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Fang XM, Li J, Wang NF, Zhang T, Yu LY. Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Ålesund (Svalbard, High Arctic). ENVIRONMENTAL RESEARCH 2024; 262:119788. [PMID: 39159777 DOI: 10.1016/j.envres.2024.119788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/29/2024] [Accepted: 08/12/2024] [Indexed: 08/21/2024]
Abstract
Research on the microbiome and resistome in polar environments, such as the Arctic, is crucial for understanding the emergence and spread of antibiotic resistance genes (ARGs) in the environment. In this study, soil and reindeer faeces samples collected from Ny-Ålesund (Svalbard, High Arctic) were examined to analyze the microbiome, ARGs, and biocide/metal resistance genes (BMRGs). The dominant phyla in both soil and faeces were Pseudomonadota, Actinomycetota, and Bacteroidota. A total of 2618 predicted Open Reading Frames (ORFs) containing antibiotic resistance genes (ARGs) were detected. These ARGs belong to 162 different genes across 17 antibiotic classes, with rifamycin and multidrug resistance genes being the most prevalent. We focused on investigating antibiotic resistance mechanisms in the Ny-Ålesund environment by analyzing the resistance genes and their biological pathways. Procrustes analysis demonstrated a significant correlation between bacterial communities and ARG/BMRG profiles in soil and faeces samples. Correlation analysis revealed that Pseudomonadota contributed most to multidrug and triclosan resistance, while Actinomycetota were predominant contributors to rifamycin and aminoglycoside resistance. The geochemical factors, SiO42- and NH4+, were found to significantly influence the microbial composition and ARG distribution in the soil samples. Analysis of ARGs, BMRGs, virulence factors (VFs), and pathogens identified potential health risks associated with certain bacteria, such as Cryobacterium and Pseudomonas, due to the presence of different genetic elements. This study provided valuable insights into the molecular mechanisms and geochemical factors contributing to antibiotic resistance and enhanced our understanding of the evolution of antibiotic resistance genes in the environment.
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Affiliation(s)
- Xiao-Mei Fang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P.R. China; Division for Medicinal Microorganism-Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, 100050, P.R. China
| | - Jun Li
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P.R. China; Division for Medicinal Microorganism-Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, 100050, P.R. China
| | - Neng-Fei Wang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276005, P.R. China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P.R. China; Division for Medicinal Microorganism-Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, 100050, P.R. China.
| | - Li-Yan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P.R. China; Division for Medicinal Microorganism-Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, 100050, P.R. China.
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2
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Amoros J, Fattar N, Buysse M, Louni M, Bertaux J, Bouchon D, Duron O. Reassessment of the genetic basis of natural rifampin resistance in the genus Rickettsia. Microbiologyopen 2024; 13:e1431. [PMID: 39082505 PMCID: PMC11289727 DOI: 10.1002/mbo3.1431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/12/2024] [Accepted: 07/20/2024] [Indexed: 08/03/2024] Open
Abstract
Rickettsia, a genus of obligate intracellular bacteria, includes species that cause significant human diseases. This study challenges previous claims that the Leucine-973 residue in the RNA polymerase beta subunit is the primary determinant of rifampin resistance in Rickettsia. We investigated a previously untested Rickettsia species, R. lusitaniae, from the Transitional group and found it susceptible to rifampin, despite possessing the Leu-973 residue. Interestingly, we observed the conservation of this residue in several rifampin-susceptible species across most Rickettsia phylogenetic groups. Comparative genomics revealed potential alternative resistance mechanisms, including additional amino acid variants that could hinder rifampin binding and genes that could facilitate rifampin detoxification through efflux pumps. Importantly, the evolutionary history of Rickettsia genomes indicates that the emergence of natural rifampin resistance is phylogenetically constrained within the genus, originating from ancient genetic features shared among a unique set of closely related Rickettsia species. Phylogenetic patterns appear to be the most reliable predictors of natural rifampin resistance, which is confined to a distinct monophyletic subclade known as Massiliae. The distinctive features of the RNA polymerase beta subunit in certain untested Rickettsia species suggest that R. raoultii, R. amblyommatis, R. gravesii, and R. kotlanii may also be naturally rifampin-resistant species.
