeeping and alternative Eσ can be modulated by regulatory factors that bind E and/or σ 5,9. So far, Crl is the only known σ S-dedicated regulatory factor that enhances σ S activity through a direct interaction, favouring Eσ S formation 7,10–15. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|