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Mosqueda N, Gato E, Roca I, López M, de Alegría CR, Fernández Cuenca F, Martínez-Martínez L, Pachón J, Cisneros JM, Rodríguez-Baño J, Pascual A, Vila J, Bou G, Tomás M. Characterization of plasmids carrying the blaOXA-24/40 carbapenemase gene and the genes encoding the AbkA/AbkB proteins of a toxin/antitoxin system. J Antimicrob Chemother 2014; 69:2629-33. [PMID: 24879663 DOI: 10.1093/jac/dku179] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Acinetobacter baumannii (CRAb) is a major source of nosocomial infections in Spain associated with the production of OXA-58-like or OXA-24/40-like β-lactamase enzymes. We analysed the plasmids carrying the bla(OXA-24/40)-like gene in CRAb isolates obtained a decade apart. METHODS The presence of β-lactamases was screened for by PCR (metallo-β-lactamases, carbapenem-hydrolysing class D β-lactamases, GES and KPC) in 101 CRAb isolates obtained in two multicentre studies (GEIH/REIPI-Ab-2000 and GEIH/REIPI-Ab-2010; n = 493 Acinetobacter spp). We analysed the distribution and characterization of the plasmids carrying the bla(OXA-24/40)-like gene and sequenced two plasmids, AbATCC223p (2000) and AbATCC329p (2010) from A. baumannii ATCC 17978 transformants. RESULTS Acquisition of the bla(OXA-24/40)-like gene was the main mechanism underlying resistance to carbapenems (48.7% in 2000 compared with 51.6% in 2010). This gene was mainly isolated in ST2 A. baumannii strains in both studies, although some novel STs (ST79 and ST80) appeared in 2010. The gene was located in plasmids (8-12 kbp) associated with the repAci2 or repAci2/repGR12 types. The sequences of AbATCC223p (8840 bp) and AbATCC329p (8842 bp) plasmids were similar, particularly regarding the presence of the genes encoding the AbkA/AbkB proteins associated with the toxin/antitoxin system. Moreover, the abkA/abkB gene sequences (>96% identity) were also located in plasmids harbouring the bla(OXA-58)-like gene. CONCLUSIONS The action of OXA-24/40 and OXA-58 β-lactamase-like enzymes represents the main mechanism underlying resistance to carbapenems in Spain in the last decade. AbkA/AbkB proteins in the toxin/antitoxin system may be involved in the successful dissemination of plasmids carrying the bla(OXA-24/40)-like gene, and probably also the bla(OXA-58)-like gene, thus contributing to the plasmid stability.
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Affiliation(s)
- Noraida Mosqueda
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Eva Gato
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
| | - Ignasi Roca
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - María López
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
| | - Carlos Ruíz de Alegría
- Microbiology Service, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Felipe Fernández Cuenca
- Clinical Unit for Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, and University of Seville, Seville, Spain
| | - Luis Martínez-Martínez
- Microbiology Service, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain Department of Molecular Biology, University of Cantabria, Santander, Spain
| | - Jerónimo Pachón
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine-IBiS, University Hospital Virgen del Rocío, Seville, Spain
| | - José Miguel Cisneros
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine-IBiS, University Hospital Virgen del Rocío, Seville, Spain
| | - Jesús Rodríguez-Baño
- Clinical Unit for Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, and University of Seville, Seville, Spain
| | - Alvaro Pascual
- Clinical Unit for Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, and University of Seville, Seville, Spain
| | - Jordi Vila
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Germán Bou
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
| | - María Tomás
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
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Im H, Jang SB, Pathak C, Yang YJ, Yoon HJ, Yu TK, Suh JY, Lee BJ. Crystal structure of toxin HP0892 from Helicobacter pylori with two Zn(II) at 1.8 Å resolution. Protein Sci 2014; 23:819-32. [PMID: 24677509 DOI: 10.1002/pro.2465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/05/2014] [Accepted: 03/22/2014] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance and microorganism virulence have been consistently exhibited by bacteria and archaea, which survive in conditions of environmental stress through toxin-antitoxin (TA) systems. The HP0892-HP0893 TA system is one of the two known TA systems belonging to Helicobacter pylori. The antitoxin, HP0893, binds and inhibits the HP0892 toxin and regulates the transcription of the TA operon. Here, we present the crystal structure of the zinc-bound HP0892 toxin at 1.8 Å resolution. Reorientation of residues at the mRNase active site was shown. The involved residues, namely E58A, H86A, and H58A/ H60A, were mutated and the binding affinity was monitored by ITC studies. Through the structural difference between the apo and the metal-bound state, and using a homology modeling tool, the involvement of the metal ion in mRNase active site could be identified. The most catalytically important residue, His86, reorients itself to exhibit RNase activity. His47, Glu58, and His60 are involved in metal binding where Glu58 acts as a general base and His47 and His60 may also act as a general acid in enzymatic activity. Glu58 and Asp64 are involved in substrate binding and specific sequence recognition. Arg83 is involved in phosphate binding and stabilization of the transition state, and Phe90 is involved in base packing and substrate orientation.
