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Denesyuk AI, Denessiouk K, Johnson MS, Uversky VN. Alpha and Omega Classification of β-Lactamase/Transpeptidase-like Superfamily Proteins Based on the Comparison of Their Structural Catalytic Cores. Molecules 2025; 30:2019. [PMID: 40363824 PMCID: PMC12073871 DOI: 10.3390/molecules30092019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2025] [Revised: 04/22/2025] [Accepted: 04/29/2025] [Indexed: 05/15/2025] Open
Abstract
β-Lactamase/transpeptidase-like superfamily proteins are serine proteases that use the Ser-Lys catalytic dyad to carry out their biological functions. Here, we investigate the three known families of β-lactamase/transpeptidase-like superfamily proteins, β-lactamase/D-Ala carboxypeptidase, glutaminase, and Dac-like, and describe the structural catalytic cores that govern the catalytic residues in these proteins. We show that the structural catalytic core of these proteins is a combination of three zones, the mutual three-dimensional arrangement of which correspondingly determines their belonging to one of seven and twenty-four established groups and subgroups.
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Affiliation(s)
- Alexander I. Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; (K.D.); (M.S.J.)
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; (K.D.); (M.S.J.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; (K.D.); (M.S.J.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Gatto CC, Dias LM, Paiva CA, da Silva ICR, Freire DO, Tormena RPI, Nascimento ÉCM, Martins JBL. Effects of changing ions on the crystal design, non-covalent interactions, antimicrobial activity, and molecular docking of Cu(II) complexes with a pyridoxal-hydrazone ligand. Front Chem 2024; 12:1347370. [PMID: 38361747 PMCID: PMC10867249 DOI: 10.3389/fchem.2024.1347370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
The present work reports the influence of the presence of different ions (Cl-, Br-, NO3 -, or SO4 2-) on the formation and proprieties of Cu(II) complexes with pyridoxal-benzoylhydrazone (PLBHZ). Four new complexes were successfully synthesized, [CuCl2(PLBHZ)] (1), [CuBr2(PLBHZ)] (2), [CuCl(PLBHZ)H2O]⋅NO3⋅H2O (3), and [CuSO4(PLBHZ)H2O]⋅3H2O (4), and characterized by spectroscopic and physicochemical methods. A single-crystal X-ray study reveals the Schiff base coordinated to the metal center tridentate by the ONS-donor system, resulting in distorted square pyramidal coordination geometries. Noncovalent interactions were investigated by 3D Hirshfeld surface analysis by the d norm function, 2D fingerprint plots, and full interaction maps. The ion exchange is important in forming three-dimensional networks with π⋅⋅⋅π stacking interactions and intermolecular hydrogen bonds. The in vitro biological activity of the free ligand and metal complexes was evaluated against Gram-positive and Gram-negative bacterial strains and the free pyridoxal-hydrazone ligand showed higher activity than their Cu(II) complexes. Molecular docking was used to predict the inhibitory activity of the ligand and complexes against Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli bacteria.
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Affiliation(s)
- Claudia C. Gatto
- Laboratory of Inorganic Synthesis and Crystallography, Institute of Chemistry, University of Brasilia, Brasília-DF, Brazil
| | - Lucas M. Dias
- Laboratory of Inorganic Synthesis and Crystallography, Institute of Chemistry, University of Brasilia, Brasília-DF, Brazil
| | - Clarisse A. Paiva
- Laboratory of Inorganic Synthesis and Crystallography, Institute of Chemistry, University of Brasilia, Brasília-DF, Brazil
| | - Izabel C. R. da Silva
- Graduate Program in Health Sciences and Technologies, Faculty UnB Ceilândia, University of Brasilia, Brasília-DF, Brazil
| | - Daniel O. Freire
- Graduate Program in Health Sciences and Technologies, Faculty UnB Ceilândia, University of Brasilia, Brasília-DF, Brazil
| | - Renata P. I. Tormena
- Graduate Program in Health Sciences and Technologies, Faculty UnB Ceilândia, University of Brasilia, Brasília-DF, Brazil
| | - Érica C. M. Nascimento
- Laboratory of Computational Chemistry, Institute of Chemistry, University of Brasilia, Brasília-DF, Brazil
| | - João B. L. Martins
- Laboratory of Computational Chemistry, Institute of Chemistry, University of Brasilia, Brasília-DF, Brazil
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3
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Mendes SR, Gomis-Rüth FX, Goulas T. Frozen fresh blood plasma preserves the functionality of native human α 2-macroglobulin. Sci Rep 2023; 13:4579. [PMID: 36941303 PMCID: PMC10027685 DOI: 10.1038/s41598-023-31800-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Human α2-macroglobulin (hα2M) is a large homotetrameric protein involved in the broad inhibition of endopeptidases. Following cleavage within a bait region, hα2M undergoes stepwise transitions from its native, expanded, highly flexible, active conformation to an induced, compact, triggered conformation. As a consequence, the peptidase is entrapped by an irreversible Venus flytrap mechanism. Given the importance of hα2M, biochemical studies galore over more than seven decades have attempted to ascertain its role, typically using authentic hα2M purified from frozen and non-frozen fresh blood plasma, and even outdated plasma. However, hα2M is sensitive once isolated and purified, and becomes heterogeneous during storage and/or freezing, raising concerns about the functional competence of frozen plasma-derived hα2M. We therefore used a combination of native and sodium dodecylsulfate polyacrylamide gel electrophoresis, affinity and ion-exchange chromatography, multi-angle laser light scattering after size-exclusion chromatography, free cysteine quantification, and peptidase inhibition assays with endopeptidases of two catalytic classes and three protein substrates, to characterize the biochemical and biophysical properties of hα2M purified ad hoc either from fresh plasma or frozen fresh plasma after thawing. We found no differences in the molecular or functional properties of the preparations, indicating that protective components in plasma maintain native hα2M in a functionally competent state despite freezing.
