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Cardona-Echavarría MC, Santillán C, Miranda-Blancas R, Stojanoff V, Rudiño-Piñera E. Unveiling success determinants for AMB-assisted phase expansion of fusion proteins in ARP/wARP. J Struct Biol 2024; 216:108089. [PMID: 38537893 DOI: 10.1016/j.jsb.2024.108089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024]
Abstract
Fusion proteins (FPs) are frequently utilized as a biotechnological tool in the determination of macromolecular structures using X-ray methods. Here, we explore the use of different protein tags in various FP, to obtain initial phases by using them in a partial molecular replacement (MR) and constructing the remaining FP structure with ARP/wARP. Usually, the tag is removed prior to crystallization, however leaving the tag on may facilitate crystal formation, and structural determination by expanding phases from known to unknown segments of the complex. In this study, the Protein Data Bank was mined for an up-to-date list of FPs with the most used protein tags, Maltose Binding Protein (MBP), Green Fluorescent Protein (GFP), Thioredoxin (TRX), Glutathione transferase (GST) and the Small Ubiquitin-like Modifier Protein (SUMO). Partial MR using the protein tag, followed by automatic model building, was tested on a subset of 116 FP. The efficiency of this method was analyzed and factors that influence the coordinate construction of a substantial portions of the fused protein were identified. Using MBP, GFP, and SUMO as phase generators it was possible to build at least 75 % of the protein of interest in 36 of the 116 cases tested. Our results reveal that tag selection has a significant impact; tags with greater structural stability, such as GFP, increase the success rate. Further statistical analysis identifies that resolution, Wilson B factor, solvent percentage, completeness, multiplicity, protein tag percentage in the FP (considering amino acids), and the linker length play pivotal roles using our approach. In cases where a structural homologous is absent, this method merits inclusion in the toolkit of protein crystallographers.
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Affiliation(s)
- María C Cardona-Echavarría
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C.P. 62210, Mexico; Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos C.P. 62209, Mexico.
| | | | - Ricardo Miranda-Blancas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México C.P. 04510, Mexico
| | - Vivian Stojanoff
- Brookhaven National Laboratory, Upton, NY 11973-5000, United States
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C.P. 62210, Mexico.
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2
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Anderson EE, Ilmain JK, Torres VJ. SarS and Rot are necessary for the repression of lukED and lukSF-PV in Staphylococcus aureus. Microbiol Spectr 2023; 11:e0165623. [PMID: 37800956 PMCID: PMC10715151 DOI: 10.1128/spectrum.01656-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE The leukocidins play an important role in disarming the host immune system and promoting infection. While both SarS and Rot have been established as repressors of leukocidins, the importance of each repressor in infection is unclear. Here, we demonstrate that repression by SarS and Rot is not additive and show that in addition to upregulating expression of each other, they are also able to bind concurrently to the leukocidin promoters. These findings suggest that both repressors are necessary for maximal repression of lukED and lukSF-PV and illuminate another complex relationship among Staphylococcus aureus virulence regulators.
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Affiliation(s)
- Exene E. Anderson
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Juliana K. Ilmain
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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3
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Kulkarni A, Soni I, Kelkar DS, Dharmaraja AT, Sankar RK, Beniwal G, Rajendran A, Tamhankar S, Chopra S, Kamat SS, Chakrapani H. Chemoproteomics of an Indole-Based Quinone Epoxide Identifies Druggable Vulnerabilities in Vancomycin-Resistant Staphylococcus aureus. J Med Chem 2019; 62:6785-6795. [PMID: 31241934 PMCID: PMC6660313 DOI: 10.1021/acs.jmedchem.9b00774] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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The alarming global
rise in fatalities from multidrug-resistant Staphylococcus
aureus (S. aureus)
infections has underscored a need to develop new therapies to address
this epidemic. Chemoproteomics is valuable in identifying targets
for new drugs in different human diseases including bacterial infections.
Targeting functional cysteines is particularly attractive, as they
serve critical catalytic functions that enable bacterial survival.
Here, we report an indole-based quinone epoxide scaffold with a unique
boat-like conformation that allows steric control in modulating thiol
reactivity. We extensively characterize a lead compound (4a), which potently inhibits clinically derived vancomycin-resistant S. aureus. Leveraging diverse chemoproteomic platforms,
we identify and biochemically validate important transcriptional factors
as potent targets of 4a. Interestingly, each identified
transcriptional factor has a conserved catalytic cysteine residue
that confers antibiotic tolerance to these bacteria. Thus, the chemical
tools and biological targets that we describe here prospect new therapeutic
paradigms in combatting S. aureus infections.
