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Kiran S, Tariq A, Iqbal S, Naseem Z, Siddique W, Jabeen S, Bashir R, Hussain A, Rahman M, Habib FE, Rauf W, Ali A, Sarwar Y, Jander G, Iqbal M. Punicalagin, a pomegranate polyphenol sensitizes the activity of antibiotics against three MDR pathogens of the Enterobacteriaceae. BMC Complement Med Ther 2024; 24:93. [PMID: 38365729 PMCID: PMC10870630 DOI: 10.1186/s12906-024-04376-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Multidrug resistance (MDR) in the family Enterobacteriaceae is a perniciously increasing threat to global health security. The discovery of new antimicrobials having the reversing drug resistance potential may contribute to augment and revive the antibiotic arsenal in hand. This study aimed to explore the anti-Enterobacteriaceae capability of bioactive polyphenols from Punica granatum (P. granatum) and their co-action with antibiotics against clinical isolates of Enterobacteriaceae predominantly prevalent in South Asian countries. METHODS The Kandhari P. granatum (Pakistani origin) extracts were tested for anti-Enterobacteriaceae activity by agar well diffusion assay against MDR Salmonella enterica serovar Typhi, serovar Typhimurium and Escherichia coli. Predominant compounds of active extract were determined by mass spectrometry and screened for bioactivity by agar well diffusion and minimum inhibitory concentration (MIC) assay. The active punicalagin was further evaluated at sub-inhibitory concentrations (SICs) for coactivity with nine conventional antimicrobials using a disc diffusion assay followed by time-kill experiments that proceeded with SICs of punicalagin and antimicrobials. RESULTS Among all P. granatum crude extracts, pomegranate peel methanol extract showed the largest inhibition zones of 25, 22 and 19 mm, and the MICs as 3.9, 7.8 and 7.8 mg/mL for S. typhi, S. typhimurium and E. coli, respectively. Punicalagin and ellagic acid were determined as predominant compounds by mass spectrometry. In plate assay, punicalagin (10 mg/mL) was active with hazy inhibition zones of 17, 14, and 13 mm against S. typhi, S. typhimurium and E. coli, respectively. However, in broth dilution assay punicalagin showed no MIC up to 10 mg/mL. The SICs 30 μg, 100 μg, and 500 μg of punicalagin combined with antimicrobials i.e., aminoglycoside, β-lactam, and fluoroquinolone act in synergy against MDR strains with % increase in inhibition zone values varying from 3.4 ± 2.7% to 73.8 ± 8.4%. In time-kill curves, a significant decrease in cell density was observed with the SICs of antimicrobials/punicalagin (0.03-60 μg/mL/30, 100, 500 μg/mL of punicalagin) combinations. CONCLUSIONS The P. granatum peel methanol extract exhibited antimicrobial activity against MDR Enterobacteriaceae pathogens. Punicalagin, the bacteriostatic flavonoid act as a concentration-dependent sensitizing agent for antimicrobials against Enterobacteriaceae. Our findings for the therapeutic punicalagin-antimicrobial combination prompt further evaluation of punicalagin as a potent activator for drugs, which otherwise remain less or inactive against MDR strains.
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Affiliation(s)
- Saba Kiran
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Anam Tariq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Shoaib Iqbal
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Zubera Naseem
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Waqar Siddique
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Sobia Jabeen
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Rizwan Bashir
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Ashfaq Hussain
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Moazur Rahman
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, Punjab, Pakistan
| | - Fazal-E Habib
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Waqar Rauf
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan.
| | - Aamir Ali
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Yasra Sarwar
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan
| | - Georg Jander
- Boyce Thompson Institute, Cornell University, 14850 Ithaca, New York, USA
| | - Mazhar Iqbal
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, 38000, Pakistan.
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Behera DU, Gaur M, Sahoo M, Subudhi E, Subudhi BB. Development of pharmacophore models for AcrB protein and the identification of potential adjuvant candidates for overcoming efflux-mediated colistin resistance. RSC Med Chem 2024; 15:127-138. [PMID: 38283226 PMCID: PMC10809322 DOI: 10.1039/d3md00483j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/26/2023] [Indexed: 01/30/2024] Open
Abstract
Growing multi-drug resistance (MDR) among ESKAPE pathogens is a huge challenge. Increased resistance to last-resort antibiotics, like colistin, has further aggravated this. Efflux is identified as a major route of colistin resistance. So, finding an FDA-approved efflux inhibitor for potential application as an adjuvant to colistin was the primary objective of this study. E. coli-AcrB pump inhibitors and substrates were used to develop and validate the pharmacophoric model. Drugs confirming this pharmacophore were subjected to molecular docking to identify hits for the AcrB binding pocket. The efflux inhibition potential of the top hit was validated through the in vitro evaluation of the minimum inhibitory concentration (MIC) in combination with colistin. The checkerboard assay was done to demonstrate synergism, which was further corroborated by the Time-kill assay. Ten common pharmacophore hypotheses were successfully generated using substrate/inhibitors. Following enrichment analysis, AHHNR.100 was identified as the top-ranked hypothesis, and 207 unique compounds were found to conform to this hypothesis. The multi-step docking of these compounds against the AcrB protein revealed argatroban as the top non-antibiotic hit. This significantly inhibited the efflux activity of colistin-resistant clinical isolates K. pneumoniae (n = 1) and M. morganii (n = 2). Further, their combination with colistin enhanced the susceptibility of these isolates, and the effect was found to be synergistic. Accordingly, the time-kill assay of this combination showed 8-log and 2-log reductions against K. pneumoniae and M. morganii, respectively. In conclusion, this study found argatroban as a bacterial efflux inhibitor that can be potentially used to overcome efflux-mediated resistance.
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Affiliation(s)
- Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 7978085389
- Department of Biotechnology & Food Technology, Punjabi University Patiala 147002 India
| | - Maheswata Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 7978085389
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Trinh TKH, Cabezas AJ, Joshi S, Catalano C, Siddique AB, Qiu W, Deshmukh S, des Georges A, Guo Y. pH-tunable membrane-active polymers, NCMNP2a- x, and their potential membrane protein applications. Chem Sci 2023; 14:7310-7326. [PMID: 37416719 PMCID: PMC10321531 DOI: 10.1039/d3sc01890c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Accurate 3D structures of membrane proteins are essential for comprehending their mechanisms of action and designing specific ligands to modulate their activities. However, these structures are still uncommon due to the involvement of detergents in the sample preparation. Recently, membrane-active polymers have emerged as an alternative to detergents, but their incompatibility with low pH and divalent cations has hindered their efficacy. Herein, we describe the design, synthesis, characterization, and application of a new class of pH-tunable membrane-active polymers, NCMNP2a-x. The results demonstrated that NCMNP2a-x could be used for high-resolution single-particle cryo-EM structural analysis of AcrB in various pH conditions and can effectively solubilize BcTSPO with the function preserved. Molecular dynamic simulation is consistent with experimental data that shed great insights into the working mechanism of this class of polymers. These results demonstrated that NCMNP2a-x might have broad applications in membrane protein research.
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Affiliation(s)
- Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Andres Jorge Cabezas
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
| | - Soumil Joshi
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Claudio Catalano
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Abu Bakkar Siddique
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Sanket Deshmukh
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
- Department of Chemistry & Biochemistry, City College of New York New York New York 10017 USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
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Radi MS, Munro LJ, Salcedo-Sora JE, Kim SH, Feist AM, Kell DB. Understanding Functional Redundancy and Promiscuity of Multidrug Transporters in E. coli under Lipophilic Cation Stress. MEMBRANES 2022; 12:1264. [PMID: 36557171 PMCID: PMC9783932 DOI: 10.3390/membranes12121264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Multidrug transporters (MDTs) are major contributors to microbial drug resistance and are further utilized for improving host phenotypes in biotechnological applications. Therefore, the identification of these MDTs and the understanding of their mechanisms of action in vivo are of great importance. However, their promiscuity and functional redundancy represent a major challenge towards their identification. Here, a multistep tolerance adaptive laboratory evolution (TALE) approach was leveraged to achieve this goal. Specifically, a wild-type E. coli K-12-MG1655 and its cognate knockout individual mutants ΔemrE, ΔtolC, and ΔacrB were evolved separately under increasing concentrations of two lipophilic cations, tetraphenylphosphonium (TPP+), and methyltriphenylphosphonium (MTPP+). The evolved strains showed a significant increase in MIC values of both cations and an apparent cross-cation resistance. Sequencing of all evolved mutants highlighted diverse mutational mechanisms that affect the activity of nine MDTs including acrB, mdtK, mdfA, acrE, emrD, tolC, acrA, mdtL, and mdtP. Besides regulatory mutations, several structural mutations were recognized in the proximal binding domain of acrB and the permeation pathways of both mdtK and mdfA. These details can aid in the rational design of MDT inhibitors to efficiently combat efflux-based drug resistance. Additionally, the TALE approach can be scaled to different microbes and molecules of medical and biotechnological relevance.