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Affiliation(s)
- Soraia R Mendes
- Proteolysis Lab, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028, Barcelona, Catalonia, Spain
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028, Barcelona, Catalonia, Spain.
| | - Theodoros Goulas
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly, 43100, Karditsa, Greece.
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Deekshit VK, Srikumar S. 'To be, or not to be' - the dilemma of 'silent' antimicrobial resistance genes in bacteria. J Appl Microbiol 2022; 133:2902-2914. [PMID: 35882476 DOI: 10.1111/jam.15738] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harboring silent antimicrobial resistance genes - genes whose presence is not associated with a corresponding resistant phenotype, do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance, and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance, and mechanism of silent antibiotic resistance genes in bacterial pathogens is very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance, and their importance in public health.
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Affiliation(s)
- Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Center for Science Education and Research, Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangaluru - 575018, Karnataka, India
| | - Shabarinath Srikumar
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, UAE
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Pandey D, Singhal N, Kumar M. Investigating the OXA Variants of ESKAPE Pathogens. Antibiotics (Basel) 2021; 10:antibiotics10121539. [PMID: 34943751 PMCID: PMC8699015 DOI: 10.3390/antibiotics10121539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
ESKAPE pathogens are the leading cause of nosocomial infections. The Global Priority List of WHO has categorized ESKAPE as priority 1 and 2 pathogens. Even though several mechanisms contribute to antimicrobial resistance, OXA β-lactamase has emerged as a new threat in combating nosocomial infections. In the present study we have investigated the presence of OXA and their variants, copy number, distribution on chromosomes/plasmids, subfamilies, phylogenetic relationships, amino acid identities and variabilities in ESKAPE pathogens. Our results revealed that a total of 929 OXA were present in 2258 completely assembled genomes, which could be further subdivided into 16 sub-families. Among all the ESKAPE pathogens, OXA were highly prevalent in A. baumannii, followed by P. aeruginosa and K. pneumoniae but completely absent in E. faecium and S. aureus while, only a few copies were found in Enterobacter spp. Most of the OXA variants belonged to the OXA-51-like subfamily (200 proteins), followed by OXA-50-like subfamily (189 proteins), OXA-23-like subfamily (156 proteins) and OXA-1-like subfamily (154 proteins). OXA-51-like, OXA-213-like, OXA-134-like, OXA-58-like, OXA-24-like and OXA-20-like subfamilies were present exclusively in A. baumannii. Phylogenetic tree of the subfamilies revealed that OXA-1-like and OXA-33-like, OXA-51-like and OXA-213-like and, OXA-5-like and OXA-10-like belonged to the same branches with amino acid identities as 100%, 97.10% and 80.90% respectively. This indicates that the members of these subfamily-pairs might have evolved from the same ancestor or have recently diverged. Thus, a judicious use of carbapenems is warranted to curtail the rise of new OXA enzymes and preserve them. This is the first detailed report about the OXA of ESKAPE pathogens.
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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Gavira JA, Matilla MA, Fernández M, Krell T. The structural basis for signal promiscuity in a bacterial chemoreceptor. FEBS J 2020; 288:2294-2310. [PMID: 33021055 DOI: 10.1111/febs.15580] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/10/2020] [Accepted: 09/29/2020] [Indexed: 01/05/2023]
Abstract
Signalling through chemosensory pathways is typically initiated by the binding of signal molecules to the chemoreceptor ligand binding domain (LBD). The PcaY_PP chemoreceptor from Pseudomonas putida KT2440 is characterized by an unusually broad signal range, and minimal requisites for signal binding are the presence of a C6-membered ring and that of a carboxyl group. Previous studies have shown that only some of the multiple signals recognized by this chemoreceptor are of apparent metabolic value. We report here high-resolution structures of PcaY_PP-LBD in the absence and presence of four cognate chemoeffectors and glycerol. The domain formed a four-helix bundle (4HB), and both ligand binding sites of the dimer were occupied with the high-affinity ligands protocatechuate and quinate, whereas the lower-affinity ligands benzoate and salicylate were present in only one site. Ligand binding was verified by microcalorimetric titration of site-directed mutants revealing important roles of an arginine and number of polar residues that establish an extensive hydrogen bonding network with bound ligands. The comparison of the apo and holo structures did not provide evidence for this receptor employing a transmembrane signalling mechanism that involves piston-like shifts of the final helix. Instead, ligand binding caused rigid-body scissoring movements of both monomers of the dimer. Comparisons with the 4HB domains of the Tar and Tsr chemoreceptors revealed significant structural differences. Importantly, the ligand binding site in PcaY_PP-LBD is approximately 8 Å removed from that of the Tar and Tsr receptors. Data indicate a significant amount of structural and functional diversity among 4HB domains. DATABASES: The coordinates and structure factors have been deposited in the protein data band with the following IDs: 6S1A (apo form), 6S18 (bound glycerol), 6S33 (bound protocatechuate), 6S38 (bound quinate), 6S3B (bound benzoate) and 6S37 (bound salicylate).
