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Lin J, Lv H, Wang T, Tao H, Zhong Y, Zhou Y, Tang Y, Xie F, Zhuang G, Xu C, Chu Y, Wang X, Yang Y, Song T. The global distribution of the macrolide esterase EstX from the alpha/beta hydrolase superfamily. Commun Biol 2024; 7:781. [PMID: 38944651 PMCID: PMC11214618 DOI: 10.1038/s42003-024-06473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
Macrolide antibiotics, pivotal in clinical therapeutics, are confronting resistance challenges mediated by enzymes like macrolide esterases, which are classified into Ere-type and the less studied Est-type. In this study, we provide the biochemical confirmation of EstX, an Est-type macrolide esterase that initially identified as unknown protein in the 1980s. EstX is capable of hydrolyzing four 16-membered ring macrolides, encompassing both veterinary (tylosin, tidipirosin, and tilmicosin) and human-use (leucomycin A5) antibiotics. It uses typical catalytic triad (Asp233-His261-Ser102) from alpha/beta hydrolase superfamily for ester bond hydrolysis. Further genomic context analysis suggests that the dissemination of estX is likely facilitated by mobile genetic elements such as integrons and transposons. The global distribution study indicates that bacteria harboring the estX gene, predominantly pathogenic species like Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae, are prevalent in 74 countries across 6 continents. Additionally, the emergence timeline of the estX gene suggests its proliferation may be linked to the overuse of macrolide antibiotics. The widespread prevalence and dissemination of Est-type macrolide esterase highlight an urgent need for enhanced monitoring and in-depth research, underlining its significance as an escalating public health issue.
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Affiliation(s)
- Jiafu Lin
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Hua Lv
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Tiantian Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Hongkun Tao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yi Zhong
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yang Zhou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yibo Tang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Feng Xie
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Guoqing Zhuang
- Sichuan Academy of Forestry, 610081, Chengdu, Sichuan, China
| | - Changwen Xu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Xinrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yongqiang Yang
- Center of Infectious Diseases, Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China.
| | - Tao Song
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China.
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2
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Gillieatt BF, Coleman NV. Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. FEMS Microbiol Rev 2024; 48:fuae017. [PMID: 38897736 PMCID: PMC11253441 DOI: 10.1093/femsre/fuae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/09/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024] Open
Abstract
The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.
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Affiliation(s)
- Brodie F Gillieatt
- School of Life and Environmental Sciences, The University of Sydney, F22 - LEES Building, NSW 2006, Australia
| | - Nicholas V Coleman
- School of Natural Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, 6 Wally’s Walk, Macquarie Park, NSW 2109, Australia
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3
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Bava R, Castagna F, Lupia C, Poerio G, Liguori G, Lombardi R, Naturale MD, Mercuri C, Bulotta RM, Britti D, Palma E. Antimicrobial Resistance in Livestock: A Serious Threat to Public Health. Antibiotics (Basel) 2024; 13:551. [PMID: 38927217 PMCID: PMC11200672 DOI: 10.3390/antibiotics13060551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Antimicrobial resistance represents an alarming public health problem; its importance is related to the significant clinical implications (increased morbidity, mortality, disease duration, development of comorbidities, and epidemics), as well as its economic effects on the healthcare sector. In fact, therapeutic options are severely limited by the advent and spread of germs resistant to many antibiotics. The situation worldwide is worrying, especially in light of the prevalence of Gram-negative bacteria-Klebsiella pneumoniae and Acinetobacter baumannii-which are frequently isolated in hospital environments and, more specifically, in intensive care units. The problem is compounded by the ineffective treatment of infections by patients who often self-prescribe therapy. Resistant bacteria also show resistance to the latest generation antibiotics, such as carbapenems. In fact, superbacteria, grouped under the acronym extended-spectrum betalactamase (ESBL), are becoming common. Antibiotic resistance is also found in the livestock sector, with serious repercussions on animal production. In general, this phenomenon affects all members of the biosphere and can only be addressed by adopting a holistic "One Health" approach. In this literature overview, a stock is taken of what has been learned about antibiotic resistance, and suggestions are proposed to stem its advance.
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Affiliation(s)
- Roberto Bava
- Department of Health Sciences, University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy; (R.B.); (C.L.); (R.M.B.); (D.B.); (E.P.)
| | - Fabio Castagna
- Department of Health Sciences, University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy; (R.B.); (C.L.); (R.M.B.); (D.B.); (E.P.)
- Mediterranean Ethnobotanical Conservatory, Sersale (CZ), 88054 Catanzaro, Italy
| | - Carmine Lupia
- Department of Health Sciences, University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy; (R.B.); (C.L.); (R.M.B.); (D.B.); (E.P.)
- Mediterranean Ethnobotanical Conservatory, Sersale (CZ), 88054 Catanzaro, Italy
| | - Giusi Poerio
- ATS Val Padana, Via dei Toscani, 46100 Mantova, Italy;
| | | | - Renato Lombardi
- IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), 71013 Foggia, Italy;
| | - Maria Diana Naturale
- Ministry of Health, Directorate General for Health Programming, 00144 Rome, Italy;
| | - Caterina Mercuri
- Department of Experimental and Clinical Medicine, University “Magna Graecia”, 88100 Catanzaro, Italy;
| | - Rosa Maria Bulotta
- Department of Health Sciences, University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy; (R.B.); (C.L.); (R.M.B.); (D.B.); (E.P.)
| | - Domenico Britti
- Department of Health Sciences, University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy; (R.B.); (C.L.); (R.M.B.); (D.B.); (E.P.)
| | - Ernesto Palma
- Department of Health Sciences, University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy; (R.B.); (C.L.); (R.M.B.); (D.B.); (E.P.)
- Center for Pharmacological Research, Food Safety, High Tech and Health (IRC-FSH), University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy
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4
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Xiao Y, Sheng ZM, Williams SL, Taubenberger JK. Two complete 1918 influenza A/H1N1 pandemic virus genomes characterized by next-generation sequencing using RNA isolated from formalin-fixed, paraffin-embedded autopsy lung tissue samples along with evidence of secondary bacterial co-infection. mBio 2024; 15:e0321823. [PMID: 38349163 PMCID: PMC10936189 DOI: 10.1128/mbio.03218-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
The 1918 influenza pandemic was the most devastating respiratory pandemic in modern human history, with 50-100 million deaths worldwide. Here, we characterized the complete genomes of influenza A virus (IAV) from two fatal cases during the fall wave of 1918 influenza A (H1N1) pandemic in the United States, one from Walter Reed Army Hospital in Washington, DC, and the other from Camp Jackson, SC. The two complete IAV genomes were obtained by combining Illumina deep sequencing data from both total RNA and influenza viral genome-enriched libraries along with Sanger sequencing data from PCR across the sequencing gaps. This study confirms the previously reported 1918 IAV genomes and increases the total number of available complete or near-complete influenza viral genomes of the 1918 pandemic from four to six. Sequence comparisons among them confirm that the genomes of the 1918 pandemic virus were highly conserved during the main wave of the pandemic with geographic separation in North America and Europe. Metagenomic analyses revealed bacterial co-infections in both cases. Interestingly, in the Washington, DC, case, evidence is presented of the first reported Rhodococcus-influenza virus co-infection. IMPORTANCE This study applied modern molecular biotechnology and high-throughput sequencing to formalin-fixed, paraffin-embedded autopsy lung samples from two fatal cases during the fall wave of the 1918 influenza A (H1N1) pandemic in the United States. Complete influenza genomes were obtained from both cases, which increases the total number of available complete or near-complete influenza genomes of the 1918 pandemic virus from four to six. Sequence analysis confirms that the 1918 pandemic virus was highly conserved during the main wave of the pandemic with geographic separation in North America and Europe. Metagenomic analyses revealed bacterial co-infections in both cases, including the first reported evidence of Rhodococcus-influenza co-infection. Overall, this study offers a detailed view at the molecular level of the very limited samples from the most devastating influenza pandemic in modern human history.
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Affiliation(s)
- Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Zong-Mei Sheng
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie L. Williams
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jeffery K. Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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5
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Miravet-Verde S, Mazzolini R, Segura-Morales C, Broto A, Lluch-Senar M, Serrano L. ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs. Nat Commun 2024; 15:2091. [PMID: 38453908 PMCID: PMC10920889 DOI: 10.1038/s41467-024-46112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by sequencing transposon insertions engineered to express a selection marker when they occur in-frame within a protein-coding gene. In the bacterium Mycoplasma pneumoniae, ProTInSeq identifies 83% of its annotated proteins, along with 5 proteins and 153 small ORF-encoded proteins (SEPs; ≤100 aa) that were not previously annotated. Moreover, ProTInSeq can be utilized for detecting translational noise, as well as for relative quantification and transmembrane topology estimation of fitness and non-essential proteins. By integrating various identification approaches, the number of initially annotated SEPs in this bacterium increases from 27 to 329, with a quarter of them predicted to possess antimicrobial potential. Herein, we describe a methodology complementary to Ribo-Seq and mass spectroscopy that can identify SEPs while providing other insights in a proteome with a flexible and cost-effective DNA ultra-deep sequencing approach.
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Affiliation(s)
- Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland.
| | | | - Carolina Segura-Morales
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Alicia Broto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Maria Lluch-Senar
- Pulmobiotics, Dr Aiguader 88, 08003, Barcelona, Spain.
- Institute of Biotechnology and Biomedicine "Vicent Villar Palasi" (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
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6
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Dhindwal P, Myziuk I, Ruzzini A. Macrolide esterases: current threats and opportunities. Trends Microbiol 2023; 31:1199-1201. [PMID: 37689489 DOI: 10.1016/j.tim.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/11/2023]
Abstract
Antibiotics often contain ester bonds. The macrocyclic lactones of macrolides are pre-eminent examples in which ester bonds are essential to the form and function of antibiotics. Bacterial macrolide esterases that hydrolyze these macrocyclic lactones to confer antimicrobial resistance (AMR) are the topic of this forum. We provide insight into their role in agricultural systems and discuss their emergence and their potential extensibility to bioremediation efforts.
