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Filipek J, Chalaskiewicz K, Kosmider A, Nielipinski M, Michalak A, Bednarkiewicz M, Goslawski-Zeligowski M, Prucnal F, Sekula B, Pietrzyk-Brzezinska AJ. Comprehensive structural overview of the C-terminal ligand-binding domains of the TetR family regulators. J Struct Biol 2024; 216:108071. [PMID: 38401830 DOI: 10.1016/j.jsb.2024.108071] [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: 01/05/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
TetR family regulators (TFRs) represent a large group of one-component bacterial signal transduction systems which recognize environmental signals, like the presence of antibiotics or other bactericidal compounds, and trigger the cell response by regulating the expression of genes that secure bacterial survival in harsh environmental conditions. TFRs act as homodimers, each protomer is composed of a conserved DNA-binding N-terminal domain (NTD) and a variable ligand-binding C-terminal domain (CTD). Currently, there are about 500 structures of TFRs available in the Protein Data Bank and one-fourth of them represent the structures of TFR-ligand complexes. In this review, we summarized information on the ligands interacting with TFRs and based on structural data, we compared the CTDs of the TFR family members, as well as their ligand-binding cavities. Additionally, we divided the whole TFR family, including more than half of a million sequences, into subfamilies according to calculated multiple sequence alignment and phylogenetic tree. We also highlighted structural elements characteristic of some of the subfamilies. The presented comprehensive overview of the TFR CTDs provides good bases and future directions for further studies on TFRs that are not only important targets for battling multidrug resistance but also good candidates for many biotechnological approaches, like TFR-based biosensors.
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Affiliation(s)
- Jakub Filipek
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Katarzyna Chalaskiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Aleksandra Kosmider
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maciej Nielipinski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka Michalak
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maria Bednarkiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Mieszko Goslawski-Zeligowski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Filip Prucnal
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Bartosz Sekula
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland.
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Singh A, Jain N, Shankar U, Sharma TK, Kumar A. Characterization of G-quadruplex structures in genes involved in survival and pathogenesis of Acinetobacter baumannii as a potential drug target. Int J Biol Macromol 2024; 269:131806. [PMID: 38670179 DOI: 10.1016/j.ijbiomac.2024.131806] [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: 12/13/2023] [Revised: 03/21/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024]
Abstract
Acinetobacter baumannii is a notorious pathogen that commonly thrives in hospital environments and is responsible for numerous nosocomial infections in humans. The burgeoning multi-drug resistance leaves relatively minimal options for treating the bacterial infection, posing a significant problem and prompting the identification of new approaches for tackling the same. This motivated us to focus on non-canonical nucleic acid structures, mainly G-quadruplexes, as drug targets. G-quadruplexes have recently been gaining attention due to their involvement in multiple bacterial and viral pathogenesis. Herein, we sought to explore conserved putative G-quadruplex motifs in A. baumannii. In silico analysis revealed the presence of eight conserved motifs in genes involved in bacterial survival and pathogenesis. The biophysical and biomolecular analysis confirmed stable G-quadruplex formation by the motifs and showed a high binding affinity with the well-reported G-quadruplex binding ligand, BRACO-19. BRACO-19 exposure also decreased the growth of bacteria and downregulated the expression of G-quadruplex-harboring genes. The biofilm-forming ability of the bacteria was also affected by BRACO-19 addition. Taking all these observations into account, we have shown here for the first time the potential of G-quadruplex structures as a promising drug target in Acinetobacter baumannii, for addressing the challenges posed by this infamous pathogen.
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Affiliation(s)
- Aakriti Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Department of Medical Biotechnology, Gujarat Biotechnology University, Gandhinagar 382355, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India.