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Affiliation(s)
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Alexander JAN, Radaeva M, King DT, Chambers HF, Cherkasov A, Chatterjee SS, Strynadka NCJ. Structural analysis of avibactam-mediated activation of the bla and mec divergons in methicillin-resistant Staphylococcus aureus. J Biol Chem 2020; 295:10870-10884. [PMID: 32518158 DOI: 10.1074/jbc.ra120.013029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/02/2020] [Indexed: 02/01/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infections cause significant mortality and morbidity globally. MRSA resistance to β-lactam antibiotics is mediated by two divergons that control levels of a β-lactamase, PC1, and a penicillin-binding protein poorly acylated by β-lactam antibiotics, PBP2a. Expression of genes encoding these proteins is controlled by two integral membrane proteins, BlaR1 and MecR1, which both have an extracellular β-lactam-binding sensor domain. Here, we solved the X-ray crystallographic structures of the BlaR1 and MecR1 sensor domains in complex with avibactam, a diazabicyclooctane β-lactamase inhibitor at 1.6-2.0 Å resolution. Additionally, we show that S. aureus SF8300, a clinically relevant strain from the USA300 clone of MRSA, responds to avibactam by up-regulating the expression of the blaZ and pbp2a antibiotic-resistance genes, encoding PC1 and PBP2a, respectively. The BlaR1-avibactam structure of the carbamoyl-enzyme intermediate revealed that avibactam is bound to the active-site serine in two orientations ∼180° to each other. Although a physiological role of the observed alternative pose remains to be validated, our structural results hint at the presence of a secondary sulfate-binding pocket that could be exploited in the design of future inhibitors of BlaR1/MecR1 sensor domains or the structurally similar class D β-lactamases. The MecR1-avibactam structure adopted a singular avibactam orientation similar to one of the two states observed in the BlaR1-avibactam structure. Given avibactam up-regulates expression of blaZ and pbp2a antibiotic resistance genes, we suggest further consideration and research is needed to explore what effects administering β-lactam-avibactam combinations have on treating MRSA infections.
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Affiliation(s)
- J Andrew N Alexander
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mariia Radaeva
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dustin T King
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Henry F Chambers
- Division of Infectious Disease, Dept. of Medicine, San Francisco General Hospital, San Francisco, California, USA
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Som S Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland and Institute of Marine and Environmental Technology, Baltimore, Maryland, USA ;
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada ;
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Belluzo BS, Abriata LA, Giannini E, Mihovilcevic D, Dal Peraro M, Llarrull LI. An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in β-lactam resistance. Sci Rep 2019; 9:19558. [PMID: 31862951 PMCID: PMC6925264 DOI: 10.1038/s41598-019-55923-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 12/04/2019] [Indexed: 11/13/2022] Open
Abstract
The treatment of hospital- and community-associated infections by methicillin-resistant Staphylococcus aureus (MRSA) is a perpetual challenge. This Gram-positive bacterium is resistant specifically to β-lactam antibiotics, and generally to many other antibacterial agents. Its resistance mechanisms to β-lactam antibiotics are activated only when the bacterium encounters a β-lactam. This activation is regulated by the transmembrane sensor/signal transducer proteins BlaR1 and MecR1. Neither the transmembrane/metalloprotease domain, nor the complete MecR1 and BlaR1 proteins, are isolatable for mechanistic study. Here we propose a model for full-length MecR1 based on homology modeling, residue coevolution data, a new extensive experimental mapping of transmembrane topology, partial structures, molecular simulations, and available NMR data. Our model defines the metalloprotease domain as a hydrophilic transmembrane chamber effectively sealed by the apo-sensor domain. It proposes that the amphipathic helices inserted into the gluzincin domain constitute the route for transmission of the β-lactam-binding event in the extracellular sensor domain, to the intracellular and membrane-embedded zinc-containing active site. From here, we discuss possible routes for subsequent activation of proteolytic action. This study provides the first coherent model of the structure of MecR1, opening routes for future functional investigations on how β-lactam binding culminates in the proteolytic degradation of MecI.
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Affiliation(s)
- Bruno S Belluzo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Estefanía Giannini
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Damila Mihovilcevic
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Leticia I Llarrull
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina. .,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 2000, Rosario, Argentina.
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Priyanka B, Patil RK, Dwarakanath S. A review on detection methods used for foodborne pathogens. Indian J Med Res 2017; 144:327-338. [PMID: 28139531 PMCID: PMC5320838 DOI: 10.4103/0971-5916.198677] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Foodborne pathogens have been a cause of a large number of diseases worldwide and more so in developing countries. This has a major economic impact. It is important to contain them, and to do so, early detection is very crucial. Detection and diagnostics relied on culture-based methods to begin with and have developed in the recent past parallel to the developments towards immunological methods such as enzyme-linked immunosorbent assays (ELISA) and molecular biology-based methods such as polymerase chain reaction (PCR). The aim has always been to find a rapid, sensitive, specific and cost-effective method. Ranging from culturing of microbes to the futuristic biosensor technology, the methods have had this common goal. This review summarizes the recent trends and brings together methods that have been developed over the years.
