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Evidence-Based Structural Model of the Staphylococcal Repressor Protein: Separation of Functions into Different Domains. PLoS One 2015; 10:e0139086. [PMID: 26414067 PMCID: PMC4634304 DOI: 10.1371/journal.pone.0139086] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/09/2015] [Indexed: 12/05/2022] Open
Abstract
Horizontal transfer of mobile genetic elements within Staphylococci is of high biomedical significance as such elements are frequently responsible for virulence and toxic effects. Staphylococcus-encoded repressor proteins regulate the replication of these mobile genetic elements that are located within the so-called pathogenicity islands. Here, we report structural and functional characterization of one such repressor protein, namely the Stl protein encoded by the pathogenicity island SaPIbov1. We create a 3D structural model and based on this prediction, we investigate the different functionalities of truncated and point mutant constructs. Results suggest that a helix-turn-helix motif governs the interaction of the Stl protein with its cognate DNA site: point mutations within this motif drastically decrease DNA-binding ability, whereas the interaction with the Stl-binding partner protein dUTPase is unperturbed by these point mutations. The 3D model also suggested the potential independent folding of a carboxy-terminal domain. This suggestion was fully verified by independent experiments revealing that the carboxy-terminal domain does not bind to DNA but is still capable of binding to and inhibiting dUTPase. A general model is proposed, which suggests that among the several structurally different repressor superfamilies Stl-like Staphylococcal repressor proteins belong to the helix-turn-helix transcription factor group and the HTH motif is suggested to reside within N-terminal segment.
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Szabó JE, Németh V, Papp-Kádár V, Nyíri K, Leveles I, Bendes AÁ, Zagyva I, Róna G, Pálinkás HL, Besztercei B, Ozohanics O, Vékey K, Liliom K, Tóth J, Vértessy BG. Highly potent dUTPase inhibition by a bacterial repressor protein reveals a novel mechanism for gene expression control. Nucleic Acids Res 2014; 42:11912-20. [PMID: 25274731 PMCID: PMC4231751 DOI: 10.1093/nar/gku882] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transfer of phage-related pathogenicity islands of Staphylococcus aureus (SaPI-s) was recently reported to be activated by helper phage dUTPases. This is a novel function for dUTPases otherwise involved in preservation of genomic integrity by sanitizing the dNTP pool. Here we investigated the molecular mechanism of the dUTPase-induced gene expression control using direct techniques. The expression of SaPI transfer initiating proteins is repressed by proteins called Stl. We found that Φ11 helper phage dUTPase eliminates SaPIbov1 Stl binding to its cognate DNA by binding tightly to Stl protein. We also show that dUTPase enzymatic activity is strongly inhibited in the dUTPase:Stl complex and that the dUTPase:dUTP complex is inaccessible to the Stl repressor. Our results disprove the previously proposed G-protein-like mechanism of SaPI transfer activation. We propose that the transfer only occurs if dUTP is cleared from the nucleotide pool, a condition promoting genomic stability of the virulence elements.
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Affiliation(s)
- Judit E Szabó
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Veronika Németh
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Veronika Papp-Kádár
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kinga Nyíri
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Ibolya Leveles
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Abris Á Bendes
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Imre Zagyva
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gergely Róna
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Hajnalka L Pálinkás
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Balázs Besztercei
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Olivér Ozohanics
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Vékey
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Liliom
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Judit Tóth
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta G Vértessy
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
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Leveles I, Németh V, Szabó JE, Harmat V, Nyíri K, Bendes ÁÁ, Papp-Kádár V, Zagyva I, Róna G, Ozohanics O, Vékey K, Tóth J, Vértessy BG. Structure and enzymatic mechanism of a moonlighting dUTPase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2298-308. [PMID: 24311572 DOI: 10.1107/s0907444913021136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/29/2013] [Indexed: 02/08/2023]
Abstract
Genome integrity requires well controlled cellular pools of nucleotides. dUTPases are responsible for regulating cellular dUTP levels and providing dUMP for dTTP biosynthesis. In Staphylococcus, phage dUTPases are also suggested to be involved in a moonlighting function regulating the expression of pathogenicity-island genes. Staphylococcal phage trimeric dUTPase sequences include a specific insertion that is not found in other organisms. Here, a 2.1 Å resolution three-dimensional structure of a ϕ11 phage dUTPase trimer with complete localization of the phage-specific insert, which folds into a small β-pleated mini-domain reaching out from the dUTPase core surface, is presented. The insert mini-domains jointly coordinate a single Mg2+ ion per trimer at the entrance to the threefold inner channel. Structural results provide an explanation for the role of Asp95, which is suggested to have functional significance in the moonlighting activity, as the metal-ion-coordinating moiety potentially involved in correct positioning of the insert. Enzyme-kinetics studies of wild-type and mutant constructs show that the insert has no major role in dUTP binding or cleavage and provide a description of the elementary steps (fast binding of substrate and release of products). In conclusion, the structural and kinetic data allow insights into both the phage-specific characteristics and the generally conserved traits of ϕ11 phage dUTPase.
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Affiliation(s)
- Ibolya Leveles
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 29 Karolina Street, 1113 Budapest, Hungary
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