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Affiliation(s)
| | - Isha Soni
- Division of Microbiology , CSIR-Central Drug Research Institute , Sector 10, Janakipuram Extension, Sitapur Road , Lucknow 226021 , Uttar Pradesh , India
| | | | | | | | | | | | | | - Sidharth Chopra
- Division of Microbiology , CSIR-Central Drug Research Institute , Sector 10, Janakipuram Extension, Sitapur Road , Lucknow 226021 , Uttar Pradesh , India
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Alanine substitution mutations in the DNA binding region of a global staphylococcal virulence regulator affect its structure, function, and stability. Int J Biol Macromol 2018; 113:1221-1232. [DOI: 10.1016/j.ijbiomac.2018.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/02/2018] [Accepted: 03/11/2018] [Indexed: 12/11/2022]
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6
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Xu Y, Maltesen RG, Larsen LH, Schønheyder HC, Le VQ, Nielsen JL, Nielsen PH, Thomsen TR, Nielsen KL. In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study. BMC Microbiol 2016; 16:80. [PMID: 27150914 PMCID: PMC4858865 DOI: 10.1186/s12866-016-0695-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/26/2016] [Indexed: 02/01/2023] Open
Abstract
Background Staphylococcus aureus gene expression has been sparsely studied in deep-sited infections in humans. Here, we characterized the staphylococcal transcriptome in vivo and the joint fluid metabolome in a prosthetic joint infection with an acute presentation using deep RNA sequencing and nuclear magnetic resonance spectroscopy, respectively. We compared our findings with the genome, transcriptome and metabolome of the S. aureus joint fluid isolate grown in vitro. Result From the transcriptome analysis we found increased expression of siderophore synthesis genes and multiple known virulence genes. The regulatory pattern of catabolic pathway genes indicated that the bacterial infection was sustained on amino acids, glycans and nucleosides. Upregulation of fermentation genes and the presence of ethanol in joint fluid indicated severe oxygen limitation in vivo. Conclusion This single case study highlights the capacity of combined transcriptome and metabolome analyses for elucidating the pathogenesis of prosthetic infections of major clinical importance. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0695-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yijuan Xu
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajersvej 7H, 9220, Aalborg, Denmark.,The Danish Technological Institute, Life Science Division, Aarhus, Denmark
| | - Raluca Georgiana Maltesen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajersvej 7H, 9220, Aalborg, Denmark
| | - Lone Heimann Larsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajersvej 7H, 9220, Aalborg, Denmark.,Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Carl Schønheyder
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University Hospital, Aalborg, Denmark
| | - Vang Quy Le
- Section for Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajersvej 7H, 9220, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajersvej 7H, 9220, Aalborg, Denmark
| | - Trine Rolighed Thomsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajersvej 7H, 9220, Aalborg, Denmark.,The Danish Technological Institute, Life Science Division, Aarhus, Denmark
| | - Kåre Lehmann Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajersvej 7H, 9220, Aalborg, Denmark.
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7
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Mandal S, Mahapa A, Biswas A, Jana B, Polley S, Sau K, Sau S. A Surfactant-Induced Functional Modulation of a Global Virulence Regulator from Staphylococcus aureus. PLoS One 2016; 11:e0151426. [PMID: 26989900 PMCID: PMC4798592 DOI: 10.1371/journal.pone.0151426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 02/29/2016] [Indexed: 11/24/2022] Open
Abstract
Triton X-100 (TX-100), a useful non-ionic surfactant, reduced the methicillin resistance in Staphylococcus aureus significantly. Many S. aureus proteins were expressed in the presence of TX-100. SarA, one of the TX-100-induced proteins, acts as a global virulence regulator in S. aureus. To understand the effects of TX-100 on the structure, and function of SarA, a recombinant S. aureus SarA (rSarA) and its derivative (C9W) have been investigated in the presence of varying concentrations of this surfactant using various probes. Our data have revealed that both rSarA and C9W bind to the cognate DNA with nearly similar affinity in the absence of TX-100. Interestingly, their DNA binding activities have been significantly increased in the presence of pre-micellar concentration of TX-100. The increase of TX-100 concentrations to micellar or post-micellar concentration did not greatly enhance their activities further. TX-100 molecules have altered the secondary and tertiary structures of both proteins to some extents. Size of the rSarA-TX-100 complex appears to be intermediate to those of rSarA and TX-100. Additional analyses show a relatively moderate interaction between C9W and TX-100. Binding of TX-100 to C9W has, however, occurred by a cooperative pathway particularly at micellar and higher concentrations of this surfactant. Taken together, TX-100-induced structural alteration of rSarA and C9W might be responsible for their increased DNA binding activity. As TX-100 has stabilized the somewhat weaker SarA-DNA complex effectively, it could be used to study its structure in the future.
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Affiliation(s)
- Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Anindya Biswas
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Biswanath Jana
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
- * E-mail: (KS); (SS)
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail: (KS); (SS)
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8
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Song Y, Zhang F, Li X, Zang J, Zhang X. Crystallographic studies of SarV, a global regulator from Staphylococcus aureus. Acta Crystallogr F Struct Biol Commun 2015; 71:1038-41. [PMID: 26249696 PMCID: PMC4528938 DOI: 10.1107/s2053230x15011097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/08/2015] [Indexed: 11/11/2022] Open
Abstract
SarV, a member of the SarA protein family, is a global transcriptional regulator which has been reported to be involved in the regulation of autolysis in Staphylococcus aureus. In this study, SarV from S. aureus was successfully cloned, expressed, purified and crystallized. X-ray diffraction data were collected to 2.10 Å resolution. The crystals of SarV belonged to the monoclinic space group P21, with unit-cell parameters a = 36.40, b = 119.64, c = 66.80 Å, α = γ = 90, β = 98.75°. The Matthews coefficient and the solvent content were estimated to be 2.57 Å(3) Da(-1) and 52%, respectively, suggesting the presence of four molecules in the asymmetric unit. The results of size-exclusion chromatography (SEC) indicated that S. aureus SarV exists as a homodimer in solution. Unfortunately, the structure cannot be solved by molecular replacement because of the low sequence identity of S. aureus SarV to known structures. Further phase determination by selenomethionine single-wavelength anomalous dispersion (SAD) and the heavy-atom method is in progress.