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Affiliation(s)
- B Priyanka
- Department of Applied Zoology, Mangalore University, Mangaluru, India
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11
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Sabat AJ, Pournaras S, Akkerboom V, Tsakris A, Grundmann H, Friedrich AW. Whole-genome analysis of an oxacillin-susceptible CC80 mecA-positive Staphylococcus aureus clinical isolate: insights into the mechanisms of cryptic methicillin resistance. J Antimicrob Chemother 2015. [PMID: 26198147 DOI: 10.1093/jac/dkv210] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The mec and bla systems, among other genetic factors, are critical in regulating the expression of methicillin resistance in Staphylococcus aureus. We examined by WGS a naturally occurring oxacillin-susceptible mecA-positive S. aureus isolate to identify the mechanism conferring oxacillin susceptibility. METHODS The mecA-positive oxacillin-susceptible S. aureus isolate GR2 (penicillin and oxacillin MICs 0.094 and 1 mg/L, respectively), belonging to clonal complex 80, was characterized. DNA fragment libraries were sequenced on Roche 454 and Illumina MiSeq sequencers and de novo assembly of the genome was generated using SeqMan NGen software. Plasmid curing was conducted by SDS treatment. Expression of mecA was quantified without/with β-lactam pressure. RESULTS The genome of GR2 consisted of a 2 792 802 bp chromosome and plasmids pGR2A (28 895 bp) and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a truncated/non-functional mecR1 gene and no mecI. A single copy of the bla system, with an organization unique for S. aureus, was found, harboured by plasmid pGR2A. Particularly, the blaZ gene was orientated like its regulatory genes, blaI and blaR1, and a gene encoding transposase IS66 was integrated between blaZ and the regulatory genes deleting the 5'-end of blaR1; blaI, encoding blaZ/mecA repressor, was intact. After plasmid loss, GR2 became penicillin and oxacillin resistant (MICs 0.5 and 6 mg/L, respectively). CONCLUSIONS We can conclude that after exposure to β-lactams, the non-functional BlaR1 does not cleave the mecA repressor BlaI, derepression does not occur and mecA is not efficiently expressed. Removal of the bla system after curing of pGR2A allows constitutive expression of mecA, resulting in oxacillin and penicillin resistance.
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Affiliation(s)
- Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Spyros Pournaras
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Microbiology, Medical School, University of Athens, Athens, Greece
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Athanassios Tsakris
- Department of Microbiology, Medical School, University of Athens, Athens, Greece
| | - Hajo Grundmann
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Matys A, Podlewska S, Witek K, Witek J, Bojarski AJ, Schabikowski J, Otrębska-Machaj E, Latacz G, Szymańska E, Kieć-Kononowicz K, Molnar J, Amaral L, Handzlik J. Imidazolidine-4-one derivatives in the search for novel chemosensitizers of Staphylococcus aureus MRSA: synthesis, biological evaluation and molecular modeling studies. Eur J Med Chem 2015; 101:313-25. [PMID: 26160112 DOI: 10.1016/j.ejmech.2015.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 05/14/2015] [Accepted: 06/04/2015] [Indexed: 12/11/2022]
Abstract
A series of amine derivatives of 5-aromatic imidazolidine-4-ones (7-19), representing three subgroups: piperazine derivatives of 5-arylideneimidazolones (7-13), piperazine derivatives of 5-arylideneimidazolidine-2,4-dione (14-16) and primary amines of 5-naphthyl-5-methylimidazolidine-2,4-diones (17-19), was evaluated for their ability to improve antibiotics effectiveness in two strains of Gram-positive Staphylococcus aureus: ATCC 25923 (a reference strain) and MRSA (methicillin resistant S. aureus) HEMSA 5 (a resistant clinical isolate). The latter compounds (17-19) were obtained by 4-step synthesis using Bucherer-Bergs condensation, two-phase bromoalkylation and Gabriel reactions. The naphthalen derivative: (Z)-5-(naphthalen-2-ylmethylene)-2-(piperazin-1-yl)-3H-imidazol-4(5H)-one (10) was the most potent in combination with β-lactam antibiotics and ciprofloxacin against the resistant strain. The high potency to increase efficacy of oxacillin was noted for (Z)-5-(anthracen-10-ylmethylene)-2-(piperazin-1-yl)-3H-imidazol-4(5H)one (12) too. In order to explain the mechanism of action of the compounds 10 and 12, docking studies with the use of crystal structures of a penicillin binding protein (PBP2a) and MecR1 were carried out. Their outcomes suggested that the most probable mechanism of action of the active compounds is the interaction with MecR1. Molecular dynamic experiments performed for the active compounds and compound 13 (structurally similar to 12) supported this hypothesis and provided possible explanation of activity dependencies of the tested compounds in terms of the restoration of antibiotic efficacy in S. aureus MRSA HEMSA 5.