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Affiliation(s)
- Poonam Dhindwal
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5B4
| | - Iryna Myziuk
- Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
| | - Antonio Ruzzini
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5B4; Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5.
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7
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Hu J, Lyu Y, Chen H, Li S, Sun W. Suspect and Nontarget Screening Reveal the Underestimated Risks of Antibiotic Transformation Products in Wastewater Treatment Plant Effluents. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17439-17451. [PMID: 37930269 DOI: 10.1021/acs.est.3c05008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Antibiotics are anthropogenic contaminants with a global presence and of deep concern in aquatic environments, while less is known about the occurrence and risks of their transformation products (TPs). Herein, we developed a comprehensive suspect and nontarget screening workflow based on high-resolution mass spectrometry to identify unknown antibiotic TPs in wastewater treatment plant effluents. We identified 211 compounds (35 parent antibiotics and 176 TPs) at confidence levels of ≥3 and 107 TPs originated from macrolides. TPs were quantified by 17 TPs standards and semiquantified by the predicted response factors and accounted for 55.6-95.1% (76.7% on average) of the total concentrations of parents and TPs. 22.2%, 63.1%, and 18.8% of the identified TPs were estimated to be more persistent, mobile, and toxic than their parent antibiotics, respectively. Further ecological risk assessment based on concentrations and toxicity to aquatic organisms revealed that the cumulative risks of TPs were generally higher than those of parents. Despite the newly formed N-oxide TPs, the tertiary treatment process (mainly ozonation) could decrease the averaged 20.3% of concentrations and 36.2% of the risks of antibiotic-related compounds. This study highlights the necessity to include antibiotic TPs in environmental scrutiny and risk assessment of antibiotics in different aquatic environments.
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Affiliation(s)
- Jingrun Hu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Yitao Lyu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Huan Chen
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina 29634, United States
| | - Si Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Weiling Sun
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
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8
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Ashraf MV, Pant S, Khan MAH, Shah AA, Siddiqui S, Jeridi M, Alhamdi HWS, Ahmad S. Phytochemicals as Antimicrobials: Prospecting Himalayan Medicinal Plants as Source of Alternate Medicine to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:881. [PMID: 37375828 DOI: 10.3390/ph16060881] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities. Given the promising results of plant-based antimicrobials, coupled with the slow discovery of novel antibiotics, it has become highly imperative to explore the vast repository of phytocompounds to overcome the looming catastrophe of AMR. This review summarizes the emergence of AMR towards existing antibiotics and potent phytochemicals having antimicrobial activities, along with a comprehensive overview of 123 Himalayan medicinal plants reported to possess antimicrobial phytocompounds, thus compiling the existing information that will help researchers in the exploration of phytochemicals to combat AMR.
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Affiliation(s)
- Mohammad Vikas Ashraf
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Shreekar Pant
- Centre for Biodiversity Studies, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - M A Hannan Khan
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Ali Asghar Shah
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Sazada Siddiqui
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Mouna Jeridi
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Shoeb Ahmad
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
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9
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Schaefer D, Cheng X. Recent Advances in Covalent Drug Discovery. Pharmaceuticals (Basel) 2023; 16:ph16050663. [PMID: 37242447 DOI: 10.3390/ph16050663] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
In spite of the increasing number of biologics license applications, the development of covalent inhibitors is still a growing field within drug discovery. The successful approval of some covalent protein kinase inhibitors, such as ibrutinib (BTK covalent inhibitor) and dacomitinib (EGFR covalent inhibitor), and the very recent discovery of covalent inhibitors for viral proteases, such as boceprevir, narlaprevir, and nirmatrelvir, represent a new milestone in covalent drug development. Generally, the formation of covalent bonds that target proteins can offer drugs diverse advantages in terms of target selectivity, drug resistance, and administration concentration. The most important factor for covalent inhibitors is the electrophile (warhead), which dictates selectivity, reactivity, and the type of protein binding (i.e., reversible or irreversible) and can be modified/optimized through rational designs. Furthermore, covalent inhibitors are becoming more and more common in proteolysis, targeting chimeras (PROTACs) for degrading proteins, including those that are currently considered to be 'undruggable'. The aim of this review is to highlight the current state of covalent inhibitor development, including a short historical overview and some examples of applications of PROTAC technologies and treatment of the SARS-CoV-2 virus.
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Affiliation(s)
- Daniel Schaefer
- Buchmann Institute for Molecular Life Sciences, Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, 60438 Frankfurt am Main, Germany
- Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Xinlai Cheng
- Buchmann Institute for Molecular Life Sciences, Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, 60438 Frankfurt am Main, Germany
- Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
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10
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Ren J, Qi X, Zhang J, Niu D, Shen Y, Yu C, Zhi J, Wang C, Jiang X, Zhang W, Li C. Biodegradation efficiency and mechanism of erythromycin degradation by Paracoccus versutus W7. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117372. [PMID: 36731410 DOI: 10.1016/j.jenvman.2023.117372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Continuous and excessive usage of erythromycin results in serious environmental pollution and presents a health risk to humans. Biological treatment is considered as an efficient and economical method to remove it from the environment. In this study, a novel erythromycin-degrading bacterial strain, W7, isolated from sewage sludge was identified as Paracoccus versutus. Strain W7 degraded 58.5% of 50 mg/L erythromycin in 72 h under the optimal conditions of 35 °C, pH 7.0, and 0.1% sodium citrate with yeast powder in mineral salt medium. It completely eliminated erythromycin from erythromycin fermentation residue at concentrations of 100 and 300 mg/L within 36 and 60 h, respectively. Erythromycin esterase (EreA) was found to be involved in erythromycin metabolism in this strain and was expressed successfully. EreA could hydrolyze erythromycin, and its maximum activity occurred at pH 8.5 and 35 °C. Finally, six intermediates of erythromycin degraded by strain W7 were detected by high performance liquid chromatography mass spectrometry. Based on the novel intermediates and enzymes, we determined two possible pathways of erythromycin degradation by strain W7. This study broadened our understanding of the erythromycin catabolic processes of P. versutus and developed a feasible microbial strategy for removing erythromycin from erythromycin fermentation residue, wastewater, and other erythromycin-contaminated environments.
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Affiliation(s)
- Jianjun Ren
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Xiancheng Qi
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; School of Pharmacy & School of Biological and Food Engineering, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Jian Zhang
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Dongze Niu
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Yunpeng Shen
- Yili Chuanning Biotechnology Co., Ltd. No. 156 Alamutuya Country, Yining District, Yili 835000, China
| | - Changyong Yu
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Junqiang Zhi
- Beijing General Station of Animal Husbandry, No. 21 Chaoqian Road, Changping District, Beijing, 100101, China
| | - Chongqing Wang
- Beijing General Station of Animal Husbandry, No. 21 Chaoqian Road, Changping District, Beijing, 100101, China
| | - Xingmei Jiang
- Bijie Institute of Animal Husbandry and Veterinary Sciences, Degoumajiayuan Road, Qixingguan District, Bijie 551700, China
| | - Wenfan Zhang
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Chunyu Li
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China.
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11
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Ibrahim SAEM, El-Bialy HA, Gomaa OM. Biodegradation of COVID19 antibiotic; azithromycin and its impact on soil microbial community in the presence of phenolic waste and with temperature variation. World J Microbiol Biotechnol 2023; 39:154. [PMID: 37037954 PMCID: PMC10085964 DOI: 10.1007/s11274-023-03591-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023]
Abstract
The increase in using antibiotics, especially Azithromycin have increased steadily since the beginning of COVID19 pandemic. This increase has led to its presence in water systems which consequently led to its presence upon using this water for irrigation. The aim of the present work is to study the impact of irrigation using Azithromycin containing water on soil microbial community and its catabolic activity in the presence of phenolic wastes as compost. Wild berry, red grapes, pomegranate, and spent tea waste were added to soil and the degradation was monitored after 5 and 7 days at ambient and high temperatures. The results obtained show that at 30 °C, soil microbial community collectively was able to degrade Azithromycin, while at 40 °C, addition of spent tea as compost was needed to reach higher degradation. To ensure that the degradation was biotic and depended on degradation by indigenous microflora, a 25 kGy irradiation dose was used to kill the microorganisms in the soil and this was used as negative control. The residual antibiotic was assayed using UV spectroscopy and High Performance Liquid Chromatography (HPLC). Indication of Azithromycin presence was studied using Fourier Transform Infrared Spectroscopy (FTIR) peaks and the same pattern was obtained using the 3 used detection methods, the ability to assign the peaks even in the presence of soil and not to have any overlaps, gives the chance to study this result in depth to prepare IR based sensor for quick sensing of antibiotic in environmental samples.
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Affiliation(s)
- Shaimaa Abd El Mohsen Ibrahim
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), 3 Ahmad El Zomor St, Cairo, Egypt
| | - Heba Abdalla El-Bialy
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), 3 Ahmad El Zomor St, Cairo, Egypt
| | - Ola M Gomaa
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), 3 Ahmad El Zomor St, Cairo, Egypt.