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Affiliation(s)
- Yang Song
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
| | - Fan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
| | - Xuan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
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9
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Zhu Y, Fan X, Zhang X, Jiang X, Niu L, Teng M, Li X. Structure of Rot, a global regulator of virulence genes in Staphylococcus aureus. ACTA ACUST UNITED AC 2014; 70:2467-76. [PMID: 25195759 DOI: 10.1107/s1399004714015326] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/30/2014] [Indexed: 12/13/2022]
Abstract
Staphylococcus aureus is a highly versatile pathogen that can infect human tissue by producing a large arsenal of virulence factors that are tightly regulated by a complex regulatory network. Rot, which shares sequence similarity with SarA homologues, is a global regulator that regulates numerous virulence genes. However, the recognition model of Rot for the promoter region of target genes and the putative regulation mechanism remain elusive. In this study, the 1.77 Å resolution X-ray crystal structure of Rot is reported. The structure reveals that two Rot molecules form a compact homodimer, each of which contains a typical helix-turn-helix module and a β-hairpin motif connected by a flexible loop. Fluorescence polarization results indicate that Rot preferentially recognizes AT-rich dsDNA with ~30-base-pair nucleotides and that the conserved positively charged residues on the winged-helix motif are vital for binding to the AT-rich dsDNA. It is proposed that the DNA-recognition model of Rot may be similar to that of SarA, SarR and SarS, in which the helix-turn-helix motifs of each monomer interact with the major grooves of target dsDNA and the winged motifs contact the minor grooves. Interestingly, the structure shows that Rot adopts a novel dimerization model that differs from that of other SarA homologues. As expected, perturbation of the dimer interface abolishes the dsDNA-binding ability of Rot, suggesting that Rot functions as a dimer. In addition, the results have been further confirmed in vivo by measuring the transcriptional regulation of α-toxin, a major virulence factor produced by most S. aureus strains.
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Affiliation(s)
- Yuwei Zhu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xiaojiao Fan
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xu Zhang
- Department of Microbiology and Immunology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xuguang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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10
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11
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Birukou I, Seo SM, Schindler BD, Kaatz GW, Brennan RG. Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR. Nucleic Acids Res 2013; 42:2774-88. [PMID: 24293644 PMCID: PMC3936728 DOI: 10.1093/nar/gkt1215] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The multidrug efflux pump MepA is a major contributor to multidrug resistance in Staphylococcus aureus. MepR, a member of the multiple antibiotic resistance regulator (MarR) family, represses mepA and its own gene. Here, we report the structure of a MepR–mepR operator complex. Structural comparison of DNA-bound MepR with ‘induced’ apoMepR reveals the large conformational changes needed to allow the DNA-binding winged helix-turn-helix motifs to interact with the consecutive major and minor grooves of the GTTAG signature sequence. Intriguingly, MepR makes no hydrogen bonds to major groove nucleobases. Rather, recognition-helix residues Thr60, Gly61, Pro62 and Thr63 make sequence-specifying van der Waals contacts with the TTAG bases. Removing these contacts dramatically affects MepR–DNA binding activity. The wings insert into the flanking minor grooves, whereby residue Arg87, buttressed by Asp85, interacts with the O2 of T4 and O4′ ribosyl oxygens of A23 and T4. Mutating Asp85 and Arg87, both conserved throughout the MarR family, markedly affects MepR repressor activity. The His14′:Arg59 and Arg10′:His35:Phe108 interaction networks stabilize the DNA-binding conformation of MepR thereby contributing significantly to its high affinity binding. A structure-guided model of the MepR–mepA operator complex suggests that MepR dimers do not interact directly and cooperative binding is likely achieved by DNA-mediated allosteric effects.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA, The John D. Dingell Department of Veterans Affairs Medical Center, B4333 JD Dingel VA Medical Center, 4646 John R, Detroit, MI 48201, USA and Department of Internal Medicine, Division of Infectious Diseases, Wayne State University School of Medicine, 5 Hudson, Harper University Hospital, 3990 John R, Detroit, MI 48201, USA
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13
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Gordon CP, Williams P, Chan WC. Attenuating Staphylococcus aureus virulence gene regulation: a medicinal chemistry perspective. J Med Chem 2013; 56:1389-404. [PMID: 23294220 PMCID: PMC3585718 DOI: 10.1021/jm3014635] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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Virulence gene expression in Staphylococcus aureus is tightly regulated by intricate networks of transcriptional regulators
and two-component signal transduction systems. There is now an emerging
body of evidence to suggest that the blockade of S. aureus virulence gene expression significantly attenuates infection in
experimental models. In this Perspective, we will provide insights
into medicinal chemistry strategies for the development of chemical
reagents that have the capacity to inhibit staphylococcal virulence
expression. These reagents can be broadly grouped into four categories:
(1) competitive inhibitors of the accessory gene regulator (agr) quorum sensing system, (2) inhibitors of AgrA–DNA
interactions, (3) RNAIII transcription inhibitors, and (4) inhibitors
of the SarA family of transcriptional regulators. We discuss the potential
of specific examples of antivirulence agents for the management and
treatment of staphylococcal infections.
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Affiliation(s)
- Christopher P Gordon
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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14
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Li N, Luo M, Fu YJ, Zu YG, Wang W, Zhang L, Yao LP, Zhao CJ, Sun Y. Effect of corilagin on membrane permeability of Escherichia coli, Staphylococcus aureus and Candida albicans. Phytother Res 2012. [PMID: 23192753 DOI: 10.1002/ptr.4891] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Corilagin is a member of polyphenolic tannins. Its antimicrobial activity and action mechanism against Escherichia coli, Staphylococcus aureus and Candida albicans were investigated through membrane permeability. Crystal violet staining determination, outer membrane (OM) and inner membrane (IM) permeability, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and atomic force microscopy (AFM) were used as methods for our investigation. The minimum inhibitory concentrations were 62.5, 31.25 and 62.5 µg/mL for E. coli, S. aureus and C. albicans, respectively. Crystal violet results and SDS-PAGE of supernatant proteins showed that corilagin dose-dependently affected membrane permeability of E. coli and C. albicans but not of S. aureus. OM and IM permeability assays revealed comparable results for E. coli. By using AFM, we demonstrated extensive cell surface alterations of corilagin-treated E. coli and C. albicans. SDS-PAGE of precipitated proteins revealed possible targets of corilagin, i.e. Fib, Sae R, Sar S in S. aureus and Tye 7p in C. albicans. In conclusion, corilagin inhibited the growth of E. coli and C. albicans by disrupting their membrane permeability and that of S. aureus by acting on Fib, Sae R and Sar S but not on membrane integrity.