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Affiliation(s)
- Anna Matys
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland
| | - Sabina Podlewska
- Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, PL 31-343 Kraków, Poland; Faculty of Chemistry Jagiellonian University, Ingardena 3, PL 30-060 Kraków, Poland
| | - Karolina Witek
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland
| | - Jagna Witek
- Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, PL 31-343 Kraków, Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, PL 31-343 Kraków, Poland
| | - Jakub Schabikowski
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland
| | - Ewa Otrębska-Machaj
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland
| | - Ewa Szymańska
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland
| | - Katarzyna Kieć-Kononowicz
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland
| | - Joseph Molnar
- Institute of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary
| | - Leonard Amaral
- Travel Medicine of the Centro de Malaria & Otra Doencas Tropicais (CMDT), Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Jadwiga Handzlik
- Department of Technology and Biotechnology of Drugs Jagiellonian University Medical College, Medyczna 9, PL 30-688 Kraków, Poland.
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13
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Abstract
Staphylococcus aureus is a major human and veterinary pathogen worldwide. Methicillin-resistant S. aureus (MRSA) poses a significant and enduring problem to the treatment of infection by such strains. Resistance is usually conferred by the acquisition of a nonnative gene encoding a penicillin-binding protein (PBP2a), with significantly lower affinity for β-lactams. This resistance allows cell-wall biosynthesis, the target of β-lactams, to continue even in the presence of typically inhibitory concentrations of antibiotic. PBP2a is encoded by the mecA gene, which is carried on a distinct mobile genetic element (SCCmec), the expression of which is controlled through a proteolytic signal transduction pathway comprising a sensor protein (MecR1) and a repressor (MecI). Many of the molecular and biochemical mechanisms underlying methicillin resistance in S. aureus have been elucidated, including regulatory events and the structure of key proteins. Here we review recent advances in this area.
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Affiliation(s)
- Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Gavin K. Paterson
- School of Biological, Biomedical, and Environmental Sciences, University of Hull, Hull HU6 7RX, United Kingdom
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14
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Goulas T, Cuppari A, Garcia-Castellanos R, Snipas S, Glockshuber R, Arolas JL, Gomis-Rüth FX. The pCri System: a vector collection for recombinant protein expression and purification. PLoS One 2014; 9:e112643. [PMID: 25386923 PMCID: PMC4227841 DOI: 10.1371/journal.pone.0112643] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/09/2014] [Indexed: 12/11/2022] Open
Abstract
A major bottleneck in structural, biochemical and biophysical studies of proteins is the need for large amounts of pure homogenous material, which is generally obtained by recombinant overexpression. Here we introduce a vector collection, the pCri System, for cytoplasmic and periplasmic/extracellular expression of heterologous proteins that allows the simultaneous assessment of prokaryotic and eukaryotic host cells (Escherichia coli, Bacillus subtilis, and Pichia pastoris). By using a single polymerase chain reaction product, genes of interest can be directionally cloned in all vectors within four different rare restriction sites at the 5'end and multiple cloning sites at the 3'end. In this way, a number of different fusion tags but also signal peptides can be incorporated at the N- and C-terminus of proteins, facilitating their expression, solubility and subsequent detection and purification. Fusion tags can be efficiently removed by treatment with site-specific peptidases, such as tobacco etch virus proteinase, thrombin, or sentrin specific peptidase 1, which leave only a few extra residues at the N-terminus of the protein. The combination of different expression systems in concert with the cloning approach in vectors that can fuse various tags makes the pCri System a valuable tool for high throughput studies.
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Affiliation(s)
- Theodoros Goulas
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
- * E-mail: (TG); (FXGR)
| | - Anna Cuppari
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
| | - Raquel Garcia-Castellanos
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
| | - Scott Snipas
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Department of Biology, Zurich, Switzerland
| | - Joan L. Arolas
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
| | - F. Xavier Gomis-Rüth
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, Barcelona, Spain
- * E-mail: (TG); (FXGR)
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15
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López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX. A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases. J Biol Chem 2013; 288:21279-21294. [PMID: 23733187 PMCID: PMC3774397 DOI: 10.1074/jbc.m113.476580] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/13/2013] [Indexed: 11/06/2022] Open
Abstract
In the search for structural models of integral-membrane metallopeptidases (MPs), we discovered three related proteins from thermophilic prokaryotes, which we grouped into a novel family called "minigluzincins." We determined the crystal structures of the zymogens of two of these (Pyrococcus abyssi proabylysin and Methanocaldococcus jannaschii projannalysin), which are soluble and, with ∼100 residues, constitute the shortest structurally characterized MPs to date. Despite relevant sequence and structural similarity, the structures revealed two unique mechanisms of latency maintenance through the C-terminal segments previously unseen in MPs as follows: intramolecular, through an extended tail, in proabylysin, and crosswise intermolecular, through a helix swap, in projannalysin. In addition, structural and sequence comparisons revealed large similarity with MPs of the gluzincin tribe such as thermolysin, leukotriene A4 hydrolase relatives, and cowrins. Noteworthy, gluzincins mostly contain a glutamate as third characteristic zinc ligand, whereas minigluzincins have a histidine. Sequence and structural similarity further allowed us to ascertain that minigluzincins are very similar to the catalytic domains of integral membrane MPs of the MEROPS database families M48 and M56, such as FACE1, HtpX, Oma1, and BlaR1/MecR1, which are provided with trans-membrane helices flanking or inserted into a minigluzincin-like catalytic domain. In a time where structural biochemistry of integral-membrane proteins in general still faces formidable challenges, the minigluzincin soluble minimal scaffold may contribute to our understanding of the working mechanisms of these membrane MPs and to the design of novel inhibitors through structure-aided rational drug design approaches.