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Affiliation(s)
- Mohammad S. Radi
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Lachlan J. Munro
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jesus E. Salcedo-Sora
- GeneMill, Shared Research Facilities, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
| | - Se Hyeuk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Adam M. Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
- Department of Bioengineering, University of California, 9500 Gilman Drive, La Jolla, San Diego, CA 92093, USA
| | - Douglas B. Kell
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
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Stolarek P, Bernat P, Różalski A. Combined Application of Aminoglycosides and Ascorbic Acid in the Elimination of Proteus mirabilis Rods Responsible for Causing Catheter-Associated Urinary Tract Infections (CAUTIs)-A Molecular Approach. Int J Mol Sci 2022; 23:13069. [PMID: 36361855 PMCID: PMC9659235 DOI: 10.3390/ijms232113069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/26/2023] Open
Abstract
Proteus mirabilis is a common cause of catheter-associated urinary tract infections (CAUTIs). In this study, we verified the effectiveness of amikacin or gentamicin and ascorbic acid (AA) co-therapy in eliminating uropathogenic cells, as well as searched for the molecular basis of AA activity by applying chromatographic and fluorescent techniques. Under simulated physiological conditions, a combined activity of the antibiotic and AA supported the growth (threefold) of the P. mirabilis C12 strain, but reduced catheter colonization (≤30%) in comparison to the drug monotherapy. Slight modifications in the phospholipid and fatty acid profiles, as well as limited (≤62%) 2',7'-dichlorofluorescein fluorescence, corresponding to the hydroxyl radical level, allowed for the exclusion of the hypothesis that the anti-biofilm effect of AA was related to membrane perturbations of the C12 strain. However, the reduced (≤20%) fluorescence intensity of propidium iodide, as a result of a decrease in membrane permeability, may be evidence of P. mirabilis cell defense against AA activity. Quantitative analyses of ascorbic acid over time with a simultaneous measurement of the pH values proved that AA can be an effective urine acidifier, provided that it is devoid of the presence of urease-positive cells. Therefore, it could be useful in a prevention of recurrent CAUTIs, rather than in their treatment.
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Affiliation(s)
- Paulina Stolarek
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Antoni Różalski
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
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In Vitro Activity of Robenidine Analogues NCL259 and NCL265 against Gram-Negative Pathogens. Antibiotics (Basel) 2022; 11:antibiotics11101301. [PMID: 36289959 PMCID: PMC9598656 DOI: 10.3390/antibiotics11101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Multidrug-resistant (MDR) Gram-negative pathogens, especially Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli and Enterobacter spp., are recognized by the World Health Organization as the most critical priority pathogens in urgent need of drug development. In this study, the in vitro antimicrobial activity of robenidine analogues NCL259 and NCL265 was tested against key human and animal Gram-negative clinical isolates and reference strains. NCL259 and NCL265 demonstrated moderate antimicrobial activity against these Gram-negative priority pathogens with NCL265 consistently more active, achieving lower minimum inhibitory concentrations (MICs) in the range of 2−16 µg/mL. When used in combination with sub-inhibitory concentrations of polymyxin B to permeabilize the outer membrane, NCL259 and NCL265 elicited a synergistic or additive activity against the reference strains tested, reducing the MIC of NCL259 by 8- to 256- fold and the MIC of NCL265 by 4- to 256- fold. A small minority of Klebsiella spp. isolates (three) were resistant to both NCL259 and NCL265 with MICs > 256 µg/mL. This resistance was completely reversed in the presence of the efflux pump inhibitor phenylalanine-arginine-beta-naphthylamide (PAβN) to yield MIC values of 8−16 µg/mL and 2−4 µg/mL for NCL259 and NCL256, respectively. When NCL259 and NCL265 were tested against wild-type E. coli isolate BW 25113 and its isogenic multidrug efflux pump subunit AcrB deletion mutant (∆AcrB), the MIC of both compounds against the mutant ∆AcrB isolate was reduced 16-fold compared to the wild-type parent, indicating a significant role for the AcrAB-TolC efflux pump from Enterobacterales in imparting resistance to these robenidine analogues. In vitro cytotoxicity testing revealed that NCL259 and NCL265 had much higher levels of toxicity to a range of human cell lines compared to the parent robenidine, thus precluding their further development as novel antibiotics against Gram-negative pathogens.
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Lai CKC, Ng RWY, Leung SSY, Hui M, Ip M. Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches - An overview. Adv Drug Deliv Rev 2022; 181:114078. [PMID: 34896131 DOI: 10.1016/j.addr.2021.114078] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 12/14/2022]
Abstract
Antimicrobial resistance is a normal evolutionary process for microorganisms. Antibiotics exerted accelerated selective pressure that hasten bacterial resistance through mutation, and acquisition external genes. These genes often carry multiple antibiotic resistant determinants allowing the recipient microbe an instant "super-bug" status. The extent of Antimicrobial Resistance (AMR) has reached a level of global crisis, existing antimicrobials are no long effective in treating infections caused by AMR pathogens. The great majority of clinically available antimicrobial agents are administered through oral and intra-venous routes. Overcoming antibacterial resistance by novel drug delivery approach offered new hopes, particularly in the treatment of AMR pathogens in sites less assessible through systemic circulation such as the lung and skin. In the current review, we will revisit the mechanism and incidence of important AMR pathogens. Finally, we will discuss novel drug delivery approaches including novel local antibiotic delivery systems, hybrid antibiotics, and nanoparticle-based antibiotic delivery systems.
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Affiliation(s)
- Christopher K C Lai
- Department of Microbiology, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong Special Administrative Region.
| | - Rita W Y Ng
- Department of Microbiology, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong Special Administrative Region.
| | - Sharon S Y Leung
- School of Pharmacy, The Chinese University of Hong Kong, New Territories, Hong Kong Special Administrative Region.
| | - Mamie Hui
- Department of Microbiology, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong Special Administrative Region.
| | - Margaret Ip
- Department of Microbiology, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong Special Administrative Region.
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Nazarov PA, Kuznetsova AM, Karakozova MV. Multidrug Resistance Pumps as a Keystone of Bacterial Resistance. MOSCOW UNIVERSITY BIOLOGICAL SCIENCES BULLETIN 2022; 77:193-200. [PMID: 36843647 PMCID: PMC9940100 DOI: 10.3103/s009639252204006x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/05/2022] [Accepted: 10/26/2022] [Indexed: 02/22/2023]
Abstract
Antibiotic resistance is a global problem of modern medicine. A harbinger of the onset of the postantibiotic era is the complexity and high cost of developing new antibiotics as well as their inefficiency due to the rapidly developing resistance of bacteria. Multidrug resistance (MDR) pumps, involved in the formation of resistance to xenobiotics, the export of toxins, the maintenance of cellular homeostasis, and the formation of biofilms and persistent cells, are the keystone of bacterial protection against antibiotics. MDR pumps are the basis for the nonspecific protection of bacteria, while modification of the drug target, inactivation of the drug, and switching of the target or sequestration of the target is the second specific line of their protection. Thus, the nonspecific protection of bacteria formed by MDR pumps is a barrier that prevents the penetration of antibacterial substances into the cell, which is the main factor determining the resistance of bacteria. Understanding the mechanisms of MDR pumps and a balanced assessment of their contribution to total resistance, as well as to antibiotic sensitivity, will either seriously delay the onset of the postantibiotic era or prevent its onset in the foreseeable future.
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Affiliation(s)
- P. A. Nazarov
- grid.14476.300000 0001 2342 9668Belozersky Institute of Physicochemical Biology, Moscow State University, 119234 Moscow, Russia
| | - A. M. Kuznetsova
- grid.14476.300000 0001 2342 9668Department of Biology, Moscow State University, 119234 Moscow, Russia
| | - M. V. Karakozova
- grid.454320.40000 0004 0555 3608Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
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Bharatham N, Bhowmik P, Aoki M, Okada U, Sharma S, Yamashita E, Shanbhag AP, Rajagopal S, Thomas T, Sarma M, Narjari R, Nagaraj S, Ramachandran V, Katagihallimath N, Datta S, Murakami S. Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae. Nat Commun 2021; 12:5400. [PMID: 34518546 PMCID: PMC8437966 DOI: 10.1038/s41467-021-25679-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.