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Affiliation(s)
- Na Li
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, PR China
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15
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Priest NK, Rudkin JK, Feil EJ, van den Elsen JMH, Cheung A, Peacock SJ, Laabei M, Lucks DA, Recker M, Massey RC. From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence? Nat Rev Microbiol 2012; 10:791-7. [PMID: 23070558 PMCID: PMC7097209 DOI: 10.1038/nrmicro2880] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
With the advent of high-throughput whole-genome sequencing, it is now possible to sequence a bacterial genome in a matter of hours. However, although the presence or absence of a particular gene can be determined, we do not yet have the tools to extract information about the true virulence potential of an organism from sequence data alone. Here, we focus on the important human pathogen Staphylococcus aureus and present a framework for the construction of a broad systems biology-based tool that could be used to predict virulence phenotypes from S. aureus genomic sequences using existing technology.
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Affiliation(s)
- Nicholas K. Priest
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Justine K. Rudkin
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Edward J. Feil
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Jean M. H. van den Elsen
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Ambrose Cheung
- Ambrose Cheung is at Dartmouth Medical School, Vail Building - HB 7550, Hanover, New Hampshire 03755, USA.,
| | - Sharon J. Peacock
- Sharon J. Peacock is at the Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.,
| | - Maisem Laabei
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - David A. Lucks
- David A. Lucks is at Western Infectious Disease Consultants, PC, 3885 Upham Street Suite 200, Wheat Ridge, Colorado 80033, USA.,
| | - Mario Recker
- Mario Recker is at the Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,
| | - Ruth C. Massey
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
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Cue D, Lei MG, Lee CY. Genetic regulation of the intercellular adhesion locus in staphylococci. Front Cell Infect Microbiol 2012; 2:38. [PMID: 23061050 PMCID: PMC3459252 DOI: 10.3389/fcimb.2012.00038] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/05/2012] [Indexed: 01/29/2023] Open
Abstract
The formation of biofilms by Staphylococcus aureus and Staphylococcus epidermidis is an important aspect of many staphylococcal infections, most notably endocarditis, osteomyelitis and infections associated with indwelling medical devices. The major constituents of staphylococcal biofilms are polysaccharides, such as poly N-acetyl glucosamine (PIA/PNAG), cell surface and secreted bacterial proteins, and extracellular DNA. The exact composition of biofilms often varies considerably between different strains of staphylococci and between different sites of infection by the same strain. PIA/PNAG is synthesized by the products of four genes, icaADBC, that are encoded in a single operon. A fifth gene, icaR, is a negative regulator of icaADBC. Expression of icaADBC is tightly regulated, but can often be induced in vitro by growing staphylococci in the presence of high salt, high glucose, or ethanol. Regulation of icaADBC is complex and numerous regulatory factors have been implicated in control of icaADBC. Many of these are well known global transcriptional regulatory factors like SarA and sigmaB, whereas other regulators, such as IcaR, seem to affect expression of relatively few genes. Here, we will summarize how various regulatory factors affect the production of PIA/PNAG in staphylococci.
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Affiliation(s)
- David Cue
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock AR, USA
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17
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Korem M, Gov Y, Rosenberg M. Global gene expression in Staphylococcus aureus following exposure to alcohol. Microb Pathog 2009; 48:74-84. [PMID: 19900530 DOI: 10.1016/j.micpath.2009.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 10/26/2009] [Accepted: 11/02/2009] [Indexed: 12/23/2022]
Abstract
It was recently shown that, as in yeast, alcohols selectively increase the hemolytic properties of certain staphylococci strains. This phenomenon has been called 'microbial alcohol-conferred hemolysis'(MACH). Here we present the changes in gene expression by Staphylococcus aureus 8325-4, in response to ethanol. Ethanol upregulated the expression of multiple toxins and increase the pathogen potential of S. aureus strain 8325-4. Ethanol also increased the level of genes considered necessary for production and viability of biofilm, such as: icaAD, sdrDE, pyr, and ure. Increased urease activity appeared to be an important factor in the ethanol response along with macromolecule repair mechanisms. Oxidative-stress responses, such as increased expression of sodA1, sodA2 and upregulation of zinc-containing alcohol dehydrogenase, alcohol-acetaldehyde dehydrogenase (adhE) and two aldehyde dehydrogenases (aldA1, aldA2), which can generate more reducing power, were also induced. Upregulation of fatty acid metabolism appears to be important in enabling the bacteria to handle excess amounts of ethanol which ultimately may lead to synthesis of lytic lypids. The patterns of regulation were confirmed by quantitive reverse transcriptase PCR (QRT-PCR). These results, taken together, suggest that exposure to ethanol increases pathogenic traits and induce oxidative-stress responses.
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Affiliation(s)
- Moshe Korem
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Ramat Aviv 69978, Israel
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18
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Ballal A, Manna AC. Expression of the sarA family of genes in different strains of Staphylococcus aureus. MICROBIOLOGY-SGM 2009; 155:2342-2352. [PMID: 19389785 DOI: 10.1099/mic.0.027417-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Expression of genes involved in the pathogenesis of Staphylococcus aureus is controlled by global regulatory loci, including two-component regulatory systems and transcriptional regulators. The staphylococcal-specific SarA family of transcription regulators control large numbers of target genes involved in virulence, autolysis, biofilm formation, stress responses and metabolic processes, and are recognized as potential therapeutic targets. Expression of some of these important regulators has been examined, mostly in laboratory strains, while the pattern of expression of these genes in other strains, especially clinical isolates, is largely unknown. In this report, a comparative analysis of 10 sarA-family genes was conducted in six different S. aureus strains, including two laboratory (RN6390, SH1000) and four clinical (MW2, Newman, COL and UAMS-1) strains, by Northern and Western blot analyses. Transcription of most of the sarA-family genes showed a strong growth phase-dependence in all strains tested. Among these genes, no difference was observed in expression of the sarA, sarV, sarT and sarU genes, while a major difference was observed in expression of the sarX gene only in strain RN6390. Expression of mgrA, rot, sarZ, sarR and sarS was observed in all strains, but the level of expression varied from strain to strain.