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3
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Shi J, Cheng J, Liu S, Zhu Y, Zhu M. Acinetobacter baumannii: an evolving and cunning opponent. Front Microbiol 2024; 15:1332108. [PMID: 38318341 PMCID: PMC10838990 DOI: 10.3389/fmicb.2024.1332108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Acinetobacter baumannii is one of the most common multidrug-resistant pathogens causing nosocomial infections. The prevalence of multidrug-resistant A. baumannii infections is increasing because of several factors, including unregulated antibiotic use. A. baumannii drug resistance rate is high; in particular, its resistance rates for tigecycline and polymyxin-the drugs of last resort for extensively drug-resistant A. baumannii-has been increasing annually. Patients with a severe infection of extensively antibiotic-resistant A. baumannii demonstrate a high mortality rate along with a poor prognosis, which makes treating them challenging. Through carbapenem enzyme production and other relevant mechanisms, A. baumannii has rapidly acquired a strong resistance to carbapenem antibiotics-once considered a class of strong antibacterials for A. baumannii infection treatment. Therefore, understanding the resistance mechanism of A. baumannii is particularly crucial. This review summarizes mechanisms underlying common antimicrobial resistance in A. baumannii, particularly those underlying tigecycline and polymyxin resistance. This review will serve as a reference for reasonable antibiotic use at clinics, as well as new antibiotic development.
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Affiliation(s)
- Jingchao Shi
- Open Laboratory Medicine, Hangzhou Xixi Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
- Graduate School, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianghao Cheng
- Open Laboratory Medicine, Hangzhou Xixi Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Shourong Liu
- Department of Infectious Disease, Hangzhou Xixi Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Yufeng Zhu
- Open Laboratory Medicine, Hangzhou Xixi Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Mingli Zhu
- Open Laboratory Medicine, Hangzhou Xixi Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
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Sikandar A, Popoff A, Jumde RP, Mándi A, Kaur A, Elgaher WAM, Rosenberger L, Hüttel S, Jansen R, Hunter M, Köhnke J, Hirsch AKH, Kurtán T, Müller R. Revision of the Absolute Configurations of Chelocardin and Amidochelocardin. Angew Chem Int Ed Engl 2023; 62:e202306437. [PMID: 37466921 DOI: 10.1002/anie.202306437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/20/2023]
Abstract
Even with the aid of the available methods, the configurational assignment of natural products can be a challenging task that is prone to errors, and it sometimes needs to be corrected after total synthesis or single-crystal X-ray diffraction (XRD) analysis. Herein, the absolute configuration of amidochelocardin is revised using a combination of XRD, NMR spectroscopy, experimental ECD spectra, and time-dependent density-functional theory (TDDFT)-ECD calculations. As amidochelocardin was obtained via biosynthetic engineering of chelocardin, we propose the same absolute configuration for chelocardin based on the similar biosynthetic origins of the two compounds and result of TDDFT-ECD calculations. The evaluation of spectral data of two closely related analogues, 6-desmethyl-chelocardin and its semisynthetic derivative 1, also supports this conclusion.
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Affiliation(s)
- Asfandyar Sikandar
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Alexander Popoff
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Ravindra P Jumde
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Attila Mándi
- Department of Organic Chemistry University of Debrecen, P. O. Box 400, 4002, Debrecen, Hungary
| | - Amninder Kaur
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Walid A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Lara Rosenberger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Stephan Hüttel
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Rolf Jansen
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Maja Hunter
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Jesko Köhnke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Helmholtz International Lab for Anti-infectives, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Tibor Kurtán
- Department of Organic Chemistry University of Debrecen, P. O. Box 400, 4002, Debrecen, Hungary
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Helmholtz International Lab for Anti-infectives, Campus Building E8.1, 66123, Saarbrücken, Germany
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Sykes EME, Mateo-Estrada V, Zhanel G, Dettman J, Chapados J, Gerdis S, Akineden Ö, Khan IIU, Castillo-Ramírez S, Kumar A. Emergence of ADC-5 Cephalosporinase in environmental Acinetobacter baumannii from a German tank milk with a novel Sequence Type. Access Microbiol 2023; 5:acmi000485.v3. [PMID: 37424542 PMCID: PMC10323797 DOI: 10.1099/acmi.0.000485.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
Bacteria resistant to antibiotics arguably pose the greatest threat to human health in the twenty-first century. One such bacterium that typifies antibiotic resistance is Acinetobacter baumannii . Frequently, hospital strains of A. baumannii display multidrug resistant (MDR) or extensively drug resistant (XDR) phenotypes, often requiring the use of last resort antibiotics for treatment. In addition to hospital settings, A. baumannii has been isolated from many highly divergent sources including wastewater treatment plant effluent, soil, and agricultural run-off with global distribution. However, such isolates remain poorly characterized. In this study, we characterized a strain of A. baumannii, AB341-IK15, isolated from bulk tank milk in Germany that demonstrated resistance to ceftazidime and intermediate resistance to ceftriaxone and piperacillin/tazobactam. Further genetic characterization identified an ADC-5 cephalosporinase, first incidence in an environmental isolate; and an OXA-408 oxacillinase that may contribute to this phenotype. Interestingly, AB341-IK15 is of a novel sequence type. This research underscores the importance of studying isolates of A. baumannii of non-clinical origin to understand the antibiotic resistance and virulence potential of environmental isolates of A. baumannii as well to understand the diversity of this species.