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12
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You C, Zhang Y, Xu Y, Xu P, Li Z, Li H, Huang S, Chen Z, Li J, Xu HE, Jiang Y. Structural basis for motilin and erythromycin recognition by motilin receptor. SCIENCE ADVANCES 2023; 9:eade9020. [PMID: 36921049 PMCID: PMC10017046 DOI: 10.1126/sciadv.ade9020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Motilin is an endogenous peptide hormone almost exclusively expressed in the human gastrointestinal (GI) tract. It activates the motilin receptor (MTLR), a class A G protein-coupled receptor (GPCR), and stimulates GI motility. To our knowledge, MTLR is the first GPCR reported to be activated by macrolide antibiotics, such as erythromycin. It has attracted extensive attention as a potential drug target for GI disorders. We report two structures of Gq-coupled human MTLR bound to motilin and erythromycin. Our structures reveal the recognition mechanism of both ligands and explain the specificity of motilin and ghrelin, a related gut peptide hormone, for their respective receptors. These structures also provide the basis for understanding the different recognition modes of erythromycin by MTLR and ribosome. These findings provide a framework for understanding the physiological regulation of MTLR and guiding drug design targeting MTLR for the treatment of GI motility disorders.
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Affiliation(s)
- Chongzhao You
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yumu Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Youwei Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peiyu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhen Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huadong Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Sijie Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zecai Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingru Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - H. Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Lingang Laboratory, Shanghai 200031, China
| | - Yi Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
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13
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Zhang Y, Ouyang B, Chen Y, Zhang W, Guang C, Xu W, Mu W. Transformation of macrolides residues by a novel erythromycin esterase C (Ere C) and safety evaluation of transformed products on Caenorhabditis elegans. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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14
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Yan S, Ding N, Yao X, Song J, He W, Rehman F, Guo J. Effects of erythromycin and roxithromycin on river periphyton: Structure, functions and metabolic pathways. CHEMOSPHERE 2023; 316:137793. [PMID: 36640977 DOI: 10.1016/j.chemosphere.2023.137793] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Macrolides have been frequently detected in the surface waters worldwide, posing a threat to the aquatic microbes. Several studies have evaluated the ecotoxicological effects of macrolides on single algal and bacterial strains. However, without considering the species interaction in the aquatic microbial community, these results cannot be extrapolated to the field. Thus, the present study aimed to evaluate the effects of two macrolides (erythromycin and roxithromycin) on the structure, photosynthetic process, carbon utilization capacity, and the antibiotic metabolic pathways in river periphyton. The colonized periphyton was exposed to the graded concentration (0 μg/L (control), 0.5 μg/L (low), 5 μg/L (medium), 50 μg/L (high)) of ERY and ROX, respectively, for 7 days. Herein, high levels of ERY and ROX altered the community composition by reducing the relative abundance of Chlorophyta in the eukaryotic community. Also, the Shannon and Simpson diversity indexes of prokaryotes were reduced, although similar effects were seldomly detected in the low and medium groups. In contrast to the unchanged carbon utilization capacity, the PSII reaction center involved in the periphytic photosynthesis was significantly inhibited by macrolides at high levels. In addition, both antibiotics had been degraded by periphyton, with the removal rate of 51.63-66.87% and 41.85-48.27% for ERY and ROX, respectively, wherein the side chain and ring cleavage were the main degradation pathways. Overall, this study provides an insight into the structural and functional toxicity and degradation processes of macrolides in river periphyton.
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Affiliation(s)
- Shiwei Yan
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Ning Ding
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Xiunan Yao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Jinxi Song
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Wei He
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Fozia Rehman
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Pakistan
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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15
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Oda K, Wlodawer A. Overview of the Properties of Glutamic Peptidases That Are Present in Plant and Bacterial Pathogens and Play a Role in Celiac Disease and Cancer. Biochemistry 2023; 62:672-694. [PMID: 36705990 DOI: 10.1021/acs.biochem.2c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Seven peptidase (proteinase) families─aspartic, cysteine, metallo, serine, glutamic, threonine, and asparagine─are in the peptidase database MEROPS, version 12.4 (https://www.ebi.ac.uk/merops/). The glutamic peptidase family is assigned two clans, GA and GB, and comprises six subfamilies. This perspective summarizes the unique features of their representatives. (1) G1, scytalidoglutamic peptidase, has a β-sandwich structure containing catalytic residues glutamic acid (E) and glutamine (Q), thus the name eqolisin. Most family members are pepstatin-insensitive and act as plant pathogens. (2) G2, preneck appendage protein, originates in phages, is a transmembrane protein, and its catalytic residues consist of glutamic and aspartic acids. (3) G3, strawberry mottle virus glutamic peptidase, originates in viruses and has a β-sandwich structure with catalytic residues E and Q. Neprosin has propyl endopeptidase activity, is associated with celiac disease, has a β-sandwich structure, and contains catalytic residues E-E and Q-tryptophan. (4) G4, Tiki peptidase, of the erythromycin esterase family, is a transmembrane protein, and its catalytic residues are E-histidine pairs. (5) G5, RCE1 peptidase, is associated with cancer, is a transmembrane protein, and its catalytic residues are E-histidine and asparagine-histidine. Microcystinase, a bacterial toxin, is a transmembrane protein with catalytic residues E-histidine and asparagine-histidine. (6) G6, Ras/Rap1-specific peptidase, is a bacterial pathogen, a transmembrane protein, and its catalytic residues are E-histidine pairs. This family's common features are that their catalytic residues consist of a glutamic acid and another (variable) amino acid and that they exhibit a diversity of biological functions─plant and bacterial pathogens and involvement in celiac disease and cancer─that suggests they are viable drug targets.
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-Ku, Kyoto 606-8585, Japan
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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16
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Shalaby A, Ismail MM, El-Sharkawy H. Isolation, Identification, and Genetic Characterization of Antibiotic Resistance of Salmonella Species Isolated from Chicken Farms. J Trop Med 2022; 2022:6065831. [PMID: 36482931 PMCID: PMC9726267 DOI: 10.1155/2022/6065831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 07/30/2023] Open
Abstract
Salmonella is a major cause of foodborne outbreaks. It causes gastroenteritis in humans and animals. This micro-organism causes severe illness in chickens and has a major impact on chicken productivity and the poultry industry. This study aimed to address the prevalence of Salmonella infection in broiler chicken farms in Kafrelsheikh, Gharbia, and Menofeya provinces in Egypt during 2020-2022. This work also aimed to evaluate the genetic characterization and antibiotic resistance of the isolated Salmonella strains. Clinical signs and mortalities were observed and recorded. In total, 832 samples were collected from 52 broiler flocks, including 26 from both one-week-old and 6-week-old chicken farms from different organs (liver, intestinal content, spleen, and gallbladder). The prevalence of Salmonella infections was reported in the study region to be 36.54%. Of the 26 one-week-old farms surveyed, 11 (42.31%) and 8/26 (30.77%) of the six-week-old broiler chicken farms had Salmonella infections. Recovered isolates were serotyped as 9 (47.37%) S. enteritidis O 1,9,12, ad monophasic H: g, m: -, 6 (31.58.%) S. shangani 2, (10.53%) S. gueuletapee 1, (5.26%) S. II (salamae), and 1 (5.26%) untypable. The results showed that Salmonella infection was predominant in one-week-old chicks compared to infection in six-week-old and uninfected flocks. All Salmonella isolates were resistant to ampicillin and erythromycin, while all isolates were sensitive to ciprofloxacin, chloramphenicol, and levofloxacin. The isolates also contained 10.53% (2/19) streptomycin, 10.53% (2/21) gentamicin, 15.79% (3/19) doxycycline, and 26.32% (5/19) lincomycin and colistin. The phenotypically resistant Salmonella samples against ampicillin, erythromycin, and macrolide harbored bla TEM , bla SHV , ermB, ereA, mphA, and ermB, respectively. This baseline data on Salmonella spp. prevalence, serotyping, and antibiotic profiles are combined to define the antimicrobial resistance to this endemic disease. Elucidation of the mechanisms underlying this drug resistance should be of general importance in understanding both the treatment and prevention of Salmonella infection in this part of Egypt.
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Affiliation(s)
- Ahmed Shalaby
- Department of Poultry and Rabbit Diseases, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33511, Egypt
| | - Mahmoud M. Ismail
- Department of Poultry and Rabbit Diseases, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33511, Egypt
| | - Hanem El-Sharkawy
- Department of Poultry and Rabbit Diseases, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33511, Egypt
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17
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El-Khoury C, Mansour E, Yuliandra Y, Lai F, Hawkins BA, Du JJ, Sundberg EJ, Sluis-Cremer N, Hibbs DE, Groundwater PW. The role of adjuvants in overcoming antibacterial resistance due to enzymatic drug modification. RSC Med Chem 2022; 13:1276-1299. [PMID: 36439977 PMCID: PMC9667779 DOI: 10.1039/d2md00263a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/16/2022] [Indexed: 02/03/2023] Open
Abstract
Antibacterial resistance is a prominent issue with monotherapy often leading to treatment failure in serious infections. Many mechanisms can lead to antibacterial resistance including deactivation of antibacterial agents by bacterial enzymes. Enzymatic drug modification confers resistance to β-lactams, aminoglycosides, chloramphenicol, macrolides, isoniazid, rifamycins, fosfomycin and lincosamides. Novel enzyme inhibitor adjuvants have been developed in an attempt to overcome resistance to these agents, only a few of which have so far reached the market. This review discusses the different enzymatic processes that lead to deactivation of antibacterial agents and provides an update on the current and potential enzyme inhibitors that may restore bacterial susceptibility.