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Affiliation(s)
- Anand Ballal
- Center for Infectious Disease Research and Vaccinology, South Dakota State University, Brookings, SD 57007, USA.,Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Adhar C Manna
- Center for Infectious Disease Research and Vaccinology, South Dakota State University, Brookings, SD 57007, USA.,Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, SD 57069, USA
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19
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Di Fiore A, Fiorentino G, Vitale RM, Ronca R, Amodeo P, Pedone C, Bartolucci S, De Simone G. Structural analysis of BldR from Sulfolobus solfataricus provides insights into the molecular basis of transcriptional activation in Archaea by MarR family proteins. J Mol Biol 2009; 388:559-69. [PMID: 19298823 DOI: 10.1016/j.jmb.2009.03.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 11/28/2022]
Abstract
The multiple antibiotic resistance regulator (MarR) family constitutes a significant class of transcriptional regulators whose members control a variety of important biological functions such as regulation of response to environmental stress, control of virulence factor production, resistance to antimicrobial agents, and regulation of aromatic catabolic pathways. Although the majority of MarR family members have been characterized as transcriptional repressors, a few examples of transcriptional activators have also been reported. BldR is a newly identified member of this family that has been demonstrated to act as a transcriptional activator in stress response to aromatic compounds in the crenarchaeon Sulfolobus solfataricus. In this work, we report findings on the BldR X-ray crystal structure and present a molecular modeling study on the complex that this protein forms with its cognate DNA sequence, thus providing the first detailed description of the DNA-binding mechanism of an archaeal activator belonging to the MarR family. Two residues responsible for the high binding specificity of this transcriptional regulator were also identified. Our studies demonstrated that, in Archaea, the capability of MarR family members to act as activators or repressors is not related to a particular DNA-binding mechanism but rather could be due to the position of the binding site on the target DNA. Moreover, since genes encoding MarR proteins often control transcription of operons that encode for multisubstrate efflux pumps, our results also provided important insights for the identification of new tools to overcome the microorganism's multidrug resistance.
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Affiliation(s)
- Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, Naples, Italy
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20
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Chu HW, Thaikoottathil J, Rino JG, Zhang G, Wu Q, Moss T, Refaeli Y, Bowler R, Wenzel SE, Chen Z, Zdunek J, Breed R, Young R, Allaire E, Martin RJ. Function and regulation of SPLUNC1 protein in Mycoplasma infection and allergic inflammation. THE JOURNAL OF IMMUNOLOGY 2007; 179:3995-4002. [PMID: 17785838 DOI: 10.4049/jimmunol.179.6.3995] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Respiratory infections, including Mycoplasma pneumoniae (Mp), contribute to asthma pathobiology. To date, the mechanisms underlying the increased susceptibility of asthmatics to airway Mp infection remain unclear. Short palate, lung, and nasal epithelium clone 1 (SPLUNC1) protein is a recently described large airway epithelial cell-derived molecule that was predicted to exert host defense activities. However, SPLUNC1 function and regulation in an infectious or allergic milieu are still unknown. We determined host defense and anti-inflammatory functions of SPLUNC1 protein in Mp infection and the regulation of SPLUNC1 by Mp and allergic inflammation (e.g., IL-13). SPLUNC1 function was examined in Mp or human airway epithelial cell cultures by using SPLUNC1 recombinant protein, overexpression and RNA interference. Human and mouse bronchial epithelial SPLUNC1 was examined using immunostaining, Western blotting, ELISA, laser capture microdissection, and real-time PCR. Mouse models of Mp infection and allergic inflammation and air-liquid interface cultures of normal human primary bronchial epithelial cells were used to study SPLUNC1 regulation by Mp and IL-13. We found that: 1) SPLUNC1 protein decreased Mp levels and inhibited epithelial IL-8 production induced by Mp-derived lipoproteins; 2) normal human and mouse large airway epithelial cells expressed high levels of SPLUNC1; and 3) although Mp infection increased SPLUNC1, IL-13 significantly decreased SPLUNC1 expression and Mp clearance. Our results suggest that SPLUNC1 serves as a novel host defense protein against Mp and that an allergic setting markedly reduces SPLUNC1 expression, which may in part contribute to the persistent nature of bacterial infections in allergic airways.
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Affiliation(s)
- Hong Wei Chu
- Department of Medicine, National Jewish Medical and Research Center and the University of Colorado Health Sciences Center, Denver, CO 80206, USA.
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21
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Manna AC, Cheung AL. Transcriptional regulation of the agr locus and the identification of DNA binding residues of the global regulatory protein SarR in Staphylococcus aureus. Mol Microbiol 2007; 60:1289-301. [PMID: 16689803 DOI: 10.1111/j.1365-2958.2006.05171.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many members of the transcriptional regulator SarA protein family are winged-helix proteins that are involved in gene regulation essential to Staphylococcus aureus pathogenesis. Investigation of the mechanism by which this family of genes acts at the molecular level will likely contribute to the understanding of the pathogenesis process and enhance the potential for the development of inhibitors capable of controlling S. aureus infections. Our previously published studies demonstrate that SarR is a repressor of sarA expression. Here, we show that SarR (a member of the SarA protein family) in part regulates agr expression by direct binding to the agr intergenic promoter region as determined by gel shift and DNase I footprinting assays. Analysis of the double sarA/sarR mutant in the early phase of growth reveals its significant role in regulating agr expression as compared with single mutants. Based on the previously reported crystal structure of SarR, we conducted site-specific mutagenesis and demonstrate that K52 residues within helix-turn-helix (HTH), K80, R82 and R88 (in the wing) and L105 (in the alpha5 helix) are important for DNA binding. Interestingly, SarR and SarA binding sites on the agr promoter are confined within the same region of DNA. Additional gel shift studies with SarR and SarA suggest that these two proteins may bind the same region of the agr promoter.