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Affiliation(s)
- Nagakumar Bharatham
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Purnendu Bhowmik
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Maho Aoki
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ui Okada
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Sreevalli Sharma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Eiki Yamashita
- grid.136593.b0000 0004 0373 3971Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Anirudh P. Shanbhag
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Sreenath Rajagopal
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Teby Thomas
- grid.418280.70000 0004 1794 3160St. John’s Research Institute, Bengaluru, Karnataka India
| | - Maitrayee Sarma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Riya Narjari
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | | | - Vasanthi Ramachandran
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Nainesh Katagihallimath
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Santanu Datta
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Satoshi Murakami
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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10
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Jahn LJ, Simon D, Jensen M, Bradshaw C, Ellabaan MMH, Sommer MOA. Compatibility of Evolutionary Responses to Constituent Antibiotics Drive Resistance Evolution to Drug Pairs. Mol Biol Evol 2021; 38:2057-2069. [PMID: 33480997 PMCID: PMC8097295 DOI: 10.1093/molbev/msab006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Antibiotic combinations are considered a relevant strategy to tackle the global antibiotic resistance crisis since they are believed to increase treatment efficacy and reduce resistance evolution (WHO treatment guidelines for drug-resistant tuberculosis: 2016 update.). However, studies of the evolution of bacterial resistance to combination therapy have focused on a limited number of drugs and have provided contradictory results (Lipsitch, Levin BR. 1997; Hegreness et al. 2008; Munck et al. 2014). To address this gap in our understanding, we performed a large-scale laboratory evolution experiment, adapting eight replicate lineages of Escherichia coli to a diverse set of 22 different antibiotics and 33 antibiotic pairs. We found that combination therapy significantly limits the evolution of de novode novo resistance in E. coli, yet different drug combinations vary substantially in their propensity to select for resistance. In contrast to current theories, the phenotypic features of drug pairs are weak predictors of resistance evolution. Instead, the resistance evolution is driven by the relationship between the evolutionary trajectories that lead to resistance to a drug combination and those that lead to resistance to the component drugs. Drug combinations requiring a novel genetic response from target bacteria compared with the individual component drugs significantly reduce resistance evolution. These data support combination therapy as a treatment option to decelerate resistance evolution and provide a novel framework for selecting optimized drug combinations based on bacterial evolutionary responses.
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Affiliation(s)
- Leonie Johanna Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Daniel Simon
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mia Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Charles Bradshaw
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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11
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Duang-Nkern J, Nontaleerak B, Udomkanarat T, Saninjuk K, Sukchawalit R, Mongkolsuk S. NieR is the repressor of a NaOCl-inducible efflux system in Agrobacterium tumefaciens C58. Microbiol Res 2021; 251:126816. [PMID: 34273784 DOI: 10.1016/j.micres.2021.126816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 05/15/2021] [Accepted: 07/08/2021] [Indexed: 11/24/2022]
Abstract
The Agrobacterium tumefaciens atu4217 gene, which encodes a TetR family transcription regulator, is a repressor of the atu4218-atu4219-atu4220 operon. The Atu4218 and Atu4219 proteins belong to the HlyD family (membrane fusion protein) and the AcrB/AcrD/AcrF family (inner membrane transporter), respectively, and may form an efflux pump. The atu4220 gene encodes a short-chain dehydrogenase. Quantitative real-time PCR analysis showed induction of atu4217 and atu4218 by NaOCl but not by N-ethylmaleimide or reactive oxygen species (ROS) including H2O2, menadione and cumene hydroperoxide; therefore, the atu4218 and atu4219 were named NaOCl-inducible efflux genes nieA and nieB, respectively. The atu4217 gene, which was named nieR, serves as a repressor of nieA and nieB. DNase I footprinting assays identified 20-bp imperfect inverted repeat (IR, underlined) motifs 5'-TAGATTTAGGATGCAATCTA-3' (box A) and 5'-TAGATTTCACTTGACATCTA-3' (box R) in the intergenic region of the divergent nieA and nieR genes; these motifs were recognized by the NieR protein. Electrophoretic mobility shift assays demonstrated that NieR specifically binds to the 20-bp IR motifs and that NaOCl prevents this NieR-DNA interaction. Promoter-lacZ fusions and mutagenesis of the NieR boxes (A and R) showed a more dominant role for box A than for box R in the repression of the nieA and nieR promoters. However, full repression of either promoter required both operators. The nieR mutant strain exhibited a small colony phenotype and was more sensitive than the wild-type to NaOCl and antibiotics, including ciprofloxacin, nalidixic acid, novobiocin, and tetracycline. By contrast, the nieAB mutant strain showed no phenotype changes under the tested conditions.
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Affiliation(s)
- Jintana Duang-Nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Benya Nontaleerak
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Tham Udomkanarat
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Kritsakorn Saninjuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Rojana Sukchawalit
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
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12
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Klenotic PA, Moseng MA, Morgan CE, Yu EW. Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters. Chem Rev 2021; 121:5378-5416. [PMID: 33211490 PMCID: PMC8119314 DOI: 10.1021/acs.chemrev.0c00621] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multidrug resistant (MDR) bacteria are a global threat with many common infections becoming increasingly difficult to eliminate. While significant effort has gone into the development of potent biocides, the effectiveness of many first-line antibiotics has been diminished due to adaptive resistance mechanisms. Bacterial membrane proteins belonging to the resistance-nodulation-cell division (RND) superfamily play significant roles in mediating bacterial resistance to antimicrobials. They participate in multidrug efflux and cell wall biogenesis to transform bacterial pathogens into "superbugs" that are resistant even to last resort antibiotics. In this review, we summarize the RND superfamily of efflux transporters with a primary focus on the assembly and function of the inner membrane pumps. These pumps are critical for extrusion of antibiotics from the cell as well as the transport of lipid moieties to the outer membrane to establish membrane rigidity and stability. We analyze recently solved structures of bacterial inner membrane efflux pumps as to how they bind and transport their substrates. Our cumulative data indicate that these RND membrane proteins are able to utilize different oligomerization states to achieve particular activities, including forming MDR pumps and cell wall remodeling machineries, to ensure bacterial survival. This mechanistic insight, combined with simulated docking techniques, allows for the design and optimization of new efflux pump inhibitors to more effectively treat infections that today are difficult or impossible to cure.
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Affiliation(s)
- Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
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13
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Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases. J Mol Biol 2021; 433:167005. [PMID: 33891902 DOI: 10.1016/j.jmb.2021.167005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023]
Abstract
Infectious diseases present a major threat to public health globally. Pathogens can acquire resistance to anti-infectious agents via several means including transporter-mediated efflux. Typically, multidrug transporters feature spacious, dynamic, and chemically malleable binding sites to aid in the recognition and transport of chemically diverse substrates across cell membranes. Here, we discuss recent structural investigations of multidrug transporters involved in resistance to infectious diseases that belong to the ATP-binding cassette (ABC) superfamily, the major facilitator superfamily (MFS), the drug/metabolite transporter (DMT) superfamily, the multidrug and toxic compound extrusion (MATE) family, the small multidrug resistance (SMR) family, and the resistance-nodulation-division (RND) superfamily. These structural insights provide invaluable information for understanding and combatting multidrug resistance.
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14
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Structure-property correlation in gallic acid and 4-cyanopyridine cocrystal and binding studies with drug efflux pump in bacteria. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Farzand R, Rajakumar K, Barer MR, Freestone PPE, Mukamolova GV, Oggioni MR, O'Hare HM. A Virulence Associated Siderophore Importer Reduces Antimicrobial Susceptibility of Klebsiella pneumoniae. Front Microbiol 2021; 12:607512. [PMID: 33584611 PMCID: PMC7876324 DOI: 10.3389/fmicb.2021.607512] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/06/2021] [Indexed: 12/18/2022] Open
Abstract
The accessory genomes of many pathogenic bacteria include ABC transporters that scavenge metal by siderophore uptake and ABC transporters that contribute to antimicrobial resistance by multidrug efflux. There are mechanistic and recently recognized structural similarities between siderophore importer proteins and efflux pumps. Here we investigated the influence of siderophore importer YbtPQ on antimicrobial resistance of Klebsiella pneumoniae. YbtPQ is encoded in the yersiniabactin cluster in a prevalent mobile genetic element ICEKp, and is also common in pathogenicity islands of Escherichia coli and Yersinia species, where yersiniabactin enhances virulence. Deletion of ICEKp increased the susceptibility of K. pneumoniae to all antimicrobials tested. The mechanism was dependent on the yersiniabactin importer YbtPQ and may involve antimicrobial efflux, since it was affected by the inhibitor reserpine. The element ICEKp is naturally highly mobile, indeed the accessory genome of K. pneumoniae is recognized as a reservoir of genes for the emergence of hospital outbreak strains and for transfer to other Gram-negative pathogens. Introduction of ICEKp, or a plasmid encoding YbtPQ, to E. coli decreased its susceptibility to a broad range of antimicrobials. Thus a confirmed siderophore importer, on a rapidly evolving and highly mobile element capable of interspecies transfer, may have a secondary function exporting antimicrobials.
