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Feng J, Zheng Y, Ma W, Weng D, Peng D, Xu Y, Wang Z, Wang X. A synthetic antibiotic class with a deeply-optimized design for overcoming bacterial resistance. Nat Commun 2024; 15:6040. [PMID: 39019927 PMCID: PMC11255307 DOI: 10.1038/s41467-024-50453-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
The lack of new drugs that are effective against antibiotic-resistant bacteria has caused increasing concern in global public health. Based on this study, we report development of a modified antimicrobial drug through structure-based drug design (SBDD) and modular synthesis. The optimal modified compound, F8, was identified, which demonstrated in vitro and in vivo broad-spectrum antibacterial activity against drug-resistant bacteria and effectively mitigated the development of resistance. F8 exhibits significant bactericidal activity against bacteria resistant to antibiotics such as methicillin, polymyxin B, florfenicol (FLO), doxycycline, ampicillin and sulfamethoxazole. In a mouse model of drug-resistant bacteremia, F8 was found to increase survival and significantly reduce bacterial load in infected mice. Multi-omics analysis (transcriptomics, proteomics, and metabolomics) have indicated that ornithine carbamoyl transferase (arcB) is a antimicrobial target of F8. Further molecular docking, Isothermal Titration Calorimetry (ITC), and Differential Scanning Fluorimetry (DSF) studies verified arcB as a effective target for F8. Finally, mechanistic studies suggest that F8 competitively binds to arcB, disrupting the bacterial cell membrane and inducing a certain degree of oxidative damage. Here, we report F8 as a promising candidate drug for the development of antibiotic formulations to combat antibiotic-resistant bacteria-associated infections.
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Affiliation(s)
- Jin Feng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Youle Zheng
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wanqing Ma
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Defeng Weng
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dapeng Peng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yindi Xu
- Institute of Animal Husbandry and Veterinary Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhifang Wang
- Institute of Animal Husbandry and Veterinary Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China.
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China.
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2
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Nguyen PT, Nguyen-Thi TU, Nguyen HT, Pham MN, Nguyen TT. Halophilic lactic acid bacteria - Play a vital role in the fermented food industry. Folia Microbiol (Praha) 2024; 69:305-321. [PMID: 38372951 DOI: 10.1007/s12223-024-01149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Halophilic lactic acid bacteria have been widely found in various high-salt fermented foods. The distribution of these species in salt-fermented foods contributes significantly to the development of the product's flavor. Besides, these bacteria also have the ability to biosynthesize bioactive components which potentially apply to different areas. In this review, insights into the metabolic properties, salt stress responses, and potential applications of these bacteria have been have been elucidated. The purpose of this review highlights the important role of halophilic lactic acid bacteria in improving the quality and safety of salt-fermented products and explores the potential application of these bacteria.
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Affiliation(s)
- Phu-Tho Nguyen
- An Giang University, An Giang, Vietnam
- Vietnam National University Ho Chi Minh City (VNU-HCM), Ho Chi Minh City, Vietnam
| | | | - Huu-Thanh Nguyen
- An Giang University, An Giang, Vietnam
- Vietnam National University Ho Chi Minh City (VNU-HCM), Ho Chi Minh City, Vietnam
| | - Minh-Nhut Pham
- Hutech Institute of Applied Science, HUTECH University, Ho Chi Minh City, Vietnam
| | - Thi-Tho Nguyen
- Hutech Institute of Applied Science, HUTECH University, Ho Chi Minh City, Vietnam.