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Affiliation(s)
- Adhar C Manna
- Division of Basic Biomedical Sciences, University of South Dakota School of Medicine, Vermillion, SD 57069, USA
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22
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Manna AC, Cheung AL. Expression of SarX, a negative regulator of agr and exoprotein synthesis, is activated by MgrA in Staphylococcus aureus. J Bacteriol 2006; 188:4288-99. [PMID: 16740935 PMCID: PMC1482969 DOI: 10.1128/jb.00297-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The expression of genes involved in the pathogenesis of Staphylococcus aureus is known to be controlled by global regulatory loci, including agr, sarA, saeRS, arlRS, and sarA-like genes. As part of our continuing efforts to understand the regulatory mechanisms that involve sarA-like genes, we describe here the characterization of a novel transcriptional regulator called SarX, a member of the SarA protein family. The transcription of sarX was growth phase dependent and was expressed maximally during the stationary phase of growth, which was significantly decreased in the mgrA mutant. MgrA acted as an activator of sarX expression as confirmed by transcriptional fusion and Northern blot analyses. Purified MgrA protein bound to the upstream region of the sarX promoter as demonstrated by gel shift assay. The expression levels of various potential target genes involved in virulence and regulation, specifically those affected by sarA and mgrA, were analyzed with isogenic sarX mutant strains. Our data indicated that SarX acted as a repressor of the agr locus and consequently target genes regulated by the agr system. We propose that SarX is an important regulator in the SarA protein family and may be part of the common pathway by which agr and members of the sarA gene family control virulence in S. aureus.
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Affiliation(s)
- Adhar C Manna
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, 414 E. Clark Street, Vermillion, SD 57069, USA.
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23
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Liu Y, Manna AC, Pan CH, Kriksunov IA, Thiel DJ, Cheung AL, Zhang G. Structural and function analyses of the global regulatory protein SarA from Staphylococcus aureus. Proc Natl Acad Sci U S A 2006; 103:2392-7. [PMID: 16455801 PMCID: PMC1413715 DOI: 10.1073/pnas.0510439103] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sarA locus in Staphylococcus aureus controls the expression of many virulence genes. The sarA regulatory molecule, SarA, is a 14.7-kDa protein (124 residues) that binds to the promoter region of target genes. Here we report the 2.6 A-resolution x-ray crystal structure of the dimeric winged helix SarA protein, which differs from the published SarA structure dramatically. In the crystal packing, multiple dimers of SarA form a scaffold, possibly via divalent cations. Mutations of individual residues within the DNA-binding helix-turn-helix and the winged region as well as within the metal-binding pocket implicate basic residues R84 and R90 within the winged region to be critical in DNA binding, whereas acidic residues D88 and E89 (wing), D8 and E11 (metal-binding pocket), and cysteine 9 are essential for SarA function. These data suggest that the winged region of the winged helix protein participates in DNA binding and activation, whereas the putative divalent cation binding pocket is only involved in gene function.
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Affiliation(s)
- Yingfang Liu
- *Integrated Department of Immunology, National Jewish Medical and Research Center, Biomolecular Structure Program and Department of Pharmacology, School of Medicine, University of Colorado Health Science Center, 1400 Jackson Street, Denver, CO 80206
| | - Adhar C. Manna
- Departments of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755; and
| | - Cheol-Ho Pan
- *Integrated Department of Immunology, National Jewish Medical and Research Center, Biomolecular Structure Program and Department of Pharmacology, School of Medicine, University of Colorado Health Science Center, 1400 Jackson Street, Denver, CO 80206
| | - Irina A. Kriksunov
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Daniel J. Thiel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Ambrose L. Cheung
- Departments of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755; and
- To whom correspondence may be addressed. E-mail:
or
| | - Gongyi Zhang
- *Integrated Department of Immunology, National Jewish Medical and Research Center, Biomolecular Structure Program and Department of Pharmacology, School of Medicine, University of Colorado Health Science Center, 1400 Jackson Street, Denver, CO 80206
- To whom correspondence may be addressed. E-mail:
or
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24
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Tran HJ, Heroven AK, Winkler L, Spreter T, Beatrix B, Dersch P. Analysis of RovA, a transcriptional regulator of Yersinia pseudotuberculosis virulence that acts through antirepression and direct transcriptional activation. J Biol Chem 2005; 280:42423-32. [PMID: 16257976 DOI: 10.1074/jbc.m504464200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The transcription factor RovA of Yersinia pseudotuberculosis and analogous proteins in other Enterobacteriaceae activate the expression of virulence genes that play a crucial role in stress adaptation and pathogenesis. In this study, we demonstrate that the RovA protein forms dimers independent of DNA binding, stimulates RNA polymerase, most likely via its C-terminal domain, and counteracts transcriptional repression by the histone-like protein H-NS. As the molecular function of the RovA family is largely uncharacterized, random mutagenesis and terminal deletions were used to identify functionally important domains. Our analysis showed that a winged-helix motif in the center of the molecule is essential and directly involved in DNA binding. Terminal deletions and amino acid changes within both termini also abrogate RovA activation and DNA-binding functions, most likely due to their implication in dimer formation. Finally, we show that the last four amino acids of RovA are crucial for activation of gene transcription. Successive deletions of these residues result in a continuous loss of RovA activity. Their removal reduced the capacity of RovA to activate RNA polymerase and abolished transcription of RovA-activated promoters in the presence of H-NS, although dimerization and DNA binding functions were retained. Our structural model implies that the final amino acids of RovA play a role in protein-protein interactions, adjusting RovA activity.