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Affiliation(s)
- Robeena Farzand
- Leicester Microbial Sciences and Infectious Diseases Network, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.,Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Kumar Rajakumar
- Leicester Microbial Sciences and Infectious Diseases Network, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Michael R Barer
- Leicester Microbial Sciences and Infectious Diseases Network, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Primrose P E Freestone
- Leicester Microbial Sciences and Infectious Diseases Network, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Galina V Mukamolova
- Leicester Microbial Sciences and Infectious Diseases Network, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Marco R Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Helen M O'Hare
- Leicester Microbial Sciences and Infectious Diseases Network, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.,Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
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16
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Williams AN, Sorout N, Cameron AJ, Stavrinides J. The Integration of Genome Mining, Comparative Genomics, and Functional Genetics for Biosynthetic Gene Cluster Identification. Front Genet 2020; 11:600116. [PMID: 33343637 PMCID: PMC7744662 DOI: 10.3389/fgene.2020.600116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022] Open
Abstract
Antimicrobial resistance is a worldwide health crisis for which new antibiotics are needed. One strategy for antibiotic discovery is identifying unique antibiotic biosynthetic gene clusters that may produce novel compounds. The aim of this study was to demonstrate how an integrated approach that combines genome mining, comparative genomics, and functional genetics can be used to successfully identify novel biosynthetic gene clusters that produce antimicrobial natural products. Secondary metabolite clusters of an antibiotic producer are first predicted using genome mining tools, generating a list of candidates. Comparative genomic approaches are then used to identify gene suites present in the antibiotic producer that are absent in closely related non-producers. Gene sets that are common to the two lists represent leading candidates, which can then be confirmed using functional genetics approaches. To validate this strategy, we identified the genes responsible for antibiotic production in Pantoea agglomerans B025670, a strain identified in a large-scale bioactivity survey. The genome of B025670 was first mined with antiSMASH, which identified 24 candidate regions. We then used the comparative genomics platform, EDGAR, to identify genes unique to B025670 that were not present in closely related strains with contrasting antibiotic production profiles. The candidate lists generated by antiSMASH and EDGAR were compared with standalone BLAST. Among the common regions was a 14 kb cluster consisting of 14 genes with predicted enzymatic, transport, and unknown functions. Site-directed mutagenesis of the gene cluster resulted in a reduction in antimicrobial activity, suggesting involvement in antibiotic production. An integrated approach that combines genome mining, comparative genomics, and functional genetics yields a powerful, yet simple strategy for identifying potentially novel antibiotics.
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17
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Zaide G, Elia U, Cohen-Gihon I, Israeli M, Rotem S, Israeli O, Ehrlich S, Cohen H, Lazar S, Beth-Din A, Shafferman A, Zvi A, Cohen O, Chitlaru T. Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. Microorganisms 2020; 8:microorganisms8121896. [PMID: 33265965 PMCID: PMC7760947 DOI: 10.3390/microorganisms8121896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracishtrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H2O2-sensitive phenotype.
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18
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Ching C, Zaman MH. Development and selection of low-level multi-drug resistance over an extended range of sub-inhibitory ciprofloxacin concentrations in Escherichia coli. Sci Rep 2020; 10:8754. [PMID: 32471975 PMCID: PMC7260183 DOI: 10.1038/s41598-020-65602-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/30/2020] [Indexed: 01/13/2023] Open
Abstract
To better combat bacterial antibiotic resistance, a growing global health threat, it is imperative to understand its drivers and underlying biological mechanisms. One potential driver of antibiotic resistance is exposure to sub-inhibitory concentrations of antibiotics. This occurs in both the environment and clinic, from agricultural contamination to incorrect dosing and usage of poor-quality medicines. To better understand this driver, we tested the effect of a broad range of ciprofloxacin concentrations on antibiotic resistance development in Escherichia coli. We observed the emergence of stable, low-level multi-drug resistance that was both time and concentration dependent. Furthermore, we identified a spectrum of single mutations in strains with resistant phenotypes, both previously described and novel. Low-level class-wide resistance, which often goes undetected in the clinic, may allow for bacterial survival and establishment of a reservoir for outbreaks of high-level antibiotic resistant infections.
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Affiliation(s)
- Carly Ching
- Boston University, Department of Biomedical Engineering, Boston, MA, USA
| | - Muhammad H Zaman
- Boston University, Department of Biomedical Engineering, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston University, Boston, MA, USA.
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19
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Kapach G, Nuri R, Schmidt C, Danin A, Ferrera S, Savidor A, Gerlach RG, Shai Y. Loss of the Periplasmic Chaperone Skp and Mutations in the Efflux Pump AcrAB-TolC Play a Role in Acquired Resistance to Antimicrobial Peptides in Salmonella typhimurium. Front Microbiol 2020; 11:189. [PMID: 32210923 PMCID: PMC7075815 DOI: 10.3389/fmicb.2020.00189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/27/2020] [Indexed: 01/01/2023] Open
Abstract
Bacterial resistance to antibiotics is a major concern worldwide, leading to an extensive search for alternative drugs. Promising candidates are antimicrobial peptides (AMPs), innate immunity molecules, shown to be highly efficient against multidrug resistant bacteria. Therefore, it is essential to study bacterial resistance mechanisms against them. For that purpose, we used experimental evolution, and isolated a Salmonella enterica serovar typhimurium-resistant line to the AMP 4DK5L7. This AMP displayed promising features including widespread activity against Gram-negative bacteria and protection from proteolytic degradation. However, the resistance that evolved in the isolated strain was particularly high. Whole genome sequencing revealed that five spontaneous mutations had evolved. Of these, three are novel in the context of acquired AMP resistance. Two mutations are related to the AcrAB-TolC multidrug efflux pump. One occurred in AcrB, the substrate-binding domain of the system, and the second in RamR, a transcriptional regulator of the system. Together, the mutations increased the minimal inhibitory concentration (MIC) by twofold toward this AMP. Moreover, the mutation in AcrB induced hypersusceptibility toward ampicillin and colistin. The last mutation occurred in Skp, a periplasmic chaperone that participates in the biogenesis of outer membrane proteins (OMPs). This mutation increased the MIC by twofold to 4DK5L7 and by fourfold to another AMP, seg5D. Proteomic analysis revealed that the mutation abolished Skp expression, reduced OMP abundance, and increased DegP levels. DegP, a protease that was reported to have an additional chaperone activity, escorts OMPs through the periplasm along with Skp, but is also associated with AMP resistance. In conclusion, our data demonstrate that both loss of Skp and manipulation of the AcrAB-TolC system are alternative strategies of AMP acquired resistance in Salmonella typhimurium and might represent a common mechanism in other Gram-negative bacteria.
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Affiliation(s)
- Gal Kapach
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Reut Nuri
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adi Danin
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Ferrera
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Roman G Gerlach
- Project Group 5, Robert Koch Institute, Wernigerode, Germany
| | - Yechiel Shai
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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20
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Xia J, Sun H, Zhang XX, Zhang T, Ren H, Ye L. Aromatic compounds lead to increased abundance of antibiotic resistance genes in wastewater treatment bioreactors. WATER RESEARCH 2019; 166:115073. [PMID: 31542545 DOI: 10.1016/j.watres.2019.115073] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/29/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Various aromatic compounds in wastewater, especially industrial wastewater, are treated by biological processes in bioreactors which are regarded as hotspots and reservoirs of antibiotic resistance genes (ARGs). Yet, little is known about the relationship between the aromatic compound degradation process and antibiotic resistance. Here, we report on the co-occurrence of ARGs and aromatic degradation genes (ADGs) in bacteria in bioreactors. We confirmed this by bioreactor experiments and bioinformatics analysis of over 10,000 publicly available bacterial genomes. We observed a significant enrichment of ARGs in bioreactors treating wastewater that contained p-aminophenol and p-nitrophenol. The potential hosts harboring ARGs and ADGs were mainly Pseudomonas, Leucobacter, Xanthobacter, Acinetobacter, and Burkholderiaceae. Genome analysis revealed that 67.6% of the publicly available bacterial genomes harboring ADGs also harbor ARGs. Over 80% of Burkholderiales, Xanthomonales, Enterobacteriaceae, Acinetobacter, Pseudomonas, and Nocardiaceae genomes harbor both ARGs and ADGs, which strongly suggests the co-occurrence of these genes. Furthermore, bacteria carrying ADGs harbored more than twice the number of ARGs than bacteria only carrying ARGs. Network analysis suggested that multidrug, beta-lactam, aminoglycoside, macrolide-lincosamide-streptogramin, and polymyxin resistance genes are the major ARGs associated with ADGs. Taken together, the presented findings improve the understanding of ARG prevalence in biological wastewater treatment plants, and highlight the potential risk of the effect of regular aromatic compounds on the selection and spread of ARGs.
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Affiliation(s)
- Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China; School of Public Health, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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21
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Kobylka J, Kuth MS, Müller RT, Geertsma ER, Pos KM. AcrB: a mean, keen, drug efflux machine. Ann N Y Acad Sci 2019; 1459:38-68. [PMID: 31588569 DOI: 10.1111/nyas.14239] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria are intrinsically resistant against cytotoxic substances by means of their outer membrane and a network of multidrug efflux systems, acting in synergy. Efflux pumps from various superfamilies with broad substrate preferences sequester and pump drugs across the inner membrane to supply the highly polyspecific and powerful tripartite resistance-nodulation-cell division (RND) efflux pumps with compounds to be extruded across the outer membrane barrier. In Escherichia coli, the tripartite efflux system AcrAB-TolC is the archetype RND multiple drug efflux pump complex. The homotrimeric inner membrane component acriflavine resistance B (AcrB) is the drug specificity and energy transduction center for the drug/proton antiport process. Drugs are bound and expelled via a cycle of mainly three consecutive states in every protomer, constituting a flexible alternating access channel system. This review recapitulates the molecular basis of drug and inhibitor binding, including mechanistic insights into drug efflux by AcrB. It also summarizes 17 years of mutational analysis of the gene acrB, reporting the effect of every substitution on the ability of E. coli to confer resistance toward antibiotics (http://goethe.link/AcrBsubstitutions). We emphasize the functional robustness of AcrB toward single-site substitutions and highlight regions that are more sensitive to perturbation.