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Affiliation(s)
- Ellen M. E. Sykes
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, Canada
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Julie Chapados
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Ömer Akineden
- Institute of Veterinary Food Science, University of Giessen, Giessen, Germany
| | - Izhar I. U. Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, Canada
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Sun C, Yu Y, Hua X. Resistance mechanisms of tigecycline in Acinetobacter baumannii. Front Cell Infect Microbiol 2023; 13:1141490. [PMID: 37228666 PMCID: PMC10203620 DOI: 10.3389/fcimb.2023.1141490] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/14/2023] [Indexed: 05/27/2023] Open
Abstract
Acinetobacter baumannii is widely distributed in nature and in hospital settings and is a common pathogen causing various infectious diseases. Currently, the drug resistance rate of A. baumannii has been persistently high, showing a worryingly high resistance rate to various antibiotics commonly used in clinical practice, which greatly limits antibiotic treatment options. Tigecycline and polymyxins show rapid and effective bactericidal activity against CRAB, and they are both widely considered to be the last clinical line of defense against multidrug resistant A. baumannii. This review focuses with interest on the mechanisms of tigecycline resistance in A. baumannii. With the explosive increase in the incidence of tigecycline-resistant A. baumannii, controlling and treating such resistance events has been considered a global challenge. Accordingly, there is a need to systematically investigate the mechanisms of tigecycline resistance in A. baumannii. Currently, the resistance mechanism of A. baumannii to tigecycline is complex and not completely clear. This article reviews the proposed resistance mechanisms of A. baumannii to tigecycline, with a view to providing references for the rational clinical application of tigecycline and the development of new candidate antibiotics.
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Affiliation(s)
- Chunli Sun
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, Haining, Zhejiang, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoting Hua
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, Haining, Zhejiang, China
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Song Q, Wu H, Zhang P, Tian K, Zhu H, Qiao J. LssR plays a positive regulatory role in acid and nisin tolerance response of Lactococcus lactis. J Dairy Sci 2022; 105:6483-6498. [PMID: 35840402 DOI: 10.3168/jds.2022-21842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/14/2022] [Indexed: 11/19/2022]
Abstract
In Lactococcus lactis, different regulation mechanisms can be activated to overcome the effects of adverse environmental stresses. Here, a TetR family regulator LssR was demonstrated as a positive regulator in the activation of the mechanisms involved in acid and nisin tolerance of L. lactis. The deletion of lssR led to the reduction of tolerance of L. lactis NZ9000 to nisin and acid stress, and the survival rates of NZ9000 under nisin and acid stress were roughly 20-fold, 10-fold (pH 3.0, hydrochloric acid), and 8.9-fold (pH 4.0, lactic acid) of the lssR mutant NZΔlssR, respectively. Moreover, the lssR mutant NZΔlssR also displayed a lower intracellular pH stability and a changed cell surface morphology. Subsequently, transcriptome analysis revealed that genes related to the arginine deiminase pathway, the surface polysaccharides biosynthesis, carbohydrates transport and metabolism, multidrug resistance, cell repair proteins and chaperones were predominantly down transcribed in NZΔlssR. The transcript levels of the arginine deiminase pathway and the surface polysaccharides biosynthesis-associated genes under acid and nisin stresses were compared between the wild type NZ9000 and NZΔlssR using real-time fluorescence quantitative PCR. It revealed that the arginine deiminase pathway genes (arcD1C1C2T) and the surface polysaccharides biosynthesis genes (cgT, gmhB, gmhA, hddA, tagH and tarS) were proposed to be the main regulatory mechanisms of LssR in response to the acid and nisin stresses. Overall, the important role of LssR in the acid and nisin stresses response was demonstrated and the putative regulation mechanism of LssR was revealed.
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Affiliation(s)
- Qianqian Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hao Wu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Peng Zhang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Kairen Tian
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.
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