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Affiliation(s)
- Julien Amoros
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
| | - Noor Fattar
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
| | - Marie Buysse
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
| | | | | | | | - Olivier Duron
- MIVEGEC, CNRS, IRDUniversity of MontpellierMontpellierFrance
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3
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Mashayekhi-Sardoo H, Rezaee R, Riahi-Zanjani B, Karimi G. Alleviation of microcystin-leucine arginine -induced hepatotoxicity: An updated overview. Toxicon 2024; 243:107715. [PMID: 38636613 DOI: 10.1016/j.toxicon.2024.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024]
Abstract
OBJECTIVES Contamination of surface waters is a major health threat for all living creatures. Some types of blue-green algae that naturally occur in fresh water, are able to produce various toxins, like Microcystins (MCs). Microcystin-leucine arginine (MC-LR) produced by Microcystis aeruginosa is the most toxic and abundant isoforms of MCs, and it causes hepatotoxicity. The present article reviews preclinical experiments examined different treatments, including herbal derivatives, dietary supplements and drugs against MC-LR hepatotoxicity. METHODS We searched scientific databases Web of Science, Embase, Medline (PubMed), Scopus, and Google Scholar using relevant keywords to find suitable studies until November 2023. RESULTS MC-LR through Organic anion transporting polypeptide superfamily transporters (OATPs) penetrates and accumulates in hepatocytes, and it inhibits protein phosphatases (PP1 and PP2A). Consequently, MC-LR disturbs many signaling pathways and induces oxidative stress thus damages cellular macromolecules. Some protective agents, especially plants rich in flavonoids, and natural supplements, as well as chemoprotectants were shown to diminish MC-LR hepatotoxicity. CONCLUSION The reviewed agents through blocking the OATP transporters (nontoxic nostocyclopeptide-M1, captopril, and naringin), then inhibition of MC-LR uptake (naringin, rifampin, cyclosporin-A, silymarin and captopril), and finally at restoration of PPAse activity (silybin, quercetin, morin, naringin, rifampin, captopril, azo dyes) exert hepatoprotective effect against MC-LR.
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Affiliation(s)
- Habibeh Mashayekhi-Sardoo
- Bio Environmental Health Hazard Research Center, Jiroft University of Medical Sciences, Jiroft, Iran; Jiroft University of Medical Sciences, Jiroft, Iran.
| | - Ramin Rezaee
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Bamdad Riahi-Zanjani
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Gholamreza Karimi
- Pharmaceutical Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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4
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Chen J, Cui Y, Zhang S, Wu B, Han J, Xiang H. Unveiling the repressive mechanism of a PPS-like regulator (PspR) in polyhydroxyalkanoates biosynthesis network. Appl Microbiol Biotechnol 2024; 108:265. [PMID: 38498113 PMCID: PMC10948481 DOI: 10.1007/s00253-024-13100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024]
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a type of polyhydroxyalkanoates (PHA) that exhibits numerous outstanding properties and is naturally synthesized and elaborately regulated in various microorganisms. However, the regulatory mechanism involving the specific regulator PhaR in Haloferax mediterranei, a major PHBV production model among Haloarchaea, is not well understood. In our previous study, we showed that deletion of the phosphoenolpyruvate (PEP) synthetase-like (pps-like) gene activates the cryptic phaC genes in H. mediterranei, resulting in enhanced PHBV accumulation. In this study, we demonstrated the specific function of the PPS-like protein as a negative regulator of phaR gene expression and PHBV synthesis. Chromatin immunoprecipitation (ChIP), in situ fluorescence reporting system, and in vitro electrophoretic mobility shift assay (EMSA) showed that the PPS-like protein can bind to the promoter region of phaRP. Computational modeling revealed a high structural similarity between the rifampin phosphotransferase (RPH) protein and the PPS-like protein, which has a conserved ATP-binding domain, a His domain, and a predicted DNA-binding domain. Key residues within this unique DNA-binding domain were subsequently validated through point mutation and functional evaluations. Based on these findings, we concluded that PPS-like protein, which we now renamed as PspR, has evolved into a repressor capable of regulating the key regulator PhaR, and thereby modulating PHBV synthesis. This regulatory network (PspR-PhaR) for PHA biosynthesis is likely widespread among haloarchaea, providing a novel approach to manipulate haloarchaea as a production platform for high-yielding PHA. KEY POINTS: • The repressive mechanism of a novel inhibitor PspR in the PHBV biosynthesis was demonstrated • PspR is widespread among the PHA accumulating haloarchaea • It is the first report of functional conversion from an enzyme to a trans-acting regulator in haloarchaea.