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Affiliation(s)
- Mar López-Pelegrín
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Núria Cerdà-Costa
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Francisco Martínez-Jiménez
- the Genome Biology Group, Centre Nacional d'Anàlisi Genòmic, c/Baldiri Reixac, 4, 08028 Barcelona,; the Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation, c/Dr. Aiguader, 88, 08003 Barcelona
| | - Anna Cintas-Pedrola
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Albert Canals
- the Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas and Institute for Research in Biomedicine, c/Baldiri Reixac, 10-12, 08028 Barcelona, and
| | - Juan R Peinado
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Marc A Marti-Renom
- the Genome Biology Group, Centre Nacional d'Anàlisi Genòmic, c/Baldiri Reixac, 4, 08028 Barcelona,; the Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation, c/Dr. Aiguader, 88, 08003 Barcelona
| | - Carlos López-Otín
- the Departamento de Bioquímica y Biología Molecular and Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Joan L Arolas
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona,.
| | - F Xavier Gomis-Rüth
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona,.
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16
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Arêde P, Botelho T, Guevara T, Usón I, Oliveira DC, Gomis-Rüth FX. Structure-function studies of the staphylococcal methicillin resistance antirepressor MecR2. J Biol Chem 2013; 288:21267-21278. [PMID: 23733184 DOI: 10.1074/jbc.m112.448134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Methicillin resistance in Staphylococcus aureus is elicited by the MecI-MecR1-MecA axis encoded by the mec locus. Recently, MecR2 was also identified as a regulator of mec through binding of the methicillin repressor, MecI. Here we show that plasmid-encoded full-length MecR2 restores resistance in a sensitive S. aureus mecR2 deletion mutant of the resistant strain N315. The crystal structure of MecR2 reveals an N-terminal DNA-binding domain, an intermediate scaffold domain, and a C-terminal dimerization domain that contributes to oligomerization. The protein shows structural similarity to ROK (repressors, open reading frames, and kinases) family proteins, which bind DNA and/or sugar molecules. We found that functional cell-based assays of three point mutants affecting residues participating in sugar binding in ROK proteins had no effect on the resistance phenotype. By contrast, MecR2 bound short double-stranded DNA oligonucleotides nonspecifically, and a deletion mutant affecting the N-terminal DNA-binding domain showed a certain effect on activity, thus contributing to resistance less than the wild-type protein. Similarly, a deletion mutant, in which a flexible segment of intermediate scaffold domain had been replaced by four glycines, significantly reduced MecR2 function, thus indicating that this domain may likewise be required for activity. Taken together, these results provide the structural basis for the activity of a methicillin antirepressor, MecR2, which would sequester MecI away from its cognate promoter region and facilitate its degradation.
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Affiliation(s)
- Pedro Arêde
- the Center for Microbiological Resources, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, P-2829-516 Caparica, Portugal, and
| | - Tiago Botelho
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, E-08028 Barcelona, Catalonia, Spain
| | - Tibisay Guevara
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, E-08028 Barcelona, Catalonia, Spain
| | - Isabel Usón
- the Institució Catalana de Recerca i Estudis Avançats, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Catalonia, Spain
| | - Duarte C Oliveira
- the Center for Microbiological Resources, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, P-2829-516 Caparica, Portugal, and
| | - F Xavier Gomis-Rüth
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, E-08028 Barcelona, Catalonia, Spain,.
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17
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Chancey ST, Zähner D, Stephens DS. Acquired inducible antimicrobial resistance in Gram-positive bacteria. Future Microbiol 2013; 7:959-78. [PMID: 22913355 DOI: 10.2217/fmb.12.63] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A major contributor to the emergence of antibiotic resistance in Gram-positive bacterial pathogens is the expansion of acquired, inducible genetic elements. Although acquired, inducible antibiotic resistance is not new, the interest in its molecular basis has been accelerated by the widening distribution and often 'silent' spread of the elements responsible, the diagnostic challenges of such resistance and the mounting limitations of available agents to treat Gram-positive infections. Acquired, inducible antibiotic resistance elements belong to the accessory genome of a species and are horizontally acquired by transformation/recombination or through the transfer of mobile DNA elements. The two key, but mechanistically very different, induction mechanisms are: ribosome-sensed induction, characteristic of the macrolide-lincosamide-streptogramin B antibiotics and tetracycline resistance, leading to ribosomal modifications or efflux pump activation; and resistance by cell surface-associated sensing of β-lactams (e.g., oxacillin), glycopeptides (e.g., vancomycin) and the polypeptide bacitracin, leading to drug inactivation or resistance due to cell wall alterations.