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Affiliation(s)
- Jessica Kobylka
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Miriam S Kuth
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Reinke T Müller
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
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22
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Pelling H, Bock LJ, Nzakizwanayo J, Wand ME, Denham EL, MacFarlane WM, Sutton JM, Jones BV. De-repression of the smvA efflux system arises in clinical isolates of Proteus mirabilis and reduces susceptibility to chlorhexidine and other biocides. Antimicrob Agents Chemother 2019; 63:AAC.01535-19. [PMID: 31570392 PMCID: PMC6879213 DOI: 10.1128/aac.01535-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/18/2019] [Indexed: 01/14/2023] Open
Abstract
Proteus mirabilis is a common pathogen of the catheterised urinary tract and often described as intrinsically resistant to the biocide chlorhexidine (CHD). Here we demonstrate that de-repression of the smvA efflux system has occurred in clinical isolates of P. mirabilis and reduces susceptibility to CHD and other cationic biocides. Compared to other isolates examined, P. mirabilis RS47 exhibited a significantly higher CHD MIC (≥512 μg/ml) and significantly greater expression of smvA. Comparison of the RS47 smvA and cognate smvR repressor with sequences from other isolates, indicated that RS47 encodes an inactivated smvR. Complementation of RS47 with a functional smvR from isolate RS50a (which exhibited the lowest smvA expression and lowest CHD MIC) reduced smvA expression by ∼59-fold, and markedly lowered the MIC of CHD and other cationic biocides. Although complementation of RS47 did not reduce MICs to concentrations observed in isolate RS50a, the significantly lower polymyxin B MIC of RS50a indicated that differences in LPS structure are also a factor in P. mirabilis CHD susceptibility. To determine if exposure to CHD can select for mutations in smvR, clinical isolates with the lowest CHD MICs were adapted to grow at increasing concentrations of CHD up to 512 μg/ml. Analysis of the smvR in adapted populations indicated that mutations predicted to inactivate smvR occurred following CHD exposure in some isolates. Collectively, our data show that smvA de-repression contributes to reduced biocide susceptibility in P. mirabilis, but differences in LPS structure between strains are also likely to be an important factor.
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Affiliation(s)
- H Pelling
- Dept. of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK
| | - L J Bock
- National Infections Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - J Nzakizwanayo
- Dept. of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - M E Wand
- National Infections Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - E L Denham
- Dept. of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - W M MacFarlane
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK
| | - J M Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - B V Jones
- Dept. of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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23
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Jagessar KL, Mchaourab HS, Claxton DP. The N-terminal domain of an archaeal multidrug and toxin extrusion (MATE) transporter mediates proton coupling required for prokaryotic drug resistance. J Biol Chem 2019; 294:12807-12814. [PMID: 31289123 DOI: 10.1074/jbc.ra119.009195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/05/2019] [Indexed: 12/15/2022] Open
Abstract
As a contributor to multidrug resistance, the family of multidrug and toxin extrusion (MATE) transporters couples the efflux of chemically dissimilar compounds to electrochemical ion gradients. Although divergent transport mechanisms have been proposed for these transporters, previous structural and functional analyses of members of the MATE subfamily DinF suggest that the N-terminal domain (NTD) supports substrate and ion binding. In this report, we investigated the relationship of ligand binding within the NTD to the drug resistance mechanism of the H+-dependent MATE from the hyperthermophilic archaeon Pyrococcus furiosus (PfMATE). To facilitate this study, we developed a cell growth assay in Escherichia coli to characterize the resistance conferred by PfMATE to toxic concentrations of the antimicrobial compound rhodamine 6G. Expression of WT PfMATE promoted cell growth in the presence of drug, but amino acid substitutions of conserved NTD residues compromised drug resistance. Steady-state binding analysis with purified PfMATE indicated that substrate affinity was unperturbed in these NTD variants. However, exploiting Trp fluorescence as an intrinsic reporter of conformational changes, we found that these variants impaired formation of a unique H+-stabilized structural intermediate. These results imply that disruption of H+ coupling is the origin of compromised toxin resistance in PfMATE variants. These findings support a model mechanism wherein the NTD mediates allosteric coupling to ion gradients through conformational changes to drive substrate transport in PfMATE. Furthermore, the results provide evidence for diverging transport mechanisms within a prokaryotic MATE subfamily.
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Affiliation(s)
- Kevin L Jagessar
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232
| | - Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232
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24
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Orellana-Saez M, Pacheco N, Costa JI, Mendez KN, Miossec MJ, Meneses C, Castro-Nallar E, Marcoleta AE, Poblete-Castro I. In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. Front Microbiol 2019; 10:1154. [PMID: 31178851 PMCID: PMC6543543 DOI: 10.3389/fmicb.2019.01154] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp. MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments.
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Affiliation(s)
- Matias Orellana-Saez
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicolas Pacheco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - José I Costa
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Katterinne N Mendez
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Computational Genomics Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Andrés E Marcoleta
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
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25
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Iyer R, Ye Z, Ferrari A, Duncan L, Tanudra MA, Tsao H, Wang T, Gao H, Brummel CL, Erwin AL. Evaluating LC-MS/MS To Measure Accumulation of Compounds within Bacteria. ACS Infect Dis 2018; 4:1336-1345. [PMID: 29961312 DOI: 10.1021/acsinfecdis.8b00083] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A general method for determining bacterial uptake of compounds independent of antibacterial activity would be a valuable tool in antibacterial drug discovery. LC-MS/MS assays have been described, but it has not been shown whether the data can be used directly to inform medicinal chemistry. We describe the evaluation of an LC-MS/MS assay measuring association of compounds with bacteria, using a set of over a hundred compounds (inhibitors of NAD-dependent DNA ligase, LigA) for which in vitro potency and antibacterial activity had been determined. All compounds were active against an efflux-deficient strain of Escherichia coli with reduced LigA activity ( E. coli ligA251 Δ tolC). Testing a single compound concentration and incubation time, we found that, for equipotent compounds, LC-MS/MS values were not predictive of antibacterial activity. This indicates that measured bacteria-associated compound was not necessarily exposed to the target enzyme. Our data suggest that, while exclusion from bacteria is a major reason for poor antibacterial activity of potent compounds, the distribution of compound within the bacterial cell may also be a problem. The relative importance of these factors is likely to vary from one chemical series to another. Our observations provide directions for further study of this difficult issue.
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Affiliation(s)
- Ramkumar Iyer
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Zhengqi Ye
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Annette Ferrari
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Leonard Duncan
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - M. Angela Tanudra
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Hong Tsao
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Tiansheng Wang
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Hong Gao
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Christopher L. Brummel
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Alice L. Erwin
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
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26
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Nuonming P, Khemthong S, Dokpikul T, Sukchawalit R, Mongkolsuk S. Characterization and regulation of AcrABR, a RND-type multidrug efflux system, in Agrobacterium tumefaciens C58. Microbiol Res 2018; 214:146-155. [PMID: 30031477 DOI: 10.1016/j.micres.2018.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/11/2018] [Accepted: 06/30/2018] [Indexed: 10/28/2022]
Abstract
Agrobacterium tumefaciens AcrR is the transcriptional repressor of the acrABR operon. The AcrAB efflux pump confers resistance to various toxic compounds, including antibiotics [ciprofloxacin (CIP), nalidixic acid (NAL), novobiocin (NOV) and tetracycline (TET)], a detergent [sodium dodecyl sulfate (SDS)] and a biocide [triclosan (TRI)]. The sequence to which AcrR specifically binds in the acrA promoter region was determined by EMSA and DNase I footprinting. The AcrR-DNA interaction was abolished by adding NAL, SDS and TRI. Quantitative real time-PCR analysis showed that induction of the acrA transcript occurred when wild-type cells were exposed to NAL, SDS and TRI. Indole is a signaling molecule that increases the antibiotic resistance of bacteria, at least in part, through activation of efflux pumps. Expression of the A. tumefaciens acrA transcript was also inducible by indole in a dose-dependent manner. Indole induced protection against CIP, NAL and SDS but enhanced susceptibility to NOV and TRI. Additionally, the TET resistance of A. tumefaciens was not apparently modulated by indole. A. tumefaciens AcrAB played a dominant role and was required for tolerance to high levels of the toxic compounds. Understanding the regulation of multidrug efflux pumps and bacterial adaptive responses to intracellular and extracellular signaling molecules for antibiotic resistance is essential. This information will be useful for the rational design of effective treatments for bacterial infection to overcome possible multidrug-resistant pathogens.