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Affiliation(s)
- Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yinglu Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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5
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Sudzinová P, Šanderová H, Koval' T, Skálová T, Borah N, Hnilicová J, Kouba T, Dohnálek J, Krásný L. What the Hel: recent advances in understanding rifampicin resistance in bacteria. FEMS Microbiol Rev 2023; 47:fuac051. [PMID: 36549665 PMCID: PMC10719064 DOI: 10.1093/femsre/fuac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
Rifampicin is a clinically important antibiotic that binds to, and blocks the DNA/RNA channel of bacterial RNA polymerase (RNAP). Stalled, nonfunctional RNAPs can be removed from DNA by HelD proteins; this is important for maintenance of genome integrity. Recently, it was reported that HelD proteins from high G+C Actinobacteria, called HelR, are able to dissociate rifampicin-stalled RNAPs from DNA and provide rifampicin resistance. This is achieved by the ability of HelR proteins to dissociate rifampicin from RNAP. The HelR-mediated mechanism of rifampicin resistance is discussed here, and the roles of HelD/HelR in the transcriptional cycle are outlined. Moreover, the possibility that the structurally similar HelD proteins from low G+C Firmicutes may be also involved in rifampicin resistance is explored. Finally, the discovery of the involvement of HelR in rifampicin resistance provides a blueprint for analogous studies to reveal novel mechanisms of bacterial antibiotic resistance.
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Affiliation(s)
- Petra Sudzinová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Koval'
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Tereza Skálová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Nabajyoti Borah
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Kouba
- Cryogenic Electron Microscopy Research-Service Group, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16000 Prague, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
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6
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Zheng M, Lupoli TJ. Counteracting antibiotic resistance enzymes and efflux pumps. Curr Opin Microbiol 2023; 75:102334. [PMID: 37329679 DOI: 10.1016/j.mib.2023.102334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
Bacterial pathogens are constantly evolving new resistance mechanisms against antibiotics; hence, strategies to potentiate existing antibiotics or combat mechanisms of resistance using adjuvants are always in demand. Recently, inhibitors have been identified that counteract enzymatic modification of the drugs isoniazid and rifampin, which have implications in the study of multi-drug-resistant mycobacteria. A wealth of structural studies on efflux pumps from diverse bacteria has also fueled the design of new small-molecule and peptide-based agents to prevent the active transport of antibiotics. We envision that these findings will inspire microbiologists to apply existing adjuvants to clinically relevant resistant strains, or to use described platforms to discover novel antibiotic adjuvant scaffolds.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
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7
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 248] [Impact Index Per Article: 248.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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8
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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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9
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The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions. Catalysts 2022. [DOI: 10.3390/catal12111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.
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10
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Wan L, Li H, Sun G, Zhang L, Xu H, Su F, He S, Xiao F. Mutational Pattern Induced by 5-Fluorouracil and Oxaliplatin in the Gut Microbiome. Front Microbiol 2022; 13:841458. [PMID: 35572679 PMCID: PMC9101311 DOI: 10.3389/fmicb.2022.841458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
Chemotherapeutic agents, such as 5-fluorouracil (5-FU) and oxaliplatin (Oxi), can not only kill the cancer cell but also influence the proliferation of gut microbiota; however, the interaction between these drugs and gut microbiota remains poorly understood. In this study, we developed a powerful framework for taxonomy composition and genomic variation analysis to investigate the mutagenesis effect and proliferation influence of chemotherapeutic agents, such as 5-FU and Oxi, on gut microbiota and the interaction between these drugs and gut microbiota during chemotherapy. Using the gut microbiome data, we detected 1.45 million variations among the chemotherapy groups and found the drugs significantly affected mutation signatures of gut microbiota. Oxi notably increased transversion rate, whereas 5-FU reduced the rate. Traits related to cell division and nutrient mobilization showed evidence of strong selection pressure from chemotherapeutic agents. In addition, drug-associated bacteriome shift patterns and functional alterations were found: the metabolism changes in the 5-FU group implied that gut microbiota could provide additional nicotinamide adenine dinucleotide (NAD+) to inhibit cancer cell autophagy; in the Oxi group, the ribosome and lysine biosynthesis genes were obviously enriched. Our study provides a blueprint for characterizing the role of microbes and drug–microbe interaction in the gut microbiota response to chemotherapy.