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Affiliation(s)
- Christy El-Khoury
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Elissar Mansour
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Yori Yuliandra
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Bryson A Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine Pittsburgh PA 15213 USA
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Paul W Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
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18
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Ni S, Li C, Yu Y, Niu D, Zhu J, Yin D, Wang C, Zhang W, Jiang X, Ren J. Immobilization of EreB on Acid-Modified Palygorskite for Highly Efficient Degradation of Erythromycin. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11064. [PMID: 36078780 PMCID: PMC9518184 DOI: 10.3390/ijerph191711064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Erythromycin is one of the most commonly used macrolide antibiotics. However, its pollution of the ecosystem is a significant risk to human health worldwide. Currently, there are no effective and environmentally friendly methods to resolve this issue. Although erythromycin esterase B (EreB) specifically degrades erythromycin, its non-recyclability and fragility limit the large-scale application of this enzyme. In this work, palygorskite was selected as a carrier for enzyme immobilization. The enzyme was attached to palygorskite via a crosslinking reaction to construct an effective erythromycin-degradation material (i.e., EreB@modified palygorskite), which was characterized using FT-IR, SEM, XRD, and Brunauer-Emmett-Teller techniques. The results suggested the successful modification of the material and the loading of the enzyme. The immobilized enzyme had a higher stability over varying temperatures (25-65 °C) and pH values (6.5-10.0) than the free enzyme, and the maximum rate of reaction (Vmax) and the turnover number (kcat) of the enzyme increased to 0.01 mM min-1 and 169 min-1, respectively, according to the enzyme-kinetics measurements. The EreB@modified palygorskite maintained about 45% of its activity after 10 cycles, and degraded erythromycin in polluted water to 20 mg L-1 within 300 min. These results indicate that EreB could serve as an effective immobilizing carrier for erythromycin degradation at the industrial scale.
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Affiliation(s)
- Shensheng Ni
- Institute of Urban and Rural Mining, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Chunyu Li
- Institute of Urban and Rural Mining, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Yicheng Yu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, No. 101 Shanghai Road, Tongshan District, Xuzhou 221116, China
| | - Dongze Niu
- Institute of Urban and Rural Mining, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Jie Zhu
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Dongmin Yin
- Institute of Urban and Rural Mining, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Chongqing Wang
- Beijing General Station of Animal Husbandry, No. 21 Chaoqian Road, Changping District, Beijing 100101, China
| | - Wenfan Zhang
- Institute of Urban and Rural Mining, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Xingmei Jiang
- Bijie Institute of Animal Husbandry and Veterinary Sciences, De Gou Ma Jia Yuan, Qixingguan District, Bijie 551700, China
| | - Jianjun Ren
- Institute of Urban and Rural Mining, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No. 21 Gehu Road, Wujin District, Changzhou 213164, China
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19
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The discovery of multidrug resistant Staphylococcus aureus harboring novel SaRI isolated from retail foods. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Miklasińska-Majdanik M. Mechanisms of Resistance to Macrolide Antibiotics among Staphylococcus aureus. Antibiotics (Basel) 2021; 10:antibiotics10111406. [PMID: 34827344 PMCID: PMC8615237 DOI: 10.3390/antibiotics10111406] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/29/2022] Open
Abstract
Methicillin resistant Staphylococcus aureus strains pose a serious treatment problem because of their multi-drug resistance (MDR). In staphylococcal strains, resistance to macrolides, lincosamides, and streptogramin B (MLSB) correlates with resistance to methicillin. The rapid transmission of erm genes responsible for MLSB resistance has strongly limited the clinical application of traditional macrolides such as erythromycin. On the other hand, in the age of increasing insensitivity to antibiotics the idea of implementing a therapy based on older generation drugs brings hope that the spread of antibiotic resistance will be limited. A thorough understanding of the resistance mechanisms contributes to design of antibiotics that avoid bacterial insensitivity. This review highlights the mechanisms of action of macrolides and mechanism of resistance to these antibiotics among Staphylococcus aureus.
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Affiliation(s)
- Maria Miklasińska-Majdanik
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
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21
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The lanthipeptide biosynthetic clusters of the domain Archaea. Microbiol Res 2021; 253:126884. [PMID: 34628131 DOI: 10.1016/j.micres.2021.126884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 09/27/2021] [Indexed: 11/21/2022]
Abstract
Research on Archaea's secondary metabolites is still lagging behind that of Bacteria and Eukarya. Our goal was to contribute to this knowledge gap by analyzing the lanthipeptide's clusters in Archaea. As previously proposed, Archaea encodes only class II synthetases (LanMs), which we found to be confined to the class Halobacteria (also known as haloarchaea). In total, we analyzed the phylogeny and the domains of 42 LanMs. Four types were identified, and the majority of them belong to the CCG group due to their cyclization domain, which includes LanMs of Cyanobacteria. Putative cognate peptides were predicted for most of LanMs and are a very diverse group of molecules that share a Kx(Y/F)(D/E)xx(F/Y) motif in their leader peptides. According to their homology, some of them were categorized into subfamilies, including Halolancins, Haladacins, Haloferaxcins and Halobiforcins. Many LanM genes were associated with mobile genetic elements, and their vicinities mainly encode ABC and MFS transporters, tailoring enzymes and uncharacterized proteins. Our results suggest that the biosynthesis of lanthipeptides in haloarchaea can entail distinct enzymology that must lead to the production of peptides with novel structures and unpredicted biological and ecological roles. Finally, an Haloferax mediterranei knockout, lacking its three lanM genes, was generated, and it was concluded that its antimicrobial activity is not primarily related to the production of lanthipeptides.
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22
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Mohanty H, Pachpute S, Yadav RP. Mechanism of drug resistance in bacteria: efflux pump modulation for designing of new antibiotic enhancers. Folia Microbiol (Praha) 2021; 66:727-739. [PMID: 34431062 DOI: 10.1007/s12223-021-00910-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/10/2021] [Indexed: 11/21/2022]
Abstract
Drug resistance has now become a serious concern in the domain of microbial infection. Bacteria are becoming smarter by displaying a variety of mechanisms during drug resistance. It is not only helping bacteria to adapt nicely in adverse environment but it also makes a smart system for better availability of nutritional status for microorganisms. In this domain, pathogenic bacteria are extensively studied and their mechanism for drug resistance is well explored. The common modes in bacterial resistance include degradation of antibiotics by enzymes, antibiotic target modification or inactivation by enzymatic actions, complete replacement of antibiotic targets, quorum sensing (QS) mechanism, and efflux pump-based extrusion of antibiotics. In this review, various mechanisms of drug resistance in bacteria have been highlighted with giving the importance of efflux pumps. This can be explored as a knowledge source for the management of a variety of bacterial infections, related disease and vibrant clue for next-generation drug development.
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Affiliation(s)
- Harshita Mohanty
- MGMIHS OMICS Research Center, MGM Central Research Laboratory, MGM Medical College and Hospital, MGM Institute of Health Sciences, Sector 1, Kamothe, Navi Mumbai-410209, Maharashtra, India.,Department of Molecular Biology, MGM School of Biomedical Sciences, MGM Institute of Health Sciences, Sector 1, Kamothe, Navi Mumbai-410209, Maharashtra, India
| | - Samir Pachpute
- Department of Medical Microbiology, MGM Medical College and Hospital, MGM Institute of Health Sciences, Sector 1, Kamothe, Navi Mumbai-410209, Maharashtra, India
| | - Raman P Yadav
- MGMIHS OMICS Research Center, MGM Central Research Laboratory, MGM Medical College and Hospital, MGM Institute of Health Sciences, Sector 1, Kamothe, Navi Mumbai-410209, Maharashtra, India. .,Department of Molecular Biology, MGM School of Biomedical Sciences, MGM Institute of Health Sciences, Sector 1, Kamothe, Navi Mumbai-410209, Maharashtra, India.
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Bacterial Resistance to Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10050593. [PMID: 34067579 PMCID: PMC8157006 DOI: 10.3390/antibiotics10050593] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial pathogens as causative agents of infection constitute an alarming concern in the public health sector. In particular, bacteria with resistance to multiple antimicrobial agents can confound chemotherapeutic efficacy towards infectious diseases. Multidrug-resistant bacteria harbor various molecular and cellular mechanisms for antimicrobial resistance. These antimicrobial resistance mechanisms include active antimicrobial efflux, reduced drug entry into cells of pathogens, enzymatic metabolism of antimicrobial agents to inactive products, biofilm formation, altered drug targets, and protection of antimicrobial targets. These microbial systems represent suitable focuses for investigation to establish the means for their circumvention and to reestablish therapeutic effectiveness. This review briefly summarizes the various antimicrobial resistance mechanisms that are harbored within infectious bacteria.
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24
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Chen G, Gonzalez M, Jiang Z, Zhang Q, Wang G, Chen QH. An amide mimic of desTHPdactylolide: Total synthesis and antiproliferative evaluation. Bioorg Med Chem Lett 2021; 40:127970. [PMID: 33753258 DOI: 10.1016/j.bmcl.2021.127970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/04/2021] [Accepted: 03/13/2021] [Indexed: 10/21/2022]
Abstract
(-)-Zampanolide is a unique microtubule stabilizing agent (MSA) with covalent-binding mechanism and low nanomolar anitproliferative potency towards multi-drug resistant cancer cells. MSAs have a special connection with prostate cancer by inhibiting androgen receptor nuclear translocation. Zampanolide and the structurally related dactylolide have thus been sought after by us as lead compounds for development of anti-prostate cancer agents. DesTHPdactylolide is a simplified mimic of dactylolide and has previously been synthesized by us in both configurations, with the (17R) configuration being more potent in suppressing prostate cancer cell proliferation. The current study aims to synthesize an amide mimic of (17R) desTHPdactylolide that was anticipated to be metabolically more stable than (17R) desTHPdactylolide. To this end, the amide mimic has been successfully synthesized through a 26-step transformation from 2-butyn-1-ol. Our WST-1 cell proliferation assay in five human prostate cancer cell models indicated that the lactam moiety can serve as a bioisostere for the lactone in desTHPdactylolide.
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Affiliation(s)
- Guanglin Chen
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA 93740, United States
| | - Maricarmen Gonzalez
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA 93740, United States
| | - Ziran Jiang
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA 93740, United States
| | - Qiang Zhang
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, LA 70125, United States
| | - Guangdi Wang
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, LA 70125, United States
| | - Qiao-Hong Chen
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA 93740, United States.