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Affiliation(s)
- Puttamas Nuonming
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Sasimaporn Khemthong
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Thanittra Dokpikul
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Rojana Sukchawalit
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand; Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand; Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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27
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Ramaswamy VK, Vargiu AV, Malloci G, Dreier J, Ruggerone P. Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa. Front Microbiol 2018; 9:1144. [PMID: 29910784 PMCID: PMC5992780 DOI: 10.3389/fmicb.2018.01144] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/14/2018] [Indexed: 12/14/2022] Open
Abstract
Secondary multidrug transporters of the resistance-nodulation-cell division (RND) superfamily contribute crucially to antibiotic resistance in Gram-negative bacteria. Compared to the most studied transporter AcrB of Escherichia coli, little is known about the molecular determinants of distinct polyspecificities of the most important RND transporters MexB and MexY of Pseudomonas aeruginosa. In an effort to add knowledge on this topic, we performed an exhaustive atomic-level comparison of the main putative recognition sites (access and deep binding pockets) in these two Mex transporters. We identified an underlying link between some structural, chemical and dynamical features of the binding pockets and the physicochemical nature of the corresponding substrates recognized by either one or both pumps. In particular, mosaic-like lipophilic and electrostatic surfaces of the binding pockets provide for both proteins several multifunctional sites for diffuse binding of diverse substrates. Specific lipophilicity signatures of the weakly conserved deep pocket suggest a key role of this site as a selectivity filter as in Acr transporters. Finally, the different dynamics of the bottom-loop in MexB and MexY support its possible role in binding of large substrates. Our work represents the first comparative study of the major RND transporters in P. aeruginosa and also the first structure-based study of MexY, for which no experimental structure is available yet.
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Affiliation(s)
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Jürg Dreier
- Basilea Pharmaceutica International Ltd., Basel, Switzerland
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Italy
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28
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Trans-envelope multidrug efflux pumps of Gram-negative bacteria and their synergism with the outer membrane barrier. Res Microbiol 2018; 169:351-356. [PMID: 29454787 DOI: 10.1016/j.resmic.2018.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 11/20/2022]
Abstract
Antibiotic resistance is a serious threat to public health. Significant efforts are currently directed toward containment of the spread of resistance, finding new therapeutic options concerning resistant human and animal pathogens, and addressing the gaps in the fundamental understanding of mechanisms of resistance. Experimental data and kinetic modeling revealed a major factor in resistance, the synergy between active efflux and the low permeability barrier of the outer membrane, which dramatically reduces the intracellular accumulation of many antibiotics. The structural and mechanistic particularities of trans-envelope efflux pumps amplify the effectiveness of cell envelopes as permeability barriers. An important feature of this synergism is that efflux pumps and the outer membrane barriers are mechanistically independent and select antibiotics based on different physicochemical properties. The synergism amplifies even weak polyspecificity of multidrug efflux pumps and creates a major hurdle in the discovery and development of new therapeutics against Gram-negative pathogens.
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29
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Uddin MJ, Ahn J. Characterization of β-lactamase- and efflux pump-mediated multiple antibiotic resistance in Salmonella Typhimurium. Food Sci Biotechnol 2018; 27:921-928. [PMID: 30263820 DOI: 10.1007/s10068-018-0317-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022] Open
Abstract
This study aimed to assess the β-lactamase- and efflux pump-mediated antibiotic resistance in Salmonella Typhimurium (WT-ST), ciprofloxacin-induced antibiotic-resistant S. Typhimurium (CI-ST), and clinically-acquired antibiotic-resistant S. Typhimurium (CA-ST). The β-lactamase activities were significantly increased up to 63 μmol/min/mL in CA-ST and 24 μmol/min/mL in CI-ST when compared to WT-ST (13 μmol/min/mL). The highest efflux pump activity was observed in CI-ST and CA-ST, showing more than 45%. The antibiotic susceptibilities of WT-ST, CI-ST, and CA-ST were increased in the presence of β-lactamase and efflux pump inhibitors. CA-ST showed the highest activity in AcrD, MdtABC, EmrAB, MdtK, and MacAB efflux pumps. The repressed ompF were responsible for the decreased susceptibility of CA-ST to ampicillin (MIC > 512 μg/mL). This study would provide useful information for better understating of the development of multidrug resistance in association with β-lactamase and efflux pump activities and designing new antibiotic chemotherapy in combination with inhibitors.
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Affiliation(s)
- Md Jalal Uddin
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Juhee Ahn
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
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30
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Tam HK, Malviya VN, Pos KM. High-Resolution Crystallographic Analysis of AcrB Using Designed Ankyrin Repeat Proteins (DARPins). Methods Mol Biol 2018; 1700:3-24. [PMID: 29177822 DOI: 10.1007/978-1-4939-7454-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
X-ray crystallography is still the most prominent technique in use to decipher the 3D structures of membrane proteins. For successful crystallization, sample quality is the most important parameter that should be addressed. In almost every case, highly pure, monodisperse, and stable protein sample is a prerequisite. Vapor diffusion is in general the method of choice for obtaining crystals. Here, we discuss a detailed protocol for overproduction and purification of the inner-membrane multidrug transporter AcrB and of DARPins, which are used for crystallization of the AcrB/DARPin complex, resulting in high-resolution diffraction and subsequent structure determination.
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Affiliation(s)
- Heng Keat Tam
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany.
| | | | - Klaas M Pos
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
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31
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Zhang L, Xiao WH, Wang Y, Yao MD, Jiang GZ, Zeng BX, Zhang RS, Yuan YJ. Chassis and key enzymes engineering for monoterpenes production. Biotechnol Adv 2017; 35:1022-1031. [DOI: 10.1016/j.biotechadv.2017.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/02/2017] [Accepted: 09/04/2017] [Indexed: 02/07/2023]
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32
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Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella enterica. Sci Rep 2017; 7:13418. [PMID: 29042652 PMCID: PMC5645378 DOI: 10.1038/s41598-017-14008-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/04/2017] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) in pathogenic microorganisms with multidrug resistance (MDR) constitutes a severe threat to human health. A major causative mechanism of AMR is mediated through the multidrug efflux pump (MEP). The resistance-nodulation-division superfamily (RND family) of Gram-negative bacteria is usually the major cause of MDR in clinical studies. In Salmonella enterica, the RND pump is translated from the acrAB gene, which is regulated by the activator RamA. Many MEP-caused AMR strains have high ramA gene expression due to mutations in RamR, which has a homodimeric structure comprising the dimerization domain and DNA-binding domain (DBD). Three mutations on the dimerization domain, namely Y59H, M84I, and E160D, are far from the DBD; the molecular mechanism through which they influence RamR’s binding affinity to the ramA gene promoter and consequently disrupt RamA remains unclear. The present study conducted molecular dynamics simulations, binding free energy calculations, and normal mode analysis to investigate the mechanism through which Y59H, M84I, and E160D mutations on the dimerization domain influence the binding affinity of RamR to the ramA promoter. The present results suggest that the three mutations alter the RamR structure, resulting in decreased DNA-binding affinity.
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33
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Brown K, Li W, Kaur P. Role of Aromatic and Negatively Charged Residues of DrrB in Multisubstrate Specificity Conferred by the DrrAB System of Streptomyces peucetius. Biochemistry 2017; 56:1921-1931. [PMID: 28272881 DOI: 10.1021/acs.biochem.6b01155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Resistance to the anticancer antibiotics, doxorubicin and daunorubicin, in the producer organism Streptomyces peucetius is conferred by an ABC transporter made of two proteins, DrrA and DrrB, which together form a dedicated exporter for these two antibiotics. Surprisingly, however, the DrrAB system exhibits broad substrate specificity overlapping with well-studied multidrug resistance transporters, including P-glycoprotein. Therefore, it provides an excellent model for studying the molecular basis of multispecificity in a prototype efflux system with the potential to unravel the origin and evolution of multidrug resistance. It has been suggested that multispecificity in multidrug exporters may be generally determined by the number and location of aromatic residues. Strategically placed negatively charged residues may also be critical for binding of cationic lipophilic drugs. We selected 13 aromatic and four negatively charged residues on the basis of their location in and/or near the predicted drug-binding pocket of DrrB for analysis. Indeed, mutations of most tested residues drastically inhibited doxorubicin efflux. Interestingly, several mutants lost resistance to doxorubicin and verapamil simultaneously but retained resistance to Hoechst 33342 and/or ethidium bromide, suggesting the presence of overlapping as well as independent drug-binding sites in a common drug-binding pocket of DrrB. This study provides the first comprehensive analysis of residues involved in drug binding in a bacterial multidrug resistance protein of the ABC superfamily, and it shows strong similarity in the molecular mechanism of polyspecific drug recognition between DrrAB and Pgp. Altogether, we conclude that aromatic residue-based multidrug specificity is conserved across domains and over long evolutionary periods. The significance of these findings is discussed.