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Affiliation(s)
- Li Wan
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongtao Xu
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing, China
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11
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Martinez Pomier K, Akimoto M, Byun JA, Khamina M, Melacini G. Allosteric Regulation of Cyclic Nucleotide Dependent Protein Kinases. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kinases include a wide variety of valuable drug targets, but full therapeutic exploitation requires a high degree of selectivity. A promising avenue to engineer the desired kinase selectivity relies on allosteric sites. Here we provide a focused minireview of recent progress in allosteric modulation of cyclic nucleotide-dependent kinases, including protein kinases A and G. We show how apparently diverse emerging concepts such as allosteric pluripotency, allosteric non-additive binding and uncompetitive allosteric inhibition are all manifestations of complex conformational ensembles. Such ensembles include not only the typical apo-inactive and effector-bound-active states, but also mixed intermediates that feature attributes of the former states within a single molecule. We also discuss how allosteric responses are amplified by aggregation processes, thus establishing a novel interface between the signaling and amyloid fields. Finally, we critically evaluate the challenges and opportunities for clinical translation opened by these emerging allosteric concepts.
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Affiliation(s)
| | | | - Jung Ah Byun
- McMaster University, 3710, Hamilton, Ontario, Canada
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12
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Kanglemycin A Can Overcome Rifamycin Resistance Caused by ADP-Ribosylation by Arr Protein. Antimicrob Agents Chemother 2021; 65:e0086421. [PMID: 34606341 PMCID: PMC8597724 DOI: 10.1128/aac.00864-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rifamycins, such as rifampicin (Rif), are potent inhibitors of bacterial RNA polymerase (RNAP) and are widely used antibiotics. Rifamycin resistance is usually associated with mutations in RNAP that preclude rifamycin binding. However, some bacteria have a type of ADP-ribosyl transferases, Arr, which ADP-ribosylate rifamycin molecules, thus inactivating their antimicrobial activity. Here, we directly show that ADP-ribosylation abolishes inhibition of transcription by rifampicin, the most widely used rifamycin antibiotic. We also show that a natural rifamycin, kanglemycin A (KglA), which has a unique sugar moiety at the ansa chain close to the Arr modification site, does not bind to Arr from Mycobacterium smegmatis and thus is not susceptible to inactivation. We, found, however, that kanglemycin A can still be ADP-ribosylated by the Arr of an emerging pathogen, Mycobacterium abscessus. Interestingly, the only part of Arr that exhibits no homology between the species is the part that sterically clashes with the sugar moiety of kanglemycin A in M. smegmatis Arr. This suggests that M. abscessus has encountered KglA or rifamycin with a similar sugar modification in the course of evolution. The results show that KglA could be an effective antimicrobial against some of the Arr-encoding bacteria.
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13
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Rifamycin antibiotics and the mechanisms of their failure. J Antibiot (Tokyo) 2021; 74:786-798. [PMID: 34400805 DOI: 10.1038/s41429-021-00462-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Rifamycins are a class of antibiotics that were first discovered in 1957 and are known for their use in treating tuberculosis (TB). Rifamycins exhibit bactericidal activity against many Gram-positive and Gram-negative bacteria by inhibiting RNA polymerase (RNAP); however, resistance is prevalent and the mechanisms range from primary target modification and antibiotic inactivation to cytoplasmic exclusion. Further, phenotypic resistance, in which only a subpopulation of bacteria grow in concentrations exceeding their minimum inhibitory concentration, and tolerance, which is characterized by reduced rates of bacterial cell death, have been identified as additional causes of rifamycin failure. Here we summarize current understanding and recent developments regarding this critical antibiotic class.