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Affiliation(s)
- Scott T Chancey
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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18
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Botelho TO, Guevara T, Marrero A, Arêde P, Fluxà VS, Reymond JL, Oliveira DC, Gomis-Rüth FX. Structural and functional analyses reveal that Staphylococcus aureus antibiotic resistance factor HmrA is a zinc-dependent endopeptidase. J Biol Chem 2011; 286:25697-709. [PMID: 21622555 PMCID: PMC3138305 DOI: 10.1074/jbc.m111.247437] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/07/2011] [Indexed: 12/17/2022] Open
Abstract
HmrA is an antibiotic resistance factor of methicillin-resistant Staphylococcus aureus. Molecular analysis of this protein revealed that it is not a muramidase or β-lactamase but a nonspecific double-zinc endopeptidase consisting of a catalytic domain and an inserted oligomerization domain, which probably undergo a relative interdomain hinge rotation upon substrate binding. The active-site cleft is located at the domain interface. Four HmrA protomers assemble to a large ∼170-kDa homotetrameric complex of 125 Å. All four active sites are fully accessible and ∼50-70 Å apart, far enough apart to act on a large meshwork substrate independently but simultaneously. In vivo studies with four S. aureus strains of variable resistance levels revealed that the extracellular addition of HmrA protects against loss of viability in the presence of oxacillin and that this protection depends on proteolytic activity. All of these results indicate that HmrA is a peptidase that participates in resistance mechanisms in vivo in the presence of β-lactams. Furthermore, our results have implications for most S. aureus strains of known genomic sequences and several other cocci and bacilli, which harbor close orthologs. This suggests that HmrA may be a new widespread antibiotic resistance factor in bacteria.
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Affiliation(s)
- Tiago O. Botelho
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028 Barcelona, Spain
| | - Tibisay Guevara
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028 Barcelona, Spain
| | - Aniebrys Marrero
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028 Barcelona, Spain
| | - Pedro Arêde
- the Center for Microbiological Resources, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, P-2829-516 Caparica, Portugal, and
| | - Viviana S. Fluxà
- the Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-301 Berne, Switzerland
| | - Jean-Louis Reymond
- the Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-301 Berne, Switzerland
| | - Duarte C. Oliveira
- the Center for Microbiological Resources, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, P-2829-516 Caparica, Portugal, and
| | - F. Xavier Gomis-Rüth
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028 Barcelona, Spain
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19
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Three factors that modulate the activity of class D β-lactamases and interfere with the post-translational carboxylation of Lys70. Biochem J 2011; 432:495-504. [PMID: 21108605 DOI: 10.1042/bj20101122] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The activity of class D β-lactamases is dependent on Lys70 carboxylation in the active site. Structural, kinetic and affinity studies show that this post-translational modification can be affected by the presence of a poor substrate such as moxalactam but also by the V117T substitution. Val117 is a strictly conserved hydrophobic residue located in the active site. In addition, inhibition of class D β-lactamases by chloride ions is due to a competition between the side chain carboxylate of the modified Lys70 and chloride ions. Determination of the individual kinetic constants shows that the deacylation of the acyl-enzyme is the rate-limiting step for the wild-type OXA-10 β-lactamase.
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20
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Doyle M, Feuerbaum EA, Fox KR, Hinds J, Thurston DE, Taylor PW. Response of Staphylococcus aureus to subinhibitory concentrations of a sequence-selective, DNA minor groove cross-linking pyrrolobenzodiazepine dimer. J Antimicrob Chemother 2009; 64:949-59. [PMID: 19744983 PMCID: PMC2764867 DOI: 10.1093/jac/dkp325] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES ELB-21 is a pyrrolo[2,1-c][1,4]benzodiazepine dimer with potent antistaphylococcal activity; it binds covalently to guanine residues on opposing strands of duplex DNA, interfering with regulatory proteins and transcription elongation in a sequence-selective manner. Transcriptional and proteomic alterations induced by exposure of Staphylococcus aureus clinical isolate EMRSA-16 to ELB-21 were determined in order to define more precisely the bactericidal mechanism of the drug. METHODS DNase I footprinting was used to identify high-affinity DNA binding sites. Microarrays and gel electrophoresis were used to assess the ELB-21-induced phenotype. RESULTS High-affinity interstrand binding sites in which guanine residues were separated by 4 bp, and also some intrastrand cross-linking sites of variable length were identified. Exposure of EMRSA-16 to 0.015 mg/L ELB-21 elicited a 2-fold or greater up-regulation of 168 genes in logarithmic phase and 181 genes in stationary phase; the majority of genes affected were associated with resident prophages Sa2 and Sa3, pathogenicity island SaPI4 and DNA damage repair. ELB-21 induced a marked increase in the number of viable phage particles in culture supernatants. The expression of only a limited number of genes showed a >50% reduction. Sixteen extracellular and four intracellular proteins were differentially expressed during logarithmic and stationary phases, including RecA, proteins associated with staphylococcal pathogenesis (IsaA, CspA), cell division and wall synthesis. CONCLUSIONS ELB-21 kills S. aureus by forming multiple interstrand and intrastrand DNA cross-links, resulting in induction of the DNA damage response, derepression of resident prophages and modulation of a limited number of genes involved with cell wall synthesis.