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Affiliation(s)
- Kenneth Brown
- Department of Biology, Georgia State University , Atlanta, Georgia 30303, United States
| | - Wen Li
- Department of Biology, Georgia State University , Atlanta, Georgia 30303, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University , Atlanta, Georgia 30303, United States
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34
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Puzari M, Chetia P. RND efflux pump mediated antibiotic resistance in Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa: a major issue worldwide. World J Microbiol Biotechnol 2017; 33:24. [PMID: 28044273 DOI: 10.1007/s11274-016-2190-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022]
Abstract
Therapeutic failures against diseases due to resistant Gram-negative bacteria have become a major threat nowadays as confirmed by surveillance reports across the world. One of the methods of development of multidrug resistance in Escherichia coli and Pseudomonas aeruginosa is by means of RND efflux pumps. Inhibition of these pumps might help to combat the antibiotic resistance problem, for which the structure and regulation of the pumps have to be known. Moreover, judicious antibiotic use is needed to control the situation. This paper focuses on the issue of antibiotic resistance as well as the structure, regulation and inhibition of the efflux pumps present in Escherichia coli and Pseudomonas aeruginosa.
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Affiliation(s)
- Minakshi Puzari
- Department of Life Sciences, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Pankaj Chetia
- Department of Life Sciences, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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35
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Hooper DC, Jacoby GA. Topoisomerase Inhibitors: Fluoroquinolone Mechanisms of Action and Resistance. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025320. [PMID: 27449972 DOI: 10.1101/cshperspect.a025320] [Citation(s) in RCA: 255] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quinolone antimicrobials are widely used in clinical medicine and are the only current class of agents that directly inhibit bacterial DNA synthesis. Quinolones dually target DNA gyrase and topoisomerase IV binding to specific domains and conformations so as to block DNA strand passage catalysis and stabilize DNA-enzyme complexes that block the DNA replication apparatus and generate double breaks in DNA that underlie their bactericidal activity. Resistance has emerged with clinical use of these agents and is common in some bacterial pathogens. Mechanisms of resistance include mutational alterations in drug target affinity and efflux pump expression and acquisition of resistance-conferring genes. Resistance mutations in one or both of the two drug target enzymes are commonly in a localized domain of the GyrA and ParC subunits of gyrase and topoisomerase IV, respectively, and reduce drug binding to the enzyme-DNA complex. Other resistance mutations occur in regulatory genes that control the expression of native efflux pumps localized in the bacterial membrane(s). These pumps have broad substrate profiles that include other antimicrobials as well as quinolones. Mutations of both types can accumulate with selection pressure and produce highly resistant strains. Resistance genes acquired on plasmids confer low-level resistance that promotes the selection of mutational high-level resistance. Plasmid-encoded resistance is because of Qnr proteins that protect the target enzymes from quinolone action, a mutant aminoglycoside-modifying enzyme that also modifies certain quinolones, and mobile efflux pumps. Plasmids with these mechanisms often encode additional antimicrobial resistances and can transfer multidrug resistance that includes quinolones.
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Affiliation(s)
- David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - George A Jacoby
- Lahey Hospital and Medical Center, Burlington, Massachusetts 01805
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36
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Sandoval-Motta S, Aldana M. Adaptive resistance to antibiotics in bacteria: a systems biology perspective. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:253-67. [DOI: 10.1002/wsbm.1335] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Santiago Sandoval-Motta
- Centro de Ciencias de la Complejidad; Universidad Nacional Autónoma de México; Ciudad de México Mexico
| | - Maximino Aldana
- Centro de Ciencias de la Complejidad; Universidad Nacional Autónoma de México; Ciudad de México Mexico
- Instituto de Ciencias Físicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos Mexico
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37
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Boyarskiy S, Davis López S, Kong N, Tullman-Ercek D. Transcriptional feedback regulation of efflux protein expression for increased tolerance to and production of n-butanol. Metab Eng 2015; 33:130-137. [PMID: 26656942 DOI: 10.1016/j.ymben.2015.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/28/2015] [Accepted: 11/23/2015] [Indexed: 01/11/2023]
Abstract
Microorganisms can be engineered to produce a variety of biofuels and commodity chemicals. The accumulation of these products, however, is often toxic to the cells and subsequently lowers production yields. Efflux pumps are a natural mechanism for alleviating toxicity through secretion of the product; unfortunately, pump overexpression also often inhibits growth. Tuning expression levels with inducible promoters is time-consuming and the reliance on small-molecule inducers is cost-prohibitive in industry. We design an expression regulation system utilizing a native Escherichia coli stress promoter, PgntK, to provide negative feedback to regulate transporter expression levels. We test the promoter in the context of the efflux pump AcrB and its butanol-secreting variant, AcrBv2. PgntK-driven AcrBv2 confers increased tolerance to n-butanol and increased titers of n-butanol in production. Furthermore, the system is responsive to stress from toxic overexpression of other membrane-associated proteins. Our results suggest a use for feedback regulation networks in membrane protein expression.
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Affiliation(s)
- Sergey Boyarskiy
- Joint Graduate Group in Bioengineering at UC Berkeley and UCSF, 306 Stanley Hall, Berkeley, CA 94720, United States
| | - Stephanie Davis López
- Department of Chemistry, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States
| | - Niwen Kong
- Department of Molecular and Cell Biology, University of California Berkeley, 142 LSA #3200, Berkeley, CA 94720, United States
| | - Danielle Tullman-Ercek
- Joint Graduate Group in Bioengineering at UC Berkeley and UCSF, 306 Stanley Hall, Berkeley, CA 94720, United States; Department of Chemistry, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States; Department of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States.
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38
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Reeve SM, Lombardo MN, Anderson AC. Understanding the structural mechanisms of antibiotic resistance sets the platform for new discovery. Future Microbiol 2015; 10:1727-33. [PMID: 26516790 DOI: 10.2217/fmb.15.78] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Understanding the structural basis of antibacterial resistance may enable rational design principles that avoid and subvert that resistance, thus leading to the discovery of more effective antibiotics. In this review, we explore the use of crystal structures to guide new discovery of antibiotics that are effective against resistant organisms. Structures of efflux pumps bound to substrates and inhibitors have aided the design of compounds with lower affinity for the pump or inhibitors that more effectively block the pump. Structures of β-lactamase enzymes have revealed the mechanisms of action toward key carbapenems and structures of gyrase have aided the design of compounds that are less susceptible to point mutations.
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Affiliation(s)
- Stephanie M Reeve
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269, USA
| | - Michael N Lombardo
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269, USA
| | - Amy C Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269, USA
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39
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Abstract
Quinolone antimicrobials are synthetic and widely used in clinical medicine. Resistance emerged with clinical use and became common in some bacterial pathogens. Mechanisms of resistance include two categories of mutation and acquisition of resistance-conferring genes. Resistance mutations in one or both of the two drug target enzymes, DNA gyrase and DNA topoisomerase IV, are commonly in a localized domain of the GyrA and ParE subunits of the respective enzymes and reduce drug binding to the enzyme-DNA complex. Other resistance mutations occur in regulatory genes that control the expression of native efflux pumps localized in the bacterial membrane(s). These pumps have broad substrate profiles that include quinolones as well as other antimicrobials, disinfectants, and dyes. Mutations of both types can accumulate with selection pressure and produce highly resistant strains. Resistance genes acquired on plasmids can confer low-level resistance that promotes the selection of mutational high-level resistance. Plasmid-encoded resistance is due to Qnr proteins that protect the target enzymes from quinolone action, one mutant aminoglycoside-modifying enzyme that also modifies certain quinolones, and mobile efflux pumps. Plasmids with these mechanisms often encode additional antimicrobial resistances and can transfer multidrug resistance that includes quinolones. Thus, the bacterial quinolone resistance armamentarium is large.
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Affiliation(s)
- David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - George A Jacoby
- Lahey Hospital and Medical Center, Burlington, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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40
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Li XZ, Plésiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin Microbiol Rev 2015; 28:337-418. [PMID: 25788514 PMCID: PMC4402952 DOI: 10.1128/cmr.00117-14] [Citation(s) in RCA: 924] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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41
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Motta SS, Cluzel P, Aldana M. Adaptive resistance in bacteria requires epigenetic inheritance, genetic noise, and cost of efflux pumps. PLoS One 2015; 10:e0118464. [PMID: 25781931 PMCID: PMC4363326 DOI: 10.1371/journal.pone.0118464] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
Adaptive resistance emerges when populations of bacteria are subjected to gradual increases of antibiotics. It is characterized by a rapid emergence of resistance and fast reversibility to the non-resistant phenotype when the antibiotic is removed from the medium. Recent work shows that adaptive resistance requires epigenetic inheritance and heterogeneity of gene expression patterns that are, in particular, associated with the production of porins and efflux pumps. However, the precise mechanisms by which inheritance and variability govern adaptive resistance, and what processes cause its reversibility remain unclear. Here, using an efflux pump regulatory network (EPRN) model, we show that the following three mechanisms are essential to obtain adaptive resistance in a bacterial population: 1) intrinsic variability in the expression of the EPRN transcription factors; 2) epigenetic inheritance of the transcription rate of EPRN associated genes; and 3) energetic cost of the efflux pumps activity that slows down cell growth. While the first two mechanisms acting together are responsible for the emergence and gradual increase of the resistance, the third one accounts for its reversibility. In contrast with the standard assumption, our model predicts that adaptive resistance cannot be explained by increased mutation rates. Our results identify the molecular mechanism of epigenetic inheritance as the main target for therapeutic treatments against the emergence of adaptive resistance. Finally, our theoretical framework unifies known and newly identified determinants such as the burden of efflux pumps that underlie bacterial adaptive resistance to antibiotics.