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Renn D, Shepard L, Vancea A, Karan R, Arold ST, Rueping M. Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. Front Microbiol 2021; 12:732856. [PMID: 34777282 PMCID: PMC8578733 DOI: 10.3389/fmicb.2021.732856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/05/2021] [Indexed: 11/23/2022] Open
Abstract
The Red Sea is a marine environment with unique chemical characteristics and physical topographies. Among the various habitats offered by the Red Sea, the deep-sea brine pools are the most extreme in terms of salinity, temperature and metal contents. Nonetheless, the brine pools host rich polyextremophilic bacterial and archaeal communities. These microbial communities are promising sources for various classes of enzymes adapted to harsh environments - extremozymes. Extremozymes are emerging as novel biocatalysts for biotechnological applications due to their ability to perform catalytic reactions under harsh biophysical conditions, such as those used in many industrial processes. In this review, we provide an overview of the extremozymes from different Red Sea brine pools and discuss the overall biotechnological potential of the Red Sea proteome.
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Affiliation(s)
- Dominik Renn
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Organic Chemistry, RWTH Aachen, Aachen, Germany
| | - Lera Shepard
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ram Karan
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging (ExMI), University Clinic, RWTH Aachen, Aachen, Germany
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Liu H, Prajapati V, Prajapati S, Bais H, Lu J. Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes. Front Genet 2021; 12:724217. [PMID: 34659348 PMCID: PMC8514880 DOI: 10.3389/fgene.2021.724217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
Bacillus amyloliquefaciens is a gram-positive, nonpathogenic, endospore-forming, member of a group of free-living soil bacteria with a variety of traits including plant growth promotion, production of antifungal and antibacterial metabolites, and production of industrially important enzymes. We have attempted to reconstruct the biogeographical structure according to functional traits and the evolutionary lineage of B. amyloliquefaciens using comparative genomics analysis. All the available 96 genomes of B. amyloliquefaciens strains were curated from the NCBI genome database, having a variety of important functionalities in all sectors keeping a high focus on agricultural aspects. In-depth analysis was carried out to deduce the orthologous gene groups and whole-genome similarity. Pan genome analysis revealed that shell genes, soft core genes, core genes, and cloud genes comprise 17.09, 5.48, 8.96, and 68.47%, respectively, which demonstrates that genomes are very different in the gene content. It also indicates that the strains may have flexible environmental adaptability or versatile functions. Phylogenetic analysis showed that B. amyloliquefaciens is divided into two clades, and clade 2 is further dived into two different clusters. This reflects the difference in the sequence similarity and diversification that happened in the B. amyloliquefaciens genome. The majority of plant-associated strains of B. amyloliquefaciens were grouped in clade 2 (73 strains), while food-associated strains were in clade 1 (23 strains). Genome mining has been adopted to deduce antimicrobial resistance and virulence genes and their prevalence among all strains. The genes tmrB and yuaB codes for tunicamycin resistance protein and hydrophobic coat forming protein only exist in clade 2, while clpP, which codes for serine proteases, is only in clade 1. Genome plasticity of all strains of B. amyloliquefaciens reflects their adaption to different niches.