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3
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Yang J, Luo H, Zhu X, Cai L, Zhou L, Ruan H, Chen J. Copper-doped bismuth oxychloride nanosheets assembled into sphere-like morphology for improved photocatalytic inactivation of drug-resistant bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168916. [PMID: 38036130 DOI: 10.1016/j.scitotenv.2023.168916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/02/2023]
Abstract
The devastating microbiological contamination as well as emerging drug-resistant bacteria has posed severe threats to the ecosystem and public health, which propels the continuous exploitation of safe yet efficient disinfection products and technology. Here, copper doping engineered bismuth oxychloride (Cu-BiOCl) nanocomposite with a hierarchical spherical structure was successfully prepared. It was found that due to the exposure of abundant active sites for the adsorption of both bacteria cells and molecular oxygen in the structure, the obtained Cu-BiOCl with nanosheets assembled into sphere-like morphology exhibited remarkable photocatalytic antibacterial effects. In particular, compared to the pure BiOCl, composite Cu-BiOCl possessed improved antibacterial effects against Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Methicillin-resistant Staphylococcus aureus (MRSA). The combination of physicochemical characterizations and theoretical calculations has revealed that copper doping significantly promoted the light absorbance, inhibited the recombination of electron-hole pairs, and enhanced molecular oxygen adsorption, which resulted in more generation of active species including reactive oxygen species (ROS) and h+ to achieve superior photocatalytic bacterial inactivation. Finally, transcriptome analysis on MRSA pinpointed photocatalytic inactivation induced by Cu-BiOCl may retard largely the development of drug-resistance. Therefore, the built spherical Cu-BiOCl nanocomposite has provided an ecofriendly, economical and robust strategy for the efficient removal of drug-resistant bacteria with promising potentials for environmental and healthcare utilizations.
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Affiliation(s)
- Jing Yang
- The Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; The Affiliated Chongqing Prevention and Treatment Center for Occupational Diseases, School of Public Health, Nanjing Medical University, Chongqing 400060, China
| | - Huan Luo
- The Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; The Affiliated Chongqing Prevention and Treatment Center for Occupational Diseases, School of Public Health, Nanjing Medical University, Chongqing 400060, China
| | - Xinyi Zhu
- The Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ling Cai
- The Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; The Affiliated Chongqing Prevention and Treatment Center for Occupational Diseases, School of Public Health, Nanjing Medical University, Chongqing 400060, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Liuzhu Zhou
- The Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hongjie Ruan
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Nanjing 210004, China.
| | - Jin Chen
- The Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; The Affiliated Chongqing Prevention and Treatment Center for Occupational Diseases, School of Public Health, Nanjing Medical University, Chongqing 400060, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China; Jiangsu Province Engineering Research Center of Antibody Drug, Key Laboratory of Antibody Technique of National Health Commission, Nanjing Medical University, Nanjing 211166, China.
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4
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Liu X, An L, Ren S, Zhou Y, Peng W. Comparative Proteomic Analysis Reveals Antibacterial Mechanism of Patrinia scabiosaefolia Against Methicillin Resistant Staphylococcus epidermidis. Infect Drug Resist 2022; 15:883-893. [PMID: 35281570 PMCID: PMC8912936 DOI: 10.2147/idr.s350715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose As a kind of opportunist pathogen, Staphylococcus epidermidis (MRSE) can cause nosocomial infections and easily evolve into resistant bacteria. Among these, methicillin-resistant Staphylococcus epidermidis (MRSE) exhibit significantly higher rates. Our previous study showed that Patrinia scabiosaefolia (PS) possessed strong antibacterial activity against MRSE. However, the mechanism of PS against MRSE is not clear. Methods Here, a tandem mass tag-based (TMT) proteomic analysis was performed to elucidate the potential mechanism of PS against MRSE. We compared the differential expression proteins of MRSE under PS stress. Results Based on a fold change of >1.2 or < 1/1.2 (with p value set at <0.05), a total of 248 proteins (128 up-regulated proteins, 120 down-regulated proteins) were identified. Bioinformatic analysis showed that proteins including arginine deiminase (arcA), ornithine carbamoyltransferase (arcB) and carbamate kinase (arcC), serine–tRNA ligase (serS), phenylalanine–tRNA ligase beta and subunit (pheT), DltD (dlt), d-alanyl carrier protein (dlt), accumulation-associated protein (SasG), serine-aspartate repeat-containing protein C (SdrC) and hemin transport system permease protein HrtB (VraG) played important roles in mechanism of PS against MRSE. Conclusion In summary, these results indicated that arginine deiminase pathway (ADI) pathway, protein synthesis, cell wall synthesis, biofilm formation and uptake of iron were related to mechanisms of PS against MRSE. Our findings provide an insight into the the mechanism of PS against MRSE, and may be valuable in offering new targets to develop more anti-MRSE drugs.