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Affiliation(s)
- Marie Doyle
- School of Pharmacy, University of London, London WC1N 1AX UK
| | | | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK
| | - Jason Hinds
- Division of Cellular and Molecular Medicine, St. George’s, University of London, London SW17 0RE, UK
| | | | - Peter W. Taylor
- School of Pharmacy, University of London, London WC1N 1AX UK
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21
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Staub I, Sieber SA. Beta-lactam probes as selective chemical-proteomic tools for the identification and functional characterization of resistance associated enzymes in MRSA. J Am Chem Soc 2009; 131:6271-6. [PMID: 19354235 DOI: 10.1021/ja901304n] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the development of antibiotic resistant bacterial strains, infectious diseases have become again a life threatening problem. One of the reasons for this dilemma is the limited number and breadth of current therapeutic targets for which several resistance strategies have evolved over time. To identify resistance associated targets and to understand their function, activity, and regulation, we utilized a novel strategy based on small synthetic beta-lactam molecules that were applied in activity based protein profiling experiments (ABPP) to comparatively profile in situ enzyme activities in antibiotic sensitive and resistant S. aureus strains (MRSA). Several enzyme activities which are unique to the MRSA strain including known resistant associated targets, involved in cell wall biosynthesis and antibiotic sensing, could be identified. In addition, we also identified uncharacterized enzymes which turned out to be capable of hydrolyzing beta-lactam antibiotics. This technology could therefore represent a valuable tool to monitor the activity and function of other yet unexplored resistance associated enzymes in pathogenic bacteria and help to discover new drug targets for customized therapeutic interventions.
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Affiliation(s)
- Isabell Staub
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
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22
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Jordan S, Hutchings MI, Mascher T. Cell envelope stress response in Gram-positive bacteria. FEMS Microbiol Rev 2008; 32:107-46. [PMID: 18173394 DOI: 10.1111/j.1574-6976.2007.00091.x] [Citation(s) in RCA: 282] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sina Jordan
- Department of General Microbiology, Georg-August-University, Grisebachstrasse 8, Göttingen, Germany
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23
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Cha J, Vakulenko SB, Mobashery S. Characterization of the β-Lactam Antibiotic Sensor Domain of the MecR1 Signal Sensor/Transducer Protein from Methicillin-Resistant Staphylococcus aureus. Biochemistry 2007; 46:7822-31. [PMID: 17550272 DOI: 10.1021/bi7005459] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has evolved two mechanisms for resistance to beta-lactam antibiotics. One is production of a beta-lactamase, and the other is that of penicillin-binding protein 2a (PBP 2a). The expression of these two proteins is regulated by the bla and mec operons, respectively. BlaR1 and MecR1 are beta-lactam sensor/signal transducer proteins, which experience acylation by beta-lactam antibiotics on the cell surface and transduce the signal into the cytoplasm. The C-terminal surface domain of MecR1 (MecRS) has been cloned, expressed, and purified to homogeneity. This protein has been characterized by documenting that it has a critical and unusual Nzeta-carboxylated lysine at position 394. Furthermore, the kinetics of interactions with beta-lactam antibiotics were evaluated, a process that entails conformational changes for the protein that might be critical for the signal transduction event. Kinetics of acylation of MecRS are suggestive that signal sensing may be the step where the two systems are substantially different from one another.
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Affiliation(s)
- Jooyoung Cha
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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24
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Santillana E, Beceiro A, Bou G, Romero A. Crystal structure of the carbapenemase OXA-24 reveals insights into the mechanism of carbapenem hydrolysis. Proc Natl Acad Sci U S A 2007; 104:5354-9. [PMID: 17374723 PMCID: PMC1838445 DOI: 10.1073/pnas.0607557104] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combating bacterial resistance to beta-lactams, the most widely used antibiotics, is an emergent and clinically important challenge. OXA-24 is a class D beta-lactamase isolated from a multiresistant epidemic clinical strain of Acinetobacter baumannii. We have investigated how OXA-24 specifically hydrolyzes the last resort carbapenem antibiotic, and we have determined the crystal structure of OXA-24 at a resolution of 2.5 A. The structure shows that the carbapenem's substrate specificity is determined by a hydrophobic barrier that is established through the specific arrangement of the Tyr-112 and Met-223 side chains, which define a tunnel-like entrance to the active site. The importance of these residues was further confirmed by mutagenesis studies. Biochemical and microbiological analyses of specific point mutants selected on the basis of structural criteria significantly reduced the catalytic efficiency (k(cat)/K(m)) against carbapenems, whereas the specificity for oxacillin was noticeably increased. This is the previously unrecognized crystal structure that has been obtained for a class D carbapenemase enzyme. Accordingly, this information may help to improve the development of effective new drugs to combat beta-lactam resistance. More specifically, it may help to overcome carbapenem resistance in A. baumannii, probably one of the most worrying infectious threats in hospitals worldwide.
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Affiliation(s)
- Elena Santillana
- *Departamento de Estructura y Función de Proteínas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, E-28040 Madrid, Spain; and
| | - Alejandro Beceiro
- Servicio de Microbiología-Unidad de Investigación, Complejo Hospitalario Universitario Juan Canalejo, As Xubias 84, E-15006 La Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología-Unidad de Investigación, Complejo Hospitalario Universitario Juan Canalejo, As Xubias 84, E-15006 La Coruña, Spain
| | - Antonio Romero
- *Departamento de Estructura y Función de Proteínas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, E-28040 Madrid, Spain; and
- To whom correspondence should be addressed. E-mail:
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