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Affiliation(s)
- Hien J Tran
- Junior Research Group 6, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
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25
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McLaughlin WA, Kulp DW, de la Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. ACTA ACUST UNITED AC 2005; 5:255-65. [PMID: 15704013 DOI: 10.1007/s10969-005-4902-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Accepted: 11/17/2004] [Indexed: 01/11/2023]
Abstract
A classification model of a DNA-binding protein chain was created based on identification of alpha helices within the chain likely to bind to DNA. Using the model, all chains in the Protein Data Bank were classified. For many of the chains classified with high confidence, previous documentation for DNA-binding was found, yet no sequence homology to the structures used to train the model was detected. The result indicates that the chain model can be used to supplement sequence based methods for annotating the function of DNA-binding. Four new candidates for DNA-binding were found, including two structures solved through structural genomics efforts. For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA.
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Affiliation(s)
- William A McLaughlin
- Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
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26
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De Silva RS, Kovacikova G, Lin W, Taylor RK, Skorupski K, Kull FJ. Crystal structure of the virulence gene activator AphA from Vibrio cholerae reveals it is a novel member of the winged helix transcription factor superfamily. J Biol Chem 2005; 280:13779-83. [PMID: 15647287 PMCID: PMC2652724 DOI: 10.1074/jbc.m413781200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AphA is a member of a new and largely uncharacterized family of transcriptional activators that is required for initiating virulence gene expression in Vibrio cholerae, the causative agent of the frequently fatal epidemic diarrheal disease cholera. AphA activates transcription by an unusual mechanism that appears to involve a direct interaction with the LysR-type regulator AphB at the tcpPH promoter. As a first step toward understanding the molecular basis for tcpPH activation by AphA and AphB, we have determined the crystal structure of AphA to 2.2 angstrom resolution. AphA is a dimer with an N-terminal winged helix DNA binding domain that is architecturally similar to that of the MarR family of transcriptional regulators. Unlike this family, however, AphA has a unique C-terminal antiparallel coiled coil domain that serves as its primary dimerization interface. AphA monomers are highly unstable by themselves and form a linked topology, requiring the protein to partially unfold to form the dimer. The structure of AphA also provides insights into how it cooperates with AphB to activate transcription, most likely by forming a heterotetrameric complex at the tcpPH promoter.
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Affiliation(s)
- Rukman S. De Silva
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755
| | - Gabriela Kovacikova
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire 03755
| | - Wei Lin
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire 03755
| | - Ronald K. Taylor
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire 03755
| | - Karen Skorupski
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755
| | - F. Jon Kull
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755
- To whom correspondence should be addressed: Dept. of Chemistry, 6128 Burke Laboratory, Dartmouth College, Hanover, NH, 03755. Tel.: 603-646-1552; Fax: 603-646-3946; E-mail:
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27
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Haering CH, Schoffnegger D, Nishino T, Helmhart W, Nasmyth K, Löwe J. Structure and stability of cohesin's Smc1-kleisin interaction. Mol Cell 2004; 15:951-64. [PMID: 15383284 DOI: 10.1016/j.molcel.2004.08.030] [Citation(s) in RCA: 248] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 08/24/2004] [Accepted: 08/24/2004] [Indexed: 11/20/2022]
Abstract
A multisubunit complex called cohesin forms a huge ring structure that mediates sister chromatid cohesion, possibly by entrapping sister DNAs following replication. Cohesin's kleisin subunit Scc1 completes the ring, connecting the ABC-like ATPase heads of a V-shaped Smc1/3 heterodimer. Proteolytic cleavage of Scc1 by separase triggers sister chromatid disjunction, presumably by breaking the Scc1 bridge. One half of the SMC-kleisin bridge is revealed here by a crystal structure of Smc1's ATPase complexed with Scc1's C-terminal domain. The latter forms a winged helix that binds a pair of beta strands in Smc1's ATPase head. Mutation of conserved residues within the contact interface destroys Scc1's interaction with Smc1/3 heterodimers and eliminates cohesin function. Interaction of Scc1's N terminus with Smc3 depends on prior C terminus connection with Smc1. There is little or no turnover of Smc1-Scc1 interactions within cohesin complexes in vivo because expression of noncleavable Scc1 after DNA replication does not hinder anaphase.
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Affiliation(s)
- Christian H Haering
- Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
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28
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Manna AC, Ingavale SS, Maloney M, van Wamel W, Cheung AL. Identification of sarV (SA2062), a new transcriptional regulator, is repressed by SarA and MgrA (SA0641) and involved in the regulation of autolysis in Staphylococcus aureus. J Bacteriol 2004; 186:5267-80. [PMID: 15292128 PMCID: PMC490931 DOI: 10.1128/jb.186.16.5267-5280.2004] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The expression of genes involved in the pathogenesis of Staphylococcus aureus is known to be controlled by global regulatory loci, including agr, sarA, sae, arlRS, lytSR, and sarA-like genes. Here we described a novel transcriptional regulator called sarV of the SarA protein family. The transcription of sarV is low or undetectable under in vitro conditions but is significantly augmented in sarA and mgrA (norR or rat) (SA0641) mutants. The sarA and mgrA genes act as repressors of sarV expression, as confirmed by transcriptional fusion and Northern analysis data. Purified SarA and MgrA proteins bound specifically to separate regions of the sarV promoter as determined by gel shift and DNase I footprinting assays. The expression of 19 potential target genes involved in autolysis and virulence, phenotypes affected by sarA and mgrA, was evaluated in an isogenic sarV mutant pair. Our data indicated that the sarV gene product played a role regulating some virulence genes and more genes involved in autolysis. The sarV mutant was more resistant to Triton X-100 and penicillin-induced lysis compared to the wild type and the sarA mutant, whereas hyperexpression of sarV in the parental strain or the sarV mutant rendered the resultant strain highly susceptible to lysis. Zymographic analysis of murein hydrolase activity revealed that inactivation of the sarV gene results in decreased extracellular murein hydrolase activity compared to that of wild-type S. aureus. We propose that sarV may be part of the common pathway by which mgrA and sarA gene products control autolysis in S. aureus.
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Affiliation(s)
- Adhar C Manna
- Department of Microbiology, Dartmouth Medical School, Hanover, NH 03755, USA.