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Affiliation(s)
- Xin Liu
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
- Correspondence: Xin Liu, College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China, Tel +8618886056643, Email
| | - Lili An
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Shuaijun Ren
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Yonghui Zhou
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Wei Peng
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
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5
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Ude Z, Flothkötter N, Sheehan G, Brennan M, Kavanagh K, Marmion CJ. Multi-targeted metallo-ciprofloxacin derivatives rationally designed and developed to overcome antimicrobial resistance. Int J Antimicrob Agents 2021; 58:106449. [PMID: 34644603 DOI: 10.1016/j.ijantimicag.2021.106449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/28/2021] [Accepted: 10/02/2021] [Indexed: 10/20/2022]
Abstract
Antimicrobial resistance is a major global threat to human health due to the rise, spread and persistence of multi-drug-resistant bacteria or 'superbugs'. There is an urgent need to develop novel chemotherapeutics to overcome this overarching challenge. The authors derivatized a clinically used fluoroquinolone antibiotic ciprofloxacin (Cip), and complexed it to a copper phenanthrene framework. This resulted in the development of two novel metallo-antibiotics of general formula [Cu(N,N)(CipHA)]NO3 where N,N represents a phenanthrene ligand and CipHA represents a hydroxamic acid of Cip derivative. Comprehensive studies, including a detailed proteomic study in which Staphylococcus aureus cells were exposed to the complexes, were undertaken to gain an insight into their mode of action. These new complexes possess potent antibacterial activity against S. aureus and methicillin-resistant S. aureus. In addition, they were found to be well tolerated in vivo in Galleria mellonella larvae, which has both functional and structural similarities to the innate immune system of mammals. These findings suggest that proteins involved in virulence, pathogenesis, and the synthesis of nucleotides and DNA repair mechanisms are most affected. In addition, both complexes affected similar cell pathways when compared with clinically used Cip, including cationic antimicrobial peptide resistance. The Cu-DPPZ-CipHA (DPPZ = dipyrido[3,2-a:2',3'-c]phenazine) analogue also induces cell leakage, which leads to an altered proteome indicative of reduced virulence and increased stress.
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Affiliation(s)
- Ziga Ude
- Centre for Synthesis and Chemical Biology, Department of Chemistry, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Nils Flothkötter
- Centre for Synthesis and Chemical Biology, Department of Chemistry, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Gerard Sheehan
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Marian Brennan
- School of Pharmacy and Biomolecular Sciences, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Kevin Kavanagh
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Celine J Marmion
- Centre for Synthesis and Chemical Biology, Department of Chemistry, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.
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Yang T, Yang S, Ahmed T, Nguyen K, Yu J, Cao X, Zan R, Zhang X, Shen H, Fay ME, Williams EK, Lam WA, VanEpps JS, Takayama S, Song Y. Dosage-dependent antimicrobial activity of DNA-histone microwebs against Staphylococcus aureus. ADVANCED MATERIALS INTERFACES 2021; 8:2100717. [PMID: 34540532 PMCID: PMC8447838 DOI: 10.1002/admi.202100717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Indexed: 05/15/2023]
Abstract
Neutrophil extracellular traps (NETs) is an antimicrobial cobweb-structured material produced by immune cells for clearance of pathogens in the body, but paradoxically associated with biofilm formation and exacerbated lung infections. To provide a better materials perspective on the pleiotropic roles played by NETs at diverse compositions/concentrations, a NETs-like material (called 'microwebs', abbreviated as μwebs) is synthesized for decoding the antimicrobial activity of NETs against Staphylococcus aureus in infection-relevant conditions. We show that μwebs composed of low-to-intermediate concentrations of DNA-histone complexes successfully trap and inhibit S. aureus growth and biofilm formation. However, with growing concentrations and histone proportions, the resulting microwebs appear gel-like structures accompanied by reduced antimicrobial activity that can even promote formation of S. aureus biofilms. Our simplified model of NETs provides a materials-based evidence on NETs-relevant pathology in the development of biofilms.