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Affiliation(s)
| | - Philippe Cluzel
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Maximino Aldana
- Instituto de Ciencias Físicas, UNAM, Cuernavaca, Morelos, Mexico
- * E-mail:
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42
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Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy TBK, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 2015; 10:8. [PMID: 26203325 PMCID: PMC4511580 DOI: 10.1186/1944-3277-10-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/24/2014] [Indexed: 12/21/2022] Open
Abstract
Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1(T) along with its complete genome sequence and annotation from a culture of DSM 17521(T). The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.
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Affiliation(s)
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | | | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian J Tindall
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
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43
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Saidijam M, Patching SG. Amino acid composition analysis of secondary transport proteins from Escherichia coli with relation to functional classification, ligand specificity and structure. J Biomol Struct Dyn 2015; 33:2205-20. [DOI: 10.1080/07391102.2014.998283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Massoud Saidijam
- Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan, Iran
| | - Simon G. Patching
- Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan, Iran
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44
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Compton CL, Carney DW, Groomes PV, Sello JK. Fragment-Based Strategy for Investigating and Suppressing the Efflux of Bioactive Small Molecules. ACS Infect Dis 2015; 1:53-8. [PMID: 27620145 DOI: 10.1021/id500009f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane protein-mediated drug efflux is a phenomenon that compromises our ability to treat both infectious diseases and cancer. Accordingly, there is much interest in the development of strategies for suppression of the mechanisms by which therapeutic agents are effluxed. Here, using resistance to the cyclic acyldepsipeptide (ADEP) antibacterial agents as a model, we demonstrate a new counter-efflux strategy wherein a fragment of an actively exported bioactive compound competitively interferes with its efflux and potentiates its activity. A fragment comprising the N-heptenoyldifluorophenylalanine side chain of the pharmacologically optimized ADEPs potentiates the antibacterial activity of the ADEPs against actinobacteria to a greater extent than reserpine, a well-known efflux inhibitor. Beyond their validation of a new approach to studying molecular recognition by drug efflux pumps, our findings have important implications for killing Mycobacterium tuberculosis with ADEPs and reclaiming the efficacies of therapeutic agents whose activity has been compromised by efflux pumps.
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Affiliation(s)
- Corey L. Compton
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
| | - Daniel W. Carney
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
| | - Patrice V. Groomes
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
| | - Jason K. Sello
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
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45
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Park AJ, Surette MD, Khursigara CM. Antimicrobial targets localize to the extracellular vesicle-associated proteome of Pseudomonas aeruginosa grown in a biofilm. Front Microbiol 2014; 5:464. [PMID: 25232353 PMCID: PMC4153316 DOI: 10.3389/fmicb.2014.00464] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/14/2014] [Indexed: 01/21/2023] Open
Abstract
Microbial biofilms are particularly resistant to antimicrobial therapies. These surface-attached communities are protected against host defenses and pharmacotherapy by a self-produced matrix that surrounds and fortifies them. Recent proteomic evidence also suggests that some bacteria, including the opportunistic pathogen Pseudomonas aeruginosa, undergo modifications within a biofilm that make them uniquely resistant compared to their planktonic (free-living) counterparts. This study examines 50 proteins in the resistance subproteome of both surface-associated and free-living P. aeruginosa PAO1 over three time points. Proteins were grouped into categories based on their roles in antimicrobial: (i) binding, (ii) efflux, (iii) resistance, and (iv) susceptibility. In addition, the extracellular outer membrane vesicle-associated proteome is examined and compared between the two growth modes. We show that in whole cells between 12-24% of the proteins are present at significantly different abundance levels over time, with some proteins being unique to a specific growth mode; however, the total abundance levels in the four categories remain consistent. In contrast, marked differences are seen in the protein content of the outer membrane vesicles, which contain a greater number of drug-binding proteins in vesicles purified from late-stage biofilms. These results show how the method of analysis can impact the interpretation of proteomic data (i.e., individual proteins vs. systems), and highlight the advantage of using protein-based methods to identify potential antimicrobial resistance mechanisms in extracellular sample components. Furthermore, this information has the potential to inform the development of specific antipseudomonal therapies that quench possible drug-sequestering vesicle proteins. This strategy could serve as a novel approach for combating the high-level of antimicrobial resistance in P. aeruginosa biofilms.
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Affiliation(s)
- Amber J Park
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Matthew D Surette
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
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46
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Luhe AL, Lim CY, Gerken H, Wu J, Zhao H. Furfural and hydroxymethylfurfural tolerance in Escherichia coli ΔacrR regulatory mutants. Biotechnol Appl Biochem 2014; 62:32-6. [PMID: 24716991 DOI: 10.1002/bab.1232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 04/01/2014] [Indexed: 11/05/2022]
Abstract
The presence of the highly toxic furfural and hydroxymethylfurfural (HMF) in the hydrolysate of lignocellulosic biomass prompted the investigation of the Escherichia coli ΔacrR regulatory mutant for higher tolerance to these compounds, to facilitate the production of biofuels and biochemicals, and further biocatalytic conversions. In comparison with the parental strain, the regulatory mutant with the upregulated efflux pump AcrAB-TolC produced moderately better growth and higher tolerance to concentrations of furfural and HMF between 1 and 2 g L(-1) .
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Affiliation(s)
- Annette Lin Luhe
- Industrial Biotechnology Program, Institute of Chemical & Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Jurong Island, Singapore
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47
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Rodrigues D, Kittelmann M, Eggimann F, Bachler T, Abad S, Camattari A, Glieder A, Winkler M, Lütz S. Production of Recombinant Human Aldehyde Oxidase in Escherichia coli
and Optimization of Its Application for the Preparative Synthesis of Oxidized Drug Metabolites. ChemCatChem 2014. [DOI: 10.1002/cctc.201301094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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48
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Li W, Sharma M, Kaur P. The DrrAB efflux system of Streptomyces peucetius is a multidrug transporter of broad substrate specificity. J Biol Chem 2014; 289:12633-46. [PMID: 24634217 DOI: 10.1074/jbc.m113.536136] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The soil bacterium Streptomyces peucetius produces two widely used anticancer antibiotics, doxorubicin and daunorubicin. Present within the biosynthesis gene cluster in S. peucetius is the drrAB operon, which codes for a dedicated ABC (ATP binding cassette)-type transporter for the export of these two closely related antibiotics. Because of its dedicated nature, the DrrAB system is believed to belong to the category of single-drug transporters. However, whether it also contains specificity for other known substrates of multidrug transporters has never been tested. In this study we demonstrate under both in vivo and in vitro conditions that the DrrAB system can transport not only doxorubicin but is also able to export two most commonly studied MDR substrates, Hoechst 33342 and ethidium bromide. Moreover, we demonstrate that many other substrates (including verapamil, vinblastine, and rifampicin) of the well studied multidrug transporters inhibit DrrAB-mediated Dox transport with high efficiency, indicating that they are also substrates of the DrrAB pump. Kinetic studies show that inhibition of doxorubicin transport by Hoechst 33342 and rifampicin occurs by a competitive mechanism, whereas verapamil inhibits transport by a non-competitive mechanism, thus suggesting the possibility of more than one drug binding site in the DrrAB system. This is the first in-depth study of a drug resistance system from a producer organism, and it shows that a dedicated efflux system like DrrAB contains specificity for multiple drugs. The significance of these findings in evolution of poly-specificity in drug resistance systems is discussed.
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Affiliation(s)
- Wen Li
- From the Department of Biology, Georgia State University, Atlanta, Georgia 30303
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49
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Nguyen D, Helms V, Lee PH. PRIMSIPLR: Prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins. Proteins 2014; 82:1503-11. [DOI: 10.1002/prot.24520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/08/2014] [Accepted: 01/16/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Duy Nguyen
- Center for Bioinformatics; Saarland University; D-66041 Saarbrücken Germany
| | - Volkhard Helms
- Center for Bioinformatics; Saarland University; D-66041 Saarbrücken Germany
| | - Po-Hsien Lee
- Center for Bioinformatics; Saarland University; D-66041 Saarbrücken Germany
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50
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Rayasam GV. MmpL3 a potential new target for development of novel anti-tuberculosis drugs. Expert Opin Ther Targets 2013; 18:247-56. [DOI: 10.1517/14728222.2014.859677] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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