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Affiliation(s)
- Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Vimalkumar Prajapati
- Division of Microbiology and Environmental, Biotechnology, Aspee Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, India
| | - Shobha Prajapati
- SVP-A School of Sardar Vallabhbhai National Institute of Technology, Surat, India
| | - Harsh Bais
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Surette MD, Spanogiannopoulos P, Wright GD. The Enzymes of the Rifamycin Antibiotic Resistome. Acc Chem Res 2021; 54:2065-2075. [PMID: 33877820 DOI: 10.1021/acs.accounts.1c00048] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rifamycin antibiotics include the WHO essential medicines rifampin, rifabutin, and rifapentine. These are semisynthetic derivatives of the natural product rifamycins, originally isolated from the soil bacterium Amycolatopsis rifamycinica. These antibiotics are primarily used to treat mycobacterial infections, including tuberculosis. Rifamycins act by binding to the β-subunit of bacterial RNA polymerase, inhibiting transcription, which results in cell death. These antibiotics consist of a naphthalene core spanned by a polyketide ansa bridge. This structure presents a unique 3D configuration that engages RNA polymerase through a series of hydrogen bonds between hydroxyl groups linked to the naphthalene core and C21 and C23 of the ansa bridge. This binding occurs not in the enzyme active site where template-directed RNA synthesis occurs but instead in the RNA exit tunnel, thereby blocking productive formation of full-length RNA. In their clinical use to treat tuberculosis, resistance to rifamycin antibiotics arises principally from point mutations in RNA polymerase that decrease the antibiotic's affinity for the binding site in the RNA exit tunnel. In contrast, the rifamycin resistome of environmental mycobacteria and actinomycetes is much richer and diverse. In these organisms, rifamycin resistance includes many different enzymatic mechanisms that modify and alter the antibiotic directly, thereby inactivating it. These enzymes include ADP ribosyltransferases, glycosyltransferases, phosphotransferases, and monooxygenases.ADP ribosyltransferases catalyze group transfer of ADP ribose from the cofactor NAD+, which is more commonly deployed for metabolic redox reactions. ADP ribose is transferred to the hydroxyl linked to C23 of the antibiotic, thereby sterically blocking productive interaction with RNA polymerase. Like ADP ribosyltransferases, rifamycin glycosyl transferases also modify the hydroxyl of position C23 of rifamycins, transferring a glucose moiety from the donor molecule UDP-glucose. Unlike other antibiotic resistance kinases that transfer the γ-phosphate of ATP to inactivate antibiotics such as aminoglycosides or macrolides, rifamycin phosphotransferases are ATP-dependent dikinases. These enzymes transfer the β-phosphate of ATP to the C21 hydroxyl of the rifamycin ansa bridge. The result is modification of a critical RNA polymerase binding group that blocks productive complex formation. On the other hand, rifamycin monooxygenases are FAD-dependent enzymes that hydroxylate the naphthoquinone core. The result of this modification is untethering of the ansa chain from the naphthyl moiety, disrupting the essential 3D shape necessary for productive RNA polymerase binding and inhibition that leads to cell death.All of these enzymes have homologues in bacterial metabolism that either are their direct precursors or share common ancestors to the resistance enzyme. The diversity of these resistance mechanisms, often redundant in individual bacterial isolates, speaks to the importance of protecting RNA polymerase from these compounds and validates this enzyme as a critical antibiotic target.
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Affiliation(s)
- Matthew D. Surette
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Center for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 3Z5, Canada
| | - Peter Spanogiannopoulos
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Center for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 3Z5, Canada
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Center for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 3Z5, Canada
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Brands S, Brass HUC, Klein AS, Sikkens JG, Davari MD, Pietruszka J, Ruff AJ, Schwaneberg U. KnowVolution of prodigiosin ligase PigC towards condensation of short-chain prodiginines. Catal Sci Technol 2021. [DOI: 10.1039/d0cy02297g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
One round of KnowVolution enhanced the catalytic activity of prodigiosin ligase PigC with short-chain monopyrroles, opening access to anticancer prodiginines.
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Affiliation(s)
- Stefanie Brands
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Hannah U. C. Brass
- Institute of Bioorganic Chemistry
- Bioeconomy Science Center (BioSC)
- Heinrich Heine University Düsseldorf
- 52426 Jülich
- Germany
| | - Andreas S. Klein
- Institute of Bioorganic Chemistry
- Bioeconomy Science Center (BioSC)
- Heinrich Heine University Düsseldorf
- 52426 Jülich
- Germany
| | - Jarno G. Sikkens
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry
- Bioeconomy Science Center (BioSC)
- Heinrich Heine University Düsseldorf
- 52426 Jülich
- Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
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Terekhov SS, Mokrushina YA, Nazarov AS, Zlobin A, Zalevsky A, Bourenkov G, Golovin A, Belogurov A, Osterman IA, Kulikova AA, Mitkevich VA, Lou HJ, Turk BE, Wilmanns M, Smirnov IV, Altman S, Gabibov AG. A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding. SCIENCE ADVANCES 2020; 6:eaaz9861. [PMID: 32637600 PMCID: PMC7314540 DOI: 10.1126/sciadv.aaz9861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities are self-controlled by repertoires of lethal agents, the antibiotics. In their turn, these antibiotics are regulated by bioscavengers that are selected in the course of evolution. Kinase-mediated phosphorylation represents one of the general strategies for the emergence of antibiotic resistance. A new subfamily of AmiN-like kinases, isolated from the Siberian bear microbiome, inactivates antibiotic amicoumacin by phosphorylation. The nanomolar substrate affinity defines AmiN as a phosphotransferase with a unique catalytic efficiency proximal to the diffusion limit. Crystallographic analysis and multiscale simulations revealed a catalytically perfect mechanism providing phosphorylation exclusively in the case of a closed active site that counteracts substrate promiscuity. AmiN kinase is a member of the previously unknown subfamily representing the first evidence of a specialized phosphotransferase bioscavenger.