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Affiliation(s)
- Ting Yang
- State Key Laboratory of Bioreactor Engineering, Department of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shi Yang
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tasdiq Ahmed
- Wallace H Coulter Department of Biomedical Engineering & Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology & Emory School of Medicine, Atlanta, GA 30332 USA
| | - Katherine Nguyen
- Wallace H Coulter Department of Biomedical Engineering & Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology & Emory School of Medicine, Atlanta, GA 30332 USA
| | - Jinlong Yu
- Department of Orthopedics, Shanghai No.6 People's hospital, Shanghai 200233, China
| | - Xuejun Cao
- State Key Laboratory of Bioreactor Engineering, Department of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Rui Zan
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaonong Zhang
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Shen
- Department of Orthopedics, Shanghai No.6 People's hospital, Shanghai 200233, China
| | - Meredith E Fay
- Wallace H Coulter Department of Biomedical Engineering & Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology & Emory School of Medicine, Atlanta, GA 30332 USA
| | - Evelyn Kendall Williams
- Wallace H Coulter Department of Biomedical Engineering & Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology & Emory School of Medicine, Atlanta, GA 30332 USA
| | - Wilbur A Lam
- Wallace H Coulter Department of Biomedical Engineering & Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology & Emory School of Medicine, Atlanta, GA 30332 USA
| | - J Scott VanEpps
- Department of Emergency Medicine, Michigan Center for Integrative Research in Critical Care, Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109 USA
| | - Shuichi Takayama
- Wallace H Coulter Department of Biomedical Engineering & Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology & Emory School of Medicine, Atlanta, GA 30332 USA
| | - Yang Song
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Liu WT, Chen EZ, Yang L, Peng C, Wang Q, Xu Z, Chen DQ. Emerging resistance mechanisms for 4 types of common anti-MRSA antibiotics in Staphylococcus aureus: A comprehensive review. Microb Pathog 2021; 156:104915. [PMID: 33930416 DOI: 10.1016/j.micpath.2021.104915] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/10/2023]
Abstract
Staphylococcus aureus is one of the leading hospital-associated and community-associated pathogens, which has caused a global public health concern. The emergence of methicillin-resistant S. aureus (MRSA) along with the widespread use of different classes of antibiotics has become a significant therapeutic challenge. Antibiotic resistance is a disturbing problem that poses a threat to humans. Treatment options for S. aureus resistant to β-lactam antibiotics include glycopeptide antibiotic, cyclic lipopeptide antibiotic, cephalosporins and oxazolidinone antibiotic. The most representative types of these antibiotics are vancomycin, daptomycin, ceftaroline and linezolid. The frequent use of the first-line drug vancomycin for MRSA treatment has increased the number of resistant strains, namely vancomycin intermediate resistant S. aureus (VISA) and vancomycin resistant S. aureus (VRSA). A systematic literature review of relevant published studies in PubMed before 2020 was conducted. In recent years, there have been some reports on the relevant resistant mechanisms of vancomycin, daptomycin, ceftaroline and linezolid. In this review, we have summarized the antibiotic molecular modes of action and different gene mutants at the whole-genome level, which will aid in further development on new drugs for effective MRSA treatment based on describing different resistance mechanisms of classic antibiotics.
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Affiliation(s)
- Wan-Ting Liu
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - En-Zhong Chen
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Chen Peng
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Qun Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, China; College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN38163, USA; Research Institute for Food Nutrition and Human Health, Guangzhou, 510640, China; Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand.
| | - Ding-Qiang Chen
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China.