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25
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Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance. Nat Chem Biol 2021; 17:412-420. [PMID: 33462493 PMCID: PMC7990689 DOI: 10.1038/s41589-020-00715-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/22/2020] [Accepted: 11/18/2020] [Indexed: 01/29/2023]
Abstract
Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases. Here, we present the crystal structure of the Erm-dimethylated 70S ribosome at 2.4 Å resolution, together with the structures of unmethylated 70S ribosome functional complexes alone or in combination with macrolides. Altogether, our structural data do not support previous models and, instead, suggest a principally new explanation of how A2058 dimethylation confers resistance to macrolides. Moreover, high-resolution structures of two macrolide antibiotics bound to the unmodified ribosome reveal a previously unknown role of the desosamine moiety in drug binding, laying a foundation for the rational knowledge-based design of macrolides that can overcome Erm-mediated resistance.
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26
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Oyegoke PI, Olayinka BO, Ehinmidu JO, Tytler BA. Molecular Characterization of Multidrug-resistant Bacteria Isolated From Patients With Pneumonia at Two Hospitals in North-West Nigeria. INTERNATIONAL JOURNAL OF EPIDEMIOLOGIC RESEARCH 2021. [DOI: 10.34172/ijer.2021.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background and aims: The spread of antimicrobial resistance (AMR) is a serious public health threat complicating treatment and resulting in prolonged hospitalization. The prevalence of AMR threat is not well defined due to the dearth of appropriate surveillance systems. This study sought to assess the prevalence of AMR among bacterial isolates from sputum specimens obtained from patients with pneumonia presenting at two secondary healthcare facilities in Zaria from June 1 to August 31, 2018. Methods: Standard methodology was followed in processing sputum samples that met the acceptance criteria. The antibiotic susceptibility patterns of bacterial pathogens cultured from sputum specimens obtained from June 1 to August 31, 2018) were evaluated using the recommendation of the Clinical and Laboratory Standards Institute. Finally, data were analyzed using descriptive statistics. Results: Acinetobacter spp. were the predominant pathogens accounting for 32% of recovered isolates, followed by Staphylococcus spp. (18%) and Klebsiella spp. (17%), respectively. AMR was found in 91% of the isolates. Most isolates were resistant to erythromycin (ERY) (80%) and amoxicillin (83.3%). Eventually, the multiple antibiotic resistance index ≥0.3 was observed in 76% of the isolates. Conclusion: Based on the findings, AMR rates were observed to be high, and may display a serious therapeutic challenge to the management of community-acquired pneumonia. Concerted efforts are needed to combat the worrisome AMR trends revealed in this study.
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Affiliation(s)
- Paul I Oyegoke
- Department of Pharmaceutical Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | - Busayo O Olayinka
- Department of Pharmaceutical Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | - Joseph O Ehinmidu
- Department of Pharmaceutical Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | - Babajide A Tytler
- Department of Pharmaceutics and Industrial Pharmacy, Ahmadu Bello University, Zaria, Nigeria
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27
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Zieliński M, Park J, Sleno B, Berghuis AM. Structural and functional insights into esterase-mediated macrolide resistance. Nat Commun 2021; 12:1732. [PMID: 33741980 PMCID: PMC7979712 DOI: 10.1038/s41467-021-22016-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/19/2021] [Indexed: 01/08/2023] Open
Abstract
Macrolides are a class of antibiotics widely used in both medicine and agriculture. Unsurprisingly, as a consequence of their exensive usage a plethora of resistance mechanisms have been encountered in pathogenic bacteria. One of these resistance mechanisms entails the enzymatic cleavage of the macrolides' macrolactone ring by erythromycin esterases (Eres). The most frequently identified Ere enzyme is EreA, which confers resistance to the majority of clinically used macrolides. Despite the role Eres play in macrolide resistance, research into this family enzymes has been sparse. Here, we report the first three-dimensional structures of an erythromycin esterase, EreC. EreC is an extremely close homologue of EreA, displaying more than 90% sequence identity. Two structures of this enzyme, in conjunction with in silico flexible docking studies and previously reported mutagenesis data allowed for the proposal of a detailed catalytic mechanism for the Ere family of enzymes, labeling them as metal-independent hydrolases. Also presented are substrate spectrum assays for different members of the Ere family. The results from these assays together with an examination of residue conservation for the macrolide binding site in Eres, suggests two distinct active site archetypes within the Ere enzyme family.
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Affiliation(s)
- Michał Zieliński
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Department of Biochemistry, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Barry Sleno
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montréal, QC, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
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28
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Nguyen PY, Carvalho G, Reis MAM, Oehmen A. A review of the biotransformations of priority pharmaceuticals in biological wastewater treatment processes. WATER RESEARCH 2021; 188:116446. [PMID: 33038717 DOI: 10.1016/j.watres.2020.116446] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 05/18/2023]
Abstract
Wastewater effluent discharges have been considered as one of the main sources of synthetic chemicals entering into the aquatic environment. Even though they occur at low concentrations, pharmaceutically active compounds (PhACs) can have an impact on ecological toxicity that affects aquatic organisms. Moreover, new regulations in development toward preserving water quality reinforces the increasing need to monitor and abate some PhACs in wastewater treatment plants (WWTPs), where they are typically only partially eliminated. Unlike most previous reviews, we have focussed on how the main biological and chemical molecular factors impact the biotransformations of key PhACs in biological WWTP processes. Biotransformations have been found to be an important contributor towards the removal of PhACs from WWTP effluents. This review paper critically assesses these aspects and the recent advances that have been achieved in wastewater treatment processes for biodegradation of 7 PhACs; namely the non-steroidal anti-inflammatory drug (NSAID) diclofenac (DCF); the macrolide antibiotics azithromycin (AZM), erythromycin (ERY) and clarithromycin (CLR); the two natural estrogens estrone (E1) and 17β-estradiol (E2), and the synthetic estrogen 17α-ethinylesradiol (EE2). These represent the micropollutants of the EU Watch list in Decision 2015/495/EU that are most relevant to WWTPs due to their frequent detection. The metabolic pathways, transformation products and impact of relevant factors to biological WWTP processes is addressed in this review. The biokinetics of PhAC biodegradation in different engineered bioprocesses is also discussed. Promising technologies and operational strategies that are likely to have a high impact on controlling PhAC releases are highlighted and future research needs are also proposed.
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Affiliation(s)
- P Y Nguyen
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Gilda Carvalho
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maria A M Reis
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Adrian Oehmen
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia.
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29
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Ren J, Deng L, Niu D, Wang Z, Fan B, Taoli H, Li Z, Zhang J, Li C. Isolation and identification of a novel erythromycin-degrading fungus, Curvularia sp. RJJ-5, and its degradation pathway. FEMS Microbiol Lett 2020; 368:6041717. [PMID: 33338238 DOI: 10.1093/femsle/fnaa215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Erythromycin pollution is an important risk to the ecosystem and human health worldwide. Thus, it is urgent to develop effective approaches to decontaminate erythromycin. In this study, we successfully isolated a novel erythromycin-degrading fungus from an erythromycin-contaminated site. The erythromycin biodegradation characteristics were investigated in mineral salt medium with erythromycin as the sole carbon and energy source. The metabolites of erythromycin degraded by fungus were identified and used to derive the degradation pathway. Based on morphological and phylogenetic analyses, the isolated strain was named Curvularia sp. RJJ-5 (MN759651). Optimal degradation conditions for strain RJJ-5 were 30°C, and pH 6.0 with 100 mg L-1 erythromycin substrate. The strain could degrade 75.69% erythromycin under this condition. The following metabolites were detected: 3-depyranosyloxy erythromycin A, 7,12-dyhydroxy-6-deoxyerythronolide B, 2,4,6,8,10,12-hexamethyl-3,5,6,11,12,13-hexahydroxy-9-ketopentadecanoic acid and cladinose. It was deduced that the erythromycin A was degraded to 3-depyranosyloxy erythromycin A by glycoside hydrolase in the initial reaction. These results imply that Curvularia sp. RJJ-5 is a novel erythromycin-degrading fungus that can hydrolyze erythromycin using a glycoside hydrolase and has great potential for removing erythromycin from mycelial dreg and the contaminated environment.
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Affiliation(s)
- Jianjun Ren
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Liujie Deng
- State Environmental Protection Antibiotic Mycelial Dreg Harmless Treatment and Resource Utilization Engineering Technology Center, Yili Chuanning Biotechnology Co., Ltd. No. 156 Alamutuya Country, Yining District, Yili 835000, China
| | - Dongze Niu
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Zhenzhu Wang
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Bo Fan
- School of Pharmaceutical Engineering and Life Science, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Huhe Taoli
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Zhijie Li
- State Environmental Protection Antibiotic Mycelial Dreg Harmless Treatment and Resource Utilization Engineering Technology Center, Yili Chuanning Biotechnology Co., Ltd. No. 156 Alamutuya Country, Yining District, Yili 835000, China
| | - Jin Zhang
- Lab of Agricultural and Environmental Microbiology, Hebei Cixin Environmental Technology Co., Ltd. No. 69 Nanhuan Road, Yongqing County, Langfang 065600, China
| | - Chunyu Li
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
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30
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Ren J, Wang Z, Deng L, Niu D, Fan B, Huhe T, Li Z, Zhang J, Li C. Biodegradation of erythromycin by Delftia lacustris RJJ-61 and characterization of its erythromycin esterase. J Basic Microbiol 2020; 61:55-62. [PMID: 33332633 DOI: 10.1002/jobm.202000613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 11/06/2022]
Abstract
The residual erythromycin in fermentation waste can pollute the environment and threaten human health. However, there are no effective approaches to remedy this issue. In this study, an erythromycin-degrading bacterium named RJJ-61 was isolated and identified as a strain of Delftia lacustris based on morphological and phylogenetic analyses. The degradation ability of this strain was also evaluated; it could degrade 45.18% of erythromycin at 35°C in 120 h. Furthermore, the key degradation gene ereA was cloned from strain RJJ-61 and expressed in Escherichia coli BL21; the molecular weight of the expressed protein was ~45 kDa. The enzyme activity of EreA was 108.0 mU ml-1 at 35°C and pH 7.0. Finally, the EreA protein was used to degrade erythromycin from mycelial dregs and 50% diluted solution, and the removal rates in them were 41.42% and 69.78%, respectively. In summary, D. lacustris RJJ-61 is a novel erythromycin-degrading strain that has great potential to remove erythromycin pollutants from the environment.