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Affiliation(s)
- Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anton S. Nazarov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zlobin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Arthur Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | | | - Andrey Golovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexandra A. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | | | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Arizona State University, Tempe, AZ, USA
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
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Dias MF, da Rocha Fernandes G, Cristina de Paiva M, Christina de Matos Salim A, Santos AB, Amaral Nascimento AM. Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings. WATER RESEARCH 2020; 174:115630. [PMID: 32105997 DOI: 10.1016/j.watres.2020.115630] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 05/09/2023]
Abstract
Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. blaKPC, blaGES, blaIMP, blaVIM, blaSPM and blaNDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.
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Affiliation(s)
- Marcela França Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | | | | | | | - Alexandre Bueno Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
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Jiang W, Yang W, Zhao X, Wang N, Ren H. Klebsiella pneumoniae presents antimicrobial drug resistance for β-lactam through the ESBL/PBP signaling pathway. Exp Ther Med 2020; 19:2449-2456. [PMID: 32256721 PMCID: PMC7086219 DOI: 10.3892/etm.2020.8498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Overuse and misuse of antibiotics leads to antibiotic resistance which has become a significant public health concern. Klebsiella pneumoniae is the most common pathogenic bacteria underlying nosocomial infections due to the expression of virulence factors and occurrence of antibiotic resistance. Evidence indicates that β-lactamase is involved in the antibiotic resistance of Klebsiella pneumoniae to β-lactam antibiotics. The aim of the present study was to investigate the association between the molecular biological mechanisms of antibiotic resistance of Klebsiella pneumoniae and extended-spectrum β-lactamase (ESBL). In order to assess temporal trends in prevalence and antimicrobial susceptibility, Klebsiella pneumoniae bacteria were isolated and the ESBL expression level was analyzed. Susceptibility tests were performed using automated systems. The β-lactam-resistance in Klebsiella pneumoniae was assessed by the β-lactam agar screen plate and respective MIC values were evaluated using E-test strips. The confirmatory disk diffusion methods were applied for phenotypic identification of the ESBL production of Klebsiella pneumoniae. The results showed that Klebsiella pneumoniae bacteria exhibited higher ESBL production after treatment with β-lactam compared to the control. The ESBL gene expression was upregulated in Klebsiella pneumoniae after treatment with β-lactam. Results identified that penicillin-binding proteins (PBPs) were associated with the growth and resistance to β-lactams. Zinc finger nuclease markedly inhibited the antibiotic resistance of Klebsiella pneumoniae to β-lactam. PBP knockdown abolished the inhibitory effects of zinc finger nuclease on the growth of Klebsiella pneumoniae induced by β-lactam antibiotic treatment. In conclusion, these results suggest that the resistance of Klebsiella pneumoniae bacteria to antimicrobial drugs is through the ESBL signaling pathway, which indicates that ESBL may be a potential target for abolishing resistance to β-lactam.