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8
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Bezrukov F, Prados J, Renzoni A, Panasenko OO. MazF toxin causes alterations in Staphylococcus aureus transcriptome, translatome and proteome that underlie bacterial dormancy. Nucleic Acids Res 2021; 49:2085-2101. [PMID: 33544858 PMCID: PMC7913683 DOI: 10.1093/nar/gkaa1292] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Antibiotic resistance is a serious problem which may be caused by bacterial dormancy. It has been suggested that bacterial toxin-antitoxin systems induce dormancy. We analyzed the genome-wide role of Staphylococcus aureus endoribonuclease toxin MazF using RNA-Seq, Ribo-Seq and quantitative proteomics. We characterized changes in transcriptome, translatome and proteome caused by MazF, and proposed that MazF decreases translation directly by cleaving mRNAs, and indirectly, by decreasing translation factors and by promoting ribosome hibernation. Important pathways affected during the early stage of MazF induction were identified: MazF increases cell wall thickness and decreases cell division; MazF activates SsrA-system which rescues stalled ribosomes, appearing as a result of MazF mRNA cleavage. These pathways may be promising targets for new antibacterial drugs that prevent bacteria dormancy. Finally, we described the overall impact of MazF on S. aureus cell physiology, and propose one of the mechanisms by which MazF might regulate cellular changes leading to dormancy.
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Affiliation(s)
- Fedor Bezrukov
- Department of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, UK
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Adriana Renzoni
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland.,Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
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9
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Lin J, Luo X, Gänzle MG, Luo L. Characterization of the two nonidentical ArgR regulators of Tetragenococcus halophilus and their regulatory effects on arginine metabolism. Appl Microbiol Biotechnol 2020; 104:8775-8787. [PMID: 32880693 DOI: 10.1007/s00253-020-10868-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022]
Abstract
The halophilic lactic acid bacterium Tetragenococcus halophilus has been widely used in high-salinity fermentation processes of food. Previous studies have indicated that the catabolism of arginine may contribute to the osmotic stress adaptation of T. halophilus. Unusually, in the chromosome of T. halophilus, preceding the arginine deiminase (ADI) operon, locate two co-transcribed genes, both encoding an ArgR regulator; similar structure was rarely found and the roles of the regulators have not been demonstrated. In the current study, regulatory roles of these two nonidentical ArgR regulators on the arginine metabolism of T. halophilus were investigated. The results show that these two regulators play different roles in arginine metabolism, ArgR1 acts as a negative regulator of the ADI pathway by binding to the promoter sequences and repressing the transcription of genes, and the addition of arginine or hyper-osmotic stress conditions can abolish the ArgR1 repression, whereas ArgR2 negatively regulates the genes involved in arginine biosynthesis. Our study found that despite the commonly known roles of the ArgR regulators as the activator of arginine catabolism and the repressor of arginine biosynthesis, which are found in most studied bacteria possessed one ArgR regulator, the two nonidentical ArgR regulators of T. halophilus both act as repressors, and the repression by which is regulated when sensing changes of environments. By revealing the regulation of arginine metabolism, the current study provides molecular insights and potential tools for future applications of halophiles in biotechnology. KEY POINTS: • The expression of the ADI pathway of T. halophilus is regulated by carbon sources and osmotic stress. • The arginine metabolism process of T. halophilus is fine-tuned by the two ArgR regulators. • The ADI pathway may contribute to the osmotic stress adaptation by generating more energy and accumulating citrulline which acts as compatible solute.
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Affiliation(s)
- Jieting Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Xiaotong Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Lixin Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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10
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Tan XE, Neoh HM, Cui L, Hiramatsu K, Jamal R. Oxidative stress resistance and fitness-compensatory response in vancomycin-intermediate Staphylococcus aureus (VISA). Can J Microbiol 2019; 65:623-628. [DOI: 10.1139/cjm-2019-0048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, vancomycin-intermediate Staphylococcus aureus (VISA) cells carrying vraS and (or) graR mutations were shown to be more resistant to oxidative stress. Caenorhabditis elegans infected with these strains in turn demonstrated lower survival. Altered regulation in oxidative stress response and virulence appear to be physiological adaptations associated with the VISA phenotype in the Mu50 lineage.