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Affiliation(s)
- Jianjun Ren
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, China.,National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, China
| | - Zhenzhu Wang
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, China.,National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, China
| | - Liujie Deng
- Yili Chuanning Biotechnology Co., Yili, China
| | - Dongze Niu
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, China.,National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, China
| | - Bo Fan
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Wujin District, Changzhou, China
| | - Taoli Huhe
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, China.,National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, China
| | - Zhenzhen Li
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Wujin District, Changzhou, China
| | - Jin Zhang
- Hebei Cixin Environmental Technology Co., Langfang, China
| | - Chunyu Li
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, China.,National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, China
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31
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Nadeem SF, Gohar UF, Tahir SF, Mukhtar H, Pornpukdeewattana S, Nukthamna P, Moula Ali AM, Bavisetty SCB, Massa S. Antimicrobial resistance: more than 70 years of war between humans and bacteria. Crit Rev Microbiol 2020; 46:578-599. [PMID: 32954887 DOI: 10.1080/1040841x.2020.1813687] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Development of antibiotic resistance in bacteria is one of the major issues in the present world and one of the greatest threats faced by mankind. Resistance is spread through both vertical gene transfer (parent to offspring) as well as by horizontal gene transfer like transformation, transduction and conjugation. The main mechanisms of resistance are limiting uptake of a drug, modification of a drug target, inactivation of a drug, and active efflux of a drug. The highest quantities of antibiotic concentrations are usually found in areas with strong anthropogenic pressures, for example medical source (e.g., hospitals) effluents, pharmaceutical industries, wastewater influents, soils treated with manure, animal husbandry and aquaculture (where antibiotics are generally used as in-feed preparations). Hence, the strong selective pressure applied by antimicrobial use has forced microorganisms to evolve for survival. The guts of animals and humans, wastewater treatment plants, hospital and community effluents, animal husbandry and aquaculture runoffs have been designated as "hotspots for AMR genes" because the high density of bacteria, phages, and plasmids in these settings allows significant genetic exchange and recombination. Evidence from the literature suggests that the knowledge of antibiotic resistance in the population is still scarce. Tackling antimicrobial resistance requires a wide range of strategies, for example, more research in antibiotic production, the need of educating patients and the general public, as well as developing alternatives to antibiotics (briefly discussed in the conclusions of this article).
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Affiliation(s)
- Syeda Fatima Nadeem
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Umar Farooq Gohar
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Syed Fahad Tahir
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | | | - Pikunthong Nukthamna
- Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,College of Research Methodology and Cognitive Science, Burapha University, Chonburi, Thailand
| | - Ali Muhammed Moula Ali
- Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | | | - Salvatore Massa
- Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
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32
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Baral B, Mozafari MR. Strategic Moves of "Superbugs" Against Available Chemical Scaffolds: Signaling, Regulation, and Challenges. ACS Pharmacol Transl Sci 2020; 3:373-400. [PMID: 32566906 PMCID: PMC7296549 DOI: 10.1021/acsptsci.0c00005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Indexed: 12/12/2022]
Abstract
Superbugs' resistivity against available natural products has become an alarming global threat, causing a rapid deterioration in public health and claiming tens of thousands of lives yearly. Although the rapid discovery of small molecules from plant and microbial origin with enhanced bioactivity has provided us with some hope, a rapid hike in the resistivity of superbugs has proven to be the biggest therapeutic hurdle of all times. Moreover, several distinct mechanisms endowed by these notorious superbugs make them immune to these antibiotics subsequently causing our antibiotic wardrobe to be obsolete. In this unfortunate situation, though the time frame for discovering novel "hit molecules" down the line remains largely unknown, our small hope and untiring efforts injected in hunting novel chemical scaffolds with unique molecular targets using high-throughput technologies may safeguard us against these life-threatening challenges to some extent. Amid this crisis, the current comprehensive review highlights the present status of knowledge, our search for bacteria Achilles' heel, distinct molecular signaling that an opportunistic pathogen bestows to trespass the toxicity of antibiotics, and facile strategies and appealing therapeutic targets of novel drugs. Herein, we also discuss multidimensional strategies to combat antimicrobial resistance.
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Affiliation(s)
- Bikash Baral
- Department
of Biochemistry, University of Turku, Tykistökatu 6, Turku, Finland
| | - M. R. Mozafari
- Australasian
Nanoscience and Nanotechnology Initiative, 8054 Monash University LPO, Clayton, Victoria 3168, Australia
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33
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The Novel Macrolide Resistance Genes mef(D), msr(F), and msr(H) Are Present on Resistance Islands in Macrococcus canis, Macrococcus caseolyticus, and Staphylococcus aureus. Antimicrob Agents Chemother 2020; 64:AAC.00160-20. [PMID: 32122903 DOI: 10.1128/aac.00160-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/27/2020] [Indexed: 12/27/2022] Open
Abstract
Chromosomal resistance islands containing the methicillin resistance gene mecD (McRI mecD ) have been reported in Macrococcus caseolyticus Here, we identified novel macrolide resistance genes in Macrococcus canis on similar elements, called McRI msr These elements were also integrated into the 3' end of the 30S ribosomal protein S9 gene (rpsI), delimited by characteristic attachment (att) sites, and carried a related site-specific integrase gene (int) at the 5' end. They carried novel macrolide resistance genes belonging to the msr family of ABC subfamily F (ABC-F)-type ribosomal protection protein [msr(F) and msr(H)] and the macrolide efflux mef family [mef(D)]. Highly related mef(D)-msr(F) fragments were found on diverse McRI msr elements in M. canis, M. caseolyticus, and Staphylococcus aureus Another McRI msr -like element identified in an M. canis strain lacked the classical att site at the 3' end and carried the msr(H) gene but no neighboring mef gene. The expression of the novel resistance genes in S. aureus resulted in a low-to-moderate increase in the MIC of erythromycin but not streptogramin B. In the mef(D)-msr(F) operon, the msr(F) gene was shown to be the crucial determinant for macrolide resistance. The detection of circular forms of McRI msr and the mef(D)-msr(F) fragment suggested mobility of both the island and the resistance gene subunit. The discovery of McRI msr in different Macrococcus species and S. aureus indicates that these islands have a potential for dissemination of antibiotic resistance within the Staphylococcaceae family.
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34
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Liu M, Feng P, Kakade A, Yang L, Chen G, Yan X, Ni H, Liu P, Kulshreshtha S, Abomohra AEF, Li X. Reducing residual antibiotic levels in animal feces using intestinal Escherichia coli with surface-displayed erythromycin esterase. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:122032. [PMID: 31955024 DOI: 10.1016/j.jhazmat.2020.122032] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/11/2019] [Accepted: 01/05/2020] [Indexed: 06/10/2023]
Abstract
Antibiotics are widely used in livestock and poultry industries, which results in large quantities of antibiotic residues in manure that influences subsequent treatments. In this study, an Escherichia coli strain was engineered to display erythromycin esterase on its cell surface. The engineered strain (E. coli ereA) efficiently degraded erythromycin by opening the macrocyclic 14-membered lactone ring in solution. Erythromycin (50 mg/L) was completely degraded in a solution by E. coli ereA (1 × 109 CFU/mL) within 24 h. E. coli ereA retained over 86.7 % of the initial enzyme activity after 40 days of storage at 25 °C, and 78.5 % of the initial activity after seven repeated batch reactions in solution at 25 °C. Mice were fed with E. coli ereA and real-time quantitative PCR data showed that E. coli ereA colonized in the mice large intestine. The mice group fed E. coli ereA exhibited 83.13 % decrease in erythromycin levels in their feces compared with the mice group not fed E. coli ereA. E. coli ereA eliminated antibiotics from the source preventing its release into the environment. The surface-engineered strain therefore is an effective alternative agent for treating recalcitrant antibiotics, and has the potential to be applied in livestock and poultry industries.
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Affiliation(s)
- Minrui Liu
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Pengya Feng
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Apurva Kakade
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China; Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
| | - Ling Yang
- Huangshi Product Quality Supervision and Inspection Institute, Huangshi 435000, Hubei, China
| | - Gang Chen
- Huangshi Product Quality Supervision and Inspection Institute, Huangshi 435000, Hubei, China
| | - Xiaojun Yan
- Institute of Forensic Science, Department of Public Security Hunan Province, Changsha 410001, Hunan, China
| | - Hongyuhang Ni
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Pu Liu
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Saurabh Kulshreshtha
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
| | | | - Xiangkai Li
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China.