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Affiliation(s)
- Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea
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Wen Y, Behiels E, Devreese B. Toxin-Antitoxin systems: their role in persistence, biofilm formation, and pathogenicity. Pathog Dis 2014; 70:240-9. [DOI: 10.1111/2049-632x.12145] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yurong Wen
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Ester Behiels
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Bart Devreese
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
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54
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Kang SJ, Kim DH, Lee BJ. NMR study on small proteins from Helicobacter pylori for antibiotic target discovery: a review. Molecules 2013; 18:13410-24. [PMID: 24177697 PMCID: PMC6269979 DOI: 10.3390/molecules181113410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/24/2013] [Accepted: 10/27/2013] [Indexed: 01/15/2023] Open
Abstract
Due to the widespread and increasing appearance of antibiotic resistance, a new strategy is needed for developing novel antibiotics. Especially, there are no specific antibiotics for Helicobacter pylori (H. pylori). H. pylori are bacteria that live in the stomach and are related to many serious gastric problems such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. Because of its importance as a human pathogen, it's worth studying the structure and function of the proteins from H. pylori. After the sequencing of the H. pylori strain 26695 in 1997, more than 1,600 genes were identified from H. pylori. Until now, the structures of 334 proteins from H. pylori have been determined. Among them, 309 structures were determined by X-ray crystallography and 25 structures by Nuclear Magnetic Resonance (NMR), respectively. Overall, the structures of large proteins were determined by X-ray crystallography and those of small proteins by NMR. In our lab, we have studied the structural and functional characteristics of small proteins from H. pylori. In this review, 25 NMR structures of H. pylori proteins will be introduced and their structure-function relationships will be discussed.
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Affiliation(s)
- Su-Jin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea.
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55
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Wei Y, Gao ZQ, Otsuka Y, Naka K, Yonesaki T, Zhang H, Dong YH. Structure-function studies of Escherichia coli RnlA reveal a novel toxin structure involved in bacteriophage resistance. Mol Microbiol 2013; 90:956-65. [PMID: 24112600 DOI: 10.1111/mmi.12409] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2013] [Indexed: 12/19/2022]
Abstract
Escherichia coli RnlA-RnlB is a newly identified toxin-antitoxin (TA) system that plays a role in bacteriophage resistance. RnlA functions as a toxin with mRNA endoribonuclease activity and the cognate antitoxin RnlB inhibits RnlA toxicity in E. coli cells. Interestingly, T4 phage encodes the antitoxin Dmd, which acts against RnlA to promote its own propagation, suggesting that RnlA-Dmd represents a novel TA system. Here, we have determined the crystal structure of RnlA refined to 2.10 (Dmd-binding domain), which is an organization not previously observed among known toxin structures. Small-angle X-ray scattering (SAXS) analysis revealed that RnlA forms a dimer in solution via interactions between the DBDs from both monomers. The in vitro and in vivo functional studies showed that among the three domains, only the DBD is responsible for recognition and inhibition by Dmd and subcellular location of RnlA. In particular, the helix located at the C-terminus of DBD plays a vital role in binding Dmd. Our comprehensive studies reveal the key region responsible for RnlA toxicity and provide novel insights into its structure-function relationship.
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Affiliation(s)
- Yong Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
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van Rensburg JJ, Hergenrother PJ. Detection of endogenous MazF enzymatic activity in Staphylococcus aureus. Anal Biochem 2013; 443:81-7. [PMID: 23994560 DOI: 10.1016/j.ab.2013.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/16/2013] [Accepted: 08/18/2013] [Indexed: 10/26/2022]
Abstract
The mazEFSa toxin-antitoxin (TA) system is ubiquitous in clinical isolates of Staphylococcus aureus, yet its physiological role is unclear. MazFSa is a sequence-specific endoribonuclease that inhibits the growth of S. aureus and Escherichia coli on ectopic overexpression. MazFSa preferentially cleaves RNA at UACAU sites, which are overrepresented in genes encoding pathogenicity factors. The exploitation of the inherent toxicity of MazFSa by artificial toxin activation has been proposed as an antibacterial strategy; however, enzymatic activity of endogenous MazFSa has never been detected, and tools for such analyses are lacking. Here we detail methods for detection of the ribonuclease activity of MazFSa, including a continuous fluorometric assay and a gel-based cleavage assay. Importantly, these methods allowed for the first detection of endogenous MazFSa enzymatic activity in S. aureus lysate. These robust and sensitive assays provide a toolkit for the identification, analysis, and validation of stressors that induce MazF enzymatic activity and should assist in the discovery of artificial activators of the mazEFSa TA system.
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Affiliation(s)
- Julia J van Rensburg
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Unterholzner SJ, Poppenberger B, Rozhon W. Toxin-antitoxin systems: Biology, identification, and application. Mob Genet Elements 2013; 3:e26219. [PMID: 24251069 PMCID: PMC3827094 DOI: 10.4161/mge.26219] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 02/07/2023] Open
Abstract
Toxin–antitoxin (TA) systems are small genetic elements composed of a toxin gene and its cognate antitoxin. The toxins of all known TA systems are proteins while the antitoxins are either proteins or non-coding RNAs. Based on the molecular nature of the antitoxin and its mode of interaction with the toxin the TA modules are currently grouped into five classes. In general, the toxin is more stable than the antitoxin but the latter is expressed to a higher level. If supply of the antitoxin stops, for instance under special growth conditions or by plasmid loss in case of plasmid encoded TA systems, the antitoxin is rapidly degraded and can no longer counteract the toxin. Consequently, the toxin becomes activated and can act on its cellular targets. Typically, TA toxins act on crucial cellular processes including translation, replication, cytoskeleton formation, membrane integrity, and cell wall biosynthesis. TA systems and their components are also versatile tools for a multitude of purposes in basic research and biotechnology. Currently, TA systems are frequently used for selection in cloning and for single protein expression in living bacterial cells. Since several TA toxins exhibit activity in yeast and mammalian cells they may be useful for applications in eukaryotic systems. TA modules are also considered as promising targets for the development of antibacterial drugs and their potential to combat viral infection may aid in controlling infectious diseases.
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Affiliation(s)
- Simon J Unterholzner
- 1 Biotechnology of Horticultural Crops; Technische Universität München; Freising, Germany
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