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Affiliation(s)
- Xin-Ee Tan
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Hui-min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
- Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Keiichi Hiramatsu
- Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
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11
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Dhanda G, Sarkar P, Samaddar S, Haldar J. Battle against Vancomycin-Resistant Bacteria: Recent Developments in Chemical Strategies. J Med Chem 2018; 62:3184-3205. [DOI: 10.1021/acs.jmedchem.8b01093] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Geetika Dhanda
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, Karnataka, India
| | - Paramita Sarkar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, Karnataka, India
| | - Sandip Samaddar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, Karnataka, India
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, Karnataka, India
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12
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Gardner SG, Marshall DD, Daum RS, Powers R, Somerville GA. Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility. Antimicrob Agents Chemother 2018; 62:e01608-17. [PMID: 29109158 PMCID: PMC5740343 DOI: 10.1128/aac.01608-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/28/2017] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen whose infections are increasingly difficult to treat due to increased antibiotic resistance, including resistance to vancomycin. Vancomycin-intermediate S. aureus (VISA) strains develop resistance to vancomycin through adaptive changes that are incompletely understood. Central to this adaptation are metabolic changes that permit growth in the presence of vancomycin. To define the metabolic changes associated with adaptive resistance to vancomycin in S. aureus, the metabolomes of a vancomycin-sensitive and VISA strain pair isolated from the same patient shortly after vancomycin therapy began and following vancomycin treatment failure were analyzed. The metabolic adaptations included increases in acetogenesis, carbon flow through the pentose phosphate pathway, wall teichoic acid and peptidoglycan precursor biosynthesis, purine biosynthesis, and decreased tricarboxylic acid (TCA) cycle activity. The significance of these metabolic pathways for vancomycin-intermediate susceptibility was determined by assessing the synergistic potential of human-use-approved inhibitors of these pathways in combination with vancomycin against VISA strains. Importantly, inhibitors of amino sugar and purine biosynthesis acted synergistically with vancomycin to kill a diverse set of VISA strains, suggesting that combinatorial therapy could augment the efficacy of vancomycin even in patients infected with VISA strains.
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Affiliation(s)
- Stewart G Gardner
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Robert S Daum
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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13
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Yang XY, Xu JY, Wei QX, Sun X, He QY. Comparative Proteomics of Streptococcus pneumoniae Response to Vancomycin Treatment. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:531-539. [PMID: 28934029 DOI: 10.1089/omi.2017.0098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Streptococcus pneumoniae is a gram-positive pathogen that causes otitis media, pneumonia, meningitis, and other serious diseases. Vancomycin is one of the most important drugs currently used for the treatment of gram-positive bacterial infections, representing, importantly, the last line of defense against bacteria that have developed resistance to other antibiotics. While primary efforts of most investigations focused on the antibacterial mechanism of vancomycin, few studies have been performed to assess the tolerance mechanism of bacteria to vancomycin. In this work, whole cellular proteins were extracted from S. pneumoniae D39 with or without vancomycin treatment. Subsequently, differentially expressed proteins (DEPs) were identified with two-dimensional gel electrophoresis coupled with matrix-assisted laser desorption/ionization mass spectrometry (MS)/MS. In total, 27 proteins were upregulated and four proteins were downregulated in vancomycin-treated S. pneumoniae. Gene ontology analysis indicated that these DEPs were mainly involved in the nucleic acid, protein, and carbohydrate biosynthetic processes. Verification experiments with real-time quantitative polymerase chain reaction showed that the gene expression profiles were consistent with proteomic data. These new observations may serve as a valuable resource for future investigations of vancomycin tolerance mechanisms of S. pneumoniae.
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Affiliation(s)
- Xiao-Yan Yang
- 1 The First Affiliated Hospital of Jinan University , Guangzhou, China .,2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Jing-Yu Xu
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Qiu-Xia Wei
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Xuesong Sun
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Qing-Yu He
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
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14
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The molecular mechanism and post-transcriptional regulation characteristic of Tetragenococcus halophilus acclimation to osmotic stress revealed by quantitative proteomics. J Proteomics 2017; 168:1-14. [DOI: 10.1016/j.jprot.2017.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/31/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022]
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