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35
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Jeong DW, Lee B, Heo S, Oh Y, Heo G, Lee JH. Two genes involved in clindamycin resistance of Bacillus licheniformis and Bacillus paralicheniformis identified by comparative genomic analysis. PLoS One 2020; 15:e0231274. [PMID: 32271828 PMCID: PMC7144989 DOI: 10.1371/journal.pone.0231274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/19/2020] [Indexed: 11/19/2022] Open
Abstract
We evaluated the minimum inhibitory concentrations of clindamycin and erythromycin toward 98 Bacillus licheniformis strains isolated from several types of fermented soybean foods manufactured in several districts of Korea. First, based on recent taxonomic standards for bacteria, the 98 strains were separated into 74 B. licheniformis strains and 24 B. paralicheniformis strains. Both species exhibited profiles of erythromycin resistance as an acquired characteristic. B. licheniformis strains exhibited acquired clindamycin resistance, while B. paralicheniformis strains showed unimodal clindamycin resistance, indicating an intrinsic characteristic. Comparative genomic analysis of five strains showing three different patterns of clindamycin and erythromycin resistance identified 23S rRNA (adenine 2058-N6)-dimethyltransferase gene ermC and spermidine acetyltransferase gene speG as candidates potentially involved in clindamycin resistance. Functional analysis of these genes using B. subtilis as a host showed that ermC contributes to cross-resistance to clindamycin and erythromycin, and speG confers resistance to clindamycin. ermC is located in the chromosomes of strains showing clindamycin and erythromycin resistance and no transposable element was identified in its flanking regions. The acquisition of ermC might be attributable to a homologous recombination. speG was identified in not only the five genome-analyzed strains but also eight strains randomly selected from the 98 test strains, and deletions in the structural gene or putative promoter region caused clindamycin sensitivity, which supports the finding that the clindamycin resistance of Bacillus species is an intrinsic property.
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Affiliation(s)
- Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
| | - Byunghoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, Republic of Korea
| | - Sojeong Heo
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
| | - Yeongmin Oh
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, Republic of Korea
| | - Ganghun Heo
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, Republic of Korea
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, Republic of Korea
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36
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Das B, Verma J, Kumar P, Ghosh A, Ramamurthy T. Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms. Vaccine 2020; 38 Suppl 1:A83-A92. [DOI: 10.1016/j.vaccine.2019.06.031] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/11/2019] [Accepted: 06/04/2019] [Indexed: 11/29/2022]
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37
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Biodegradation of antibiotics: The new resistance determinants – part II. N Biotechnol 2020; 54:13-27. [DOI: 10.1016/j.nbt.2019.08.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 07/17/2019] [Accepted: 08/11/2019] [Indexed: 02/06/2023]
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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39
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Cen Y, Liu Y, Xue Y, Zheng Y. Immobilization of Enzymes in/on Membranes and their Applications. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900439] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yu‐Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of Technology Hangzhou 310014 People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Yu‐Xiao Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of Technology Hangzhou 310014 People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Ya‐Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of Technology Hangzhou 310014 People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Yu‐Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of Technology Hangzhou 310014 People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of Technology Hangzhou 310014 People's Republic of China
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40
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Zhou R, Zeng S, Hou D, Liu J, Weng S, He J, Huang Z. Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment. J Environ Sci (China) 2019; 80:248-256. [PMID: 30952342 DOI: 10.1016/j.jes.2019.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis (contig Intestine_364647) and Enterococcus faecium (contig Intestine_80272) carrying efrA, efrB and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica (contig Sediment_825143) and Escherichia coli (contig Sediment_188430) carrying mexB and APH(3')-IIa were found in sediments, and Laribacter hongkongensis (contig Water_478168 and Water_369477), Shigella sonnei (contig Water_880246), and Acinetobacter baumannii (contig Water_525520) carrying sul1, sul2, ereA, qacH, OXA-21, and mphD were found in pond water. Mobile genetic elements (MGEs) analysis indicated that horizontal gene transfer (HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.
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Affiliation(s)
- Renjun Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shaoping Weng
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China; School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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Agrawal A, Ravikumar R, Varun CN, Kumar M, Chatterjee O, Advani J, Gopalakrishnan L, Nagaraj S, Mohanty V, Patil AH, Sreeramulu B, Malik A, Pinto SM, Prasad TSK. Global Proteome Profiling Reveals Drug-Resistant Traits in Elizabethkingia meningoseptica: An Opportunistic Nosocomial Pathogen. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:318-326. [PMID: 31120389 DOI: 10.1089/omi.2019.0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Elizabethkingia meningoseptica is Gram-negative, rod-shaped opportunistic bacterial pathogen increasingly reported in hospital-acquired outbreaks. This bacterium is well known to thrive in the hospital environment. One of the leading causes of meningitis in pediatric and immune-compromised patients, E. meningoseptica has been noted as a "pathogen of interest" in the context of nosocomial diseases associated with device-related infections in particular. This pathogen's multidrug-resistant phenotype and attendant lack of adequate molecular mechanistic data limit the current approaches for its effective management in hospitals and public health settings. This study provides the global proteome of E. meningoseptica. The reference strain E. meningoseptica ATCC 13253 was used for proteomic analysis using high-resolution Fourier transform mass spectrometry. The study provided translational evidence for 2506 proteins of E. meningoseptica. We identified multiple metallo-β-lactamases, transcriptional regulators, and efflux transporter proteins associated with multidrug resistance. A protein Car D, which is an enzyme of the carbapenem synthesis pathway, was also discovered in E. meningoseptica. Further, the proteomics data were harnessed for refining the genome annotation. We discovered 39 novel protein-coding genes and corrected four existing translations using proteogenomic workflow. Novel translations reported in this study enhance the molecular data on this organism, thus improving current databases. We believe that the in-depth proteomic data presented in this study offer a platform for accelerated research on this pathogen. The identification of multiple proteins, particularly those involved in drug resistance, offers new future opportunities to design novel and specific antibiotics against infections caused by E. meningoseptica.
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Affiliation(s)
- Archana Agrawal
- 1 Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Raju Ravikumar
- 1 Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Chakrakodi N Varun
- 1 Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Manish Kumar
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Oishi Chatterjee
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India.,3 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,4 School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Jayshree Advani
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Lathika Gopalakrishnan
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India.,3 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,5 Manipal Academy of Higher Education, Manipal, India
| | - Sowmya Nagaraj
- 1 Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Varshasnata Mohanty
- 3 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Arun H Patil
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India.,3 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,6 School of Biotechnology, KIIT (Deemed to be University), Bhubaneswar, India
| | | | - Aubid Malik
- 8 CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Sneha M Pinto
- 3 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India.,3 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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42
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Gomes C, Ruiz-Roldán L, Mateu J, Ochoa TJ, Ruiz J. Azithromycin resistance levels and mechanisms in Escherichia coli. Sci Rep 2019; 9:6089. [PMID: 30988366 PMCID: PMC6465286 DOI: 10.1038/s41598-019-42423-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 04/01/2019] [Indexed: 11/10/2022] Open
Abstract
Despite azithromycin being used in some countries to treat infections caused by Gram-negative pathogens, no resistance breakpoint for Escherichia coli exists. The aim of this study was to analyse the levels and mechanisms of azithromycin resistance in E. coli. The presence of chromosomal (rplD, rplV and 23S rRNA) mutations, 10 macrolide resistance genes (MRGs) and efflux pump overexpression was determined in 343 E. coli isolates. Overall, 89 (25.9%) isolates had MICs ≥ 32 mg/L to azithromycin, decreasing to 42 (12.2%) when assayed in the presence of Phe-Arg-β-Napthylamide, with 35 of these 42 possessing at least one MRG. Efflux pumps played a role in azithromycin resistance affecting the Minimal Inhibitory Concentration (MIC) levels of 91.2% isolates whereas chromosomal alterations seem to have a minimal role. At least one MRG was found in 22.7% of the isolates with mph(A) being the most commonly found gene. The mph(A) gene plays the main role in the development of azithromycin resistance and 93% of the mph(A)-carrying isolates showed a MIC of 32 mg/L. In the absence of a specific resistance breakpoint our results suggest a MIC of 32 mg/L to be considered in order to detect isolates carrying mechanisms able to confer azithromycin resistance.
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Affiliation(s)
- Cláudia Gomes
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Lidia Ruiz-Roldán
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,Molecular Microbiology Area, CIBIR, Logroño, Spain
| | - Judit Mateu
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Theresa J Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru.,Center for Infectious Diseases, University of Texas School of Public Health, Houston, Texas, USA
| | - Joaquim Ruiz
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.
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43
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Ramakrishnan B, Venkateswarlu K, Sethunathan N, Megharaj M. Local applications but global implications: Can pesticides drive microorganisms to develop antimicrobial resistance? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:177-189. [PMID: 30445319 DOI: 10.1016/j.scitotenv.2018.11.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 05/07/2023]
Abstract
Pesticides are an important agricultural input, and the introduction of new active ingredients with increased efficiencies drives their higher production and consumption worldwide. Inappropriate application and storage of these chemicals often contaminate plant tissues, air, water, or soil environments. The presence of pesticides can lead to developing tolerance, resistance or persistence and even the capabilities to degrade them by the microbiomes of theses environments. The pesticide-degrading microorganisms gain and employ several mechanisms for attraction (chemotaxis), membrane transport systems, efflux pumps, enzymes and genetical make-up with plasmid and chromosome encoded catabolic genes for degradation. Even the evolution and the mechanisms of inheritance for pesticide-degradation as a functional trait in several microorganisms are beginning to be understood. Because of the commonalities in the microbial responses of sensing and uptake, and adaptation due to the selection pressures of pesticides and antimicrobial substances including antibiotics, the pesticide-degraders have higher chances of possessing antimicrobial resistance as a surplus functional trait. This review critically examines the probabilities of pesticide contamination of soil and foliage, the knowledge gaps in the regulation and storage of pesticide chemicals, and the human implications of pesticide-degrading microorganisms with antimicrobial resistance in the global strategy of 'One Health'.
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Affiliation(s)
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapur 515055, India
| | - Nambrattil Sethunathan
- Flat No. 103, Ushodaya Apartments, Sri Venkateswara Officers Colony, Ramakrishnapuram, Secunderabad 500056, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER) and Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), University of Newcastle, ATC Building, Callaghan, NSW 2308, Australia.