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29
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Abstract
Staphylococcal protein A (Spa) is an important virulence factor of Staphylococcus aureus. Transcription of the spa determinant occurs during the exponential growth phase and is repressed when the cells enter the postexponential growth phase. Regulation of spa expression has been found to be complicated, with regulation involving multiple factors, including Agr, SarA, SarS, SarT, Rot, and MgrA. Our understanding of how these factors work on the spa promoter to regulate spa expression is incomplete. To identify regulatory sites within the spa promoter, analysis of deletion derivatives of the promoter in host strains deficient in one or more of the regulatory factors was undertaken, and several critical features of spa regulation were revealed. The transcriptional start sites of spa were determined by primer extension. The spa promoter sequences were subcloned in front of a promoterless chloramphenicol acetyltransferase reporter gene. Various lengths of spa truncations with the same 3' end were constructed, and the resultant plasmids were transduced into strains with different regulatory genetic backgrounds. Our results identified upstream promoter sequences necessary for Agr system regulation of spa expression. The cis elements for SarS activity, an activator of spa expression, and for SarA activity, a repressor of spa expression, were identified. The well-characterized SarA consensus sequence on the spa promoter was found to be insufficient for SarA repression of the spa promoter. Full repression required the presence of a second consensus site adjacent to the SarS binding site. Sequences directly upstream of the core promoter sequence were found to stimulate transcription.
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Affiliation(s)
- Jinxin Gao
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Ave., Manhattan, KS 66506, USA
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30
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McCallum N, Bischoff M, Maki H, Wada A, Berger-Bächi B. TcaR, a putative MarR-like regulator of sarS expression. J Bacteriol 2004; 186:2966-72. [PMID: 15126456 PMCID: PMC400606 DOI: 10.1128/jb.186.10.2966-2972.2004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
TcaR, which shares sequence homology with MarR-like transcriptional regulators, has been identified as a novel Staphylococcus aureus regulator affecting the expression of the global regulatory element SarS (SarH1), as well as that of the cell surface-associated protein SasF (N315-SA2439). Microarray analysis, confirmatory Northern blots, and genetic complementation experiments showed that TcaR upregulates sarS and thus spa transcription. In addition, it attenuates whole-length transcription of sasF, thereby producing a truncated transcript lacking the 3' terminus, which codes for the cell wall anchor motif. Hence, in strains containing an intact tcaR gene, TcaR is likely to decrease the amount of the surface-associated protein SasF and to increase that of the surface-associated protein A. The widely used laboratory strains derived from NCTC8325 were found to be natural, truncated mutants of tcaR, harboring an inactive TcaR and therefore expressing very low levels of sarS. The data presented here identified TcaR as a further activator of sarS, and a modulator of sasF expression that has to be taken into account in studies of virulence gene expression in S. aureus.
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Affiliation(s)
- Nadine McCallum
- Department of Medical Microbiology, University of Zürich, CH-8028 Zürich, Switzerland
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Kovacikova G, Lin W, Skorupski K. Vibrio cholerae AphA uses a novel mechanism for virulence gene activation that involves interaction with the LysR-type regulator AphB at the tcpPH promoter. Mol Microbiol 2004; 53:129-42. [PMID: 15225309 DOI: 10.1111/j.1365-2958.2004.04121.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AphA is required for expression of the Vibrio cholerae virulence cascade and for its regulation by quorum sensing. In order to activate transcription, AphA functions together with a second protein, the LysR-type regulator AphB, at the tcpPH promoter. As AphA is a member of a new and largely uncharacterized regulator family, random mutagenesis was used to gain insights into how this protein activates transcription. As shown here, 17 amino acid substitutions were identified in AphA that reduced expression of the tcpPH promoter and prevented the protein from binding DNA. The amino acids involved in DNA recognition inferred from a dominant-negative analysis were located throughout the N-terminal domain from amino acids 18 to 67. This region of AphA has a conserved domain architecture similar to that of MarR, a multiple antibiotic resistance repressor. The analogous positions of the dominant-negative mutations in AphA and MarR confirm that the DNA-binding domains of these proteins are similar and indicate that AphA is a new member of the winged helix family of transcription factors. We also show that AphB is capable of rescuing two of the DNA binding-defective AphA mutants, suggesting that the proteins interact directly on the DNA. Disruption of this interaction by insertion of half a helical turn between the two binding sites prevented AphB from rescuing the mutants and prevented the expression of the virulence cascade in a wild-type background. These results provide a novel mechanism for the initiation of virulence gene expression at tcpPH.
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Affiliation(s)
- Gabriela Kovacikova
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755, USA
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Cheung AL, Bayer AS, Zhang G, Gresham H, Xiong YQ. Regulation of virulence determinants in vitro and in vivo in Staphylococcus aureus. ACTA ACUST UNITED AC 2004; 40:1-9. [PMID: 14734180 DOI: 10.1016/s0928-8244(03)00309-2] [Citation(s) in RCA: 338] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen. In response to changing host environments, this bacterium has the capability to switch on selective sets of genes to enhance its chances for survival. This switching process is precisely controlled by global regulatory elements. There are two major groups of global regulatory elements in S. aureus, including two-component regulatory systems (TCRSs) and the SarA protein family. Presumably, the sensor proteins of the 16 TCRSs in S. aureus provide external sensing, while the response regulators, in conjunction with alternative transcription factors and the SarA protein family, function as effectors within the intricate regulatory network to respond to environmental stimuli. Sequence alignment and structural data indicate that the SarA protein family could be subdivided into three subfamilies: (1) single-domain proteins; (2) double-domain proteins; and (3) proteins homologous to the MarR protein family. Recent data using reporter gene fusions in animal models, have confirmed distinct expression profiles of selected regulatory and target genes in vitro vs. in vivo.
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Affiliation(s)
- Ambrose L Cheung
- Department of Microbiology, Dartmouth Medical School, Hanover, NH 03755, USA.
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