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44
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Trilles R, Beglov D, Chen Q, He H, Wireman R, Reed A, Chennamadhavuni S, Panek JS, Brown LE, Vajda S, Porco JA, Kelley MR, Georgiadis MM. Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1. J Med Chem 2019; 62:1971-1988. [PMID: 30653918 DOI: 10.1021/acs.jmedchem.8b01529] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential base excision repair enzyme that is upregulated in a number of cancers, contributes to resistance of tumors treated with DNA-alkylating or -oxidizing agents, and has recently been identified as an important therapeutic target. In this work, we identified hot spots for binding of small organic molecules experimentally in high resolution crystal structures of APE1 and computationally through the use of FTMAP analysis ( http://ftmap.bu.edu/ ). Guided by these hot spots, a library of drug-like macrocycles was docked and then screened for inhibition of APE1 endonuclease activity. In an iterative process, hot-spot-guided docking, characterization of inhibition of APE1 endonuclease, and cytotoxicity of cancer cells were used to design next generation macrocycles. To assess target selectivity in cells, selected macrocycles were analyzed for modulation of DNA damage. Taken together, our studies suggest that macrocycles represent a promising class of compounds for inhibition of APE1 in cancer cells.
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Affiliation(s)
- Richard Trilles
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - Dmitri Beglov
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | | | | | | | | | - Spandan Chennamadhavuni
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - James S Panek
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - Lauren E Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - Sandor Vajda
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - John A Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | | | - Millie M Georgiadis
- Department of Chemistry and Chemical Biology, Purdue School of Science , Indiana University-Purdue University Indianapolis , Indianapolis , Indiana 46202 , United States
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45
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Molecules that Inhibit Bacterial Resistance Enzymes. Molecules 2018; 24:molecules24010043. [PMID: 30583527 PMCID: PMC6337270 DOI: 10.3390/molecules24010043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/14/2022] Open
Abstract
Antibiotic resistance mediated by bacterial enzymes constitutes an unmet clinical challenge for public health, particularly for those currently used antibiotics that are recognized as "last-resort" defense against multidrug-resistant (MDR) bacteria. Inhibitors of resistance enzymes offer an alternative strategy to counter this threat. The combination of inhibitors and antibiotics could effectively prolong the lifespan of clinically relevant antibiotics and minimize the impact and emergence of resistance. In this review, we first provide a brief overview of antibiotic resistance mechanism by bacterial secreted enzymes. Furthermore, we summarize the potential inhibitors that sabotage these resistance pathways and restore the bactericidal activity of inactive antibiotics. Finally, the faced challenges and an outlook for the development of more effective and safer resistance enzyme inhibitors are discussed.
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46
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Jang SY, Hwang J, Kim BS, Lee EY, Oh BH, Kim MH. Structural basis of inactivation of Ras and Rap1 small GTPases by Ras/Rap1-specific endopeptidase from the sepsis-causing pathogen Vibrio vulnificus. J Biol Chem 2018; 293:18110-18122. [PMID: 30282804 PMCID: PMC6254334 DOI: 10.1074/jbc.ra118.004857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
Multifunctional autoprocessing repeats-in-toxin (MARTX) toxins are secreted by Gram-negative bacteria and function as primary virulence-promoting macromolecules that deliver multiple cytopathic and cytotoxic effector domains into the host cytoplasm. Among these effectors, Ras/Rap1-specific endopeptidase (RRSP) catalyzes the sequence-specific cleavage of the Switch I region of the cellular substrates Ras and Rap1 that are crucial for host innate immune defenses during infection. To dissect the molecular basis underpinning RRSP-mediated substrate inactivation, we determined the crystal structure of an RRSP from the sepsis-causing bacterial pathogen Vibrio vulnificus (VvRRSP). Structural and biochemical analyses revealed that VvRRSP is a metal-independent TIKI family endopeptidase composed of an N-terminal membrane-localization and substrate-recruitment domain (N lobe) connected via an inter-lobe linker to the C-terminal active site-coordinating core β-sheet-containing domain (C lobe). Structure-based mutagenesis identified the 2His/2Glu catalytic residues in the core catalytic domain that are shared with other TIKI family enzymes and that are essential for Ras processing. In vitro KRas cleavage assays disclosed that deleting the N lobe in VvRRSP causes complete loss of enzymatic activity. Endogenous Ras cleavage assays combined with confocal microscopy analysis of HEK293T cells indicated that the N lobe functions both in membrane localization via the first α-helix and in substrate assimilation by altering the functional conformation of the C lobe to facilitate recruitment of cellular substrates. Collectively, these results indicate that RRSP is a critical virulence factor that robustly inactivates Ras and Rap1 and augments the pathogenicity of invading bacteria via the combined effects of its N and C lobes.
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Affiliation(s)
- Song Yee Jang
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141,; the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and
| | - Jungwon Hwang
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and.
| | - Byoung Sik Kim
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and; the Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea
| | - Eun-Young Lee
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and
| | - Byung-Ha Oh
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141,.
| | - Myung Hee Kim
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and.
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47
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Biancucci M, Minasov G, Banerjee A, Herrera A, Woida PJ, Kieffer MB, Bindu L, Abreu-Blanco M, Anderson WF, Gaponenko V, Stephen AG, Holderfield M, Satchell KJF. The bacterial Ras/Rap1 site-specific endopeptidase RRSP cleaves Ras through an atypical mechanism to disrupt Ras-ERK signaling. Sci Signal 2018; 11:eaat8335. [PMID: 30279169 PMCID: PMC6309442 DOI: 10.1126/scisignal.aat8335] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Ras-extracellular signal-regulated kinase pathway is critical for controlling cell proliferation, and its aberrant activation drives the growth of various cancers. Because many pathogens produce toxins that inhibit Ras activity, efforts to develop effective Ras inhibitors to treat cancer could be informed by studies of Ras inhibition by pathogens. Vibrio vulnificus causes fatal infections in a manner that depends on multifunctional autoprocessing repeats-in-toxin, a toxin that releases bacterial effector domains into host cells. One such domain is the Ras/Rap1-specific endopeptidase (RRSP), which site-specifically cleaves the Switch I domain of the small GTPases Ras and Rap1. We solved the crystal structure of RRSP and found that its backbone shares a structural fold with the EreA/ChaN-like superfamily of enzymes. Unlike other proteases in this family, RRSP is not a metalloprotease. Through nuclear magnetic resonance analysis and nucleotide exchange assays, we determined that the processing of KRAS by RRSP did not release any fragments or cause KRAS to dissociate from its bound nucleotide but instead only locally affected its structure. However, this structural alteration of KRAS was sufficient to disable guanine nucleotide exchange factor-mediated nucleotide exchange and prevent KRAS from binding to RAF. Thus, RRSP is a bacterial effector that represents a previously unrecognized class of protease that disconnects Ras from its signaling network while inducing limited structural disturbance in its target.
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Affiliation(s)
- Marco Biancucci
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alfa Herrera
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Patrick J Woida
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew B Kieffer
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lakshman Bindu
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Maria Abreu-Blanco
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrew G Stephen
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Matthew Holderfield
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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48
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An automated on-line turbulent flow liquid-chromatography technology coupled to a high resolution mass spectrometer LTQ-Orbitrap for suspect screening of antibiotic transformation products during microalgae wastewater treatment. J Chromatogr A 2018; 1568:57-68. [DOI: 10.1016/j.chroma.2018.06.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/07/2018] [Accepted: 06/10/2018] [Indexed: 12/26/2022]
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49
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Golkar T, Zieliński M, Berghuis AM. Look and Outlook on Enzyme-Mediated Macrolide Resistance. Front Microbiol 2018; 9:1942. [PMID: 30177927 PMCID: PMC6109786 DOI: 10.3389/fmicb.2018.01942] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 07/31/2018] [Indexed: 01/14/2023] Open
Abstract
Since their discovery in the early 1950s, macrolide antibiotics have been used in both agriculture and medicine. Specifically, macrolides such as erythromycin and azithromycin have found use as substitutes for β-lactam antibiotics in patients with penicillin allergies. Given the extensive use of this class of antibiotics it is no surprise that resistance has spread among pathogenic bacteria. In these bacteria different mechanisms of resistance have been observed. Frequently observed are alterations in the target of macrolides, i.e., the ribosome, as well as upregulation of efflux pumps. However, drug modification is also increasingly observed. Two classes of enzymes have been implicated in macrolide detoxification: macrolide phosphotransferases and macrolide esterases. In this review, we present a comprehensive overview on what is known about macrolide resistance with an emphasis on the macrolide phosphotransferase and esterase enzymes. Furthermore, we explore how this information can assist in addressing resistance to macrolide antibiotics.
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Affiliation(s)
- Tolou Golkar
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Michał Zieliński
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC, Canada.,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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50
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Markley JL, Wencewicz TA. Tetracycline-Inactivating Enzymes. Front Microbiol 2018; 9:1058. [PMID: 29899733 PMCID: PMC5988894 DOI: 10.3389/fmicb.2018.01058] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/04/2018] [Indexed: 12/25/2022] Open
Abstract
Tetracyclines have been foundational antibacterial agents for more than 70 years. Renewed interest in tetracycline antibiotics is being driven by advancements in tetracycline synthesis and strategic scaffold modifications designed to overcome established clinical resistance mechanisms including efflux and ribosome protection. Emerging new resistance mechanisms, including enzymatic antibiotic inactivation, threaten recent progress on bringing these next-generation tetracyclines to the clinic. Here we review the current state of knowledge on the structure, mechanism, and inhibition of tetracycline-inactivating enzymes.
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Affiliation(s)
- Jana L Markley
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, United States
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, United States
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