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Affiliation(s)
- Wei Jiang
- Department of Infectious Disease, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Wenjie Yang
- Department of Transplantation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Xuequn Zhao
- Department of Transplantation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Na Wang
- Department of Infectious Disease, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Haixia Ren
- Department of Pharmaceutical Preparation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
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21
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Wright GD. Environmental and clinical antibiotic resistomes, same only different. Curr Opin Microbiol 2019; 51:57-63. [DOI: 10.1016/j.mib.2019.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/10/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
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Unusual Phosphoenolpyruvate (PEP) Synthetase-Like Protein Crucial to Enhancement of Polyhydroxyalkanoate Accumulation in Haloferax mediterranei Revealed by Dissection of PEP-Pyruvate Interconversion Mechanism. Appl Environ Microbiol 2019; 85:AEM.00984-19. [PMID: 31350314 DOI: 10.1128/aem.00984-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022] Open
Abstract
Phosphoenolpyruvate (PEP)/pyruvate interconversion is a major metabolic point in glycolysis and gluconeogenesis and is catalyzed by various sets of enzymes in different Archaea groups. In this study, we report the key enzymes that catalyze the anabolic and catabolic directions of the PEP/pyruvate interconversion in Haloferax mediterranei The in silico analysis showed the presence of a potassium-dependent pyruvate kinase (PYKHm [HFX_0773]) and two phosphoenol pyruvate synthetase (PPS) candidates (PPSHm [HFX_0782] and a PPS homolog protein named PPS-like [HFX_2676]) in this strain. Expression of the pyk Hm gene and pps Hm was induced by glycerol and pyruvate, respectively; whereas the pps-like gene was not induced at all. Similarly, genetic analysis and enzyme activities of purified proteins showed that PYKHm catalyzed the conversion from PEP to pyruvate and that PPSHm catalyzed the reverse reaction, while PPS-like protein displayed no function in PEP/pyruvate interconversion. Interestingly, knockout of the pps-like gene led to a 70.46% increase in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) production. The transcriptome sequencing (RNA-Seq) and quantitative reverse transcription-PCR (qRT-PCR) results showed that many genes responsible for PHBV monomer supply and for PHBV synthesis were upregulated in a pps-like gene deletion strain and thereby improved PHBV accumulation. Additionally, our phylogenetic evidence suggested that PPS-like protein diverged from PPS enzyme and evolved as a distinct protein with novel function in haloarchaea. Our findings attempt to fill the gaps in central metabolism of Archaea by providing comprehensive information about key enzymes involved in the haloarchaeal PEP/pyruvate interconversion, and we also report a high-yielding PHBV strain with great future potentials.IMPORTANCE Archaea, the third domain of life, have evolved diversified metabolic pathways to cope with their extreme habitats. Phosphoenol pyruvate (PEP)/pyruvate interconversion during carbohydrate metabolism is one such important metabolic process that is highly differentiated among Archaea However, this process is still uncharacterized in the haloarchaeal group. Haloferax mediterranei is a well-studied haloarchaeon that has the ability to produce polyhydroxyalkanoates (PHAs) under unbalanced nutritional conditions. In this study, we identified the key enzymes involved in this interconversion and discussed their differences with their counterparts from other members of the Archaea and Bacteria domains. Notably, we found a novel protein, phosphoenolpyruvate synthetase-like (PPS-like), which exhibited high homology to PPS enzyme. However, PPS-like protein has evolved some distinct sequence features and functions, and strikingly the corresponding gene deletion helped to enhance poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) synthesis significantly. Overall, we have filled the gap in knowledge about PEP/pyruvate interconversion in haloarchaea and reported an efficient strategy for improving PHBV production in H. mediterranei.
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Wencewicz TA. Crossroads of Antibiotic Resistance and Biosynthesis. J Mol Biol 2019; 431:3370-3399. [PMID: 31288031 DOI: 10.1016/j.jmb.2019.06.033] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.
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Affiliation(s)
- Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA.
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24
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Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
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Pyta K, Janas A, Szukowska M, Pecyna P, Jaworska M, Gajecka M, Bartl F, Przybylski P. Synthesis, docking and antibacterial studies of more potent amine and hydrazone rifamycin congeners than rifampicin. Eur J Med Chem 2019; 167:96-104. [PMID: 30769243 DOI: 10.1016/j.ejmech.2019.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/18/2019] [Accepted: 02/03/2019] [Indexed: 12/24/2022]
Abstract
New rifamycin congeners (1-33) with incorporated amine and hydrazone substituents leading to lipophilic and/or basic nature and altered rigidity of modified C(3) arm were synthesized and structurally characterized in detail. NMR spectroscopic studies at different temperatures indicate two types of structures of rifamycin congeners that are realized in solution: zwitterionic and non-ionic forms in dependence of the basicity of modified C(3) arm. The presence of rifamycin congeners in these two possible forms has a significant impact on the physico-chemical parameters such as lipophilicity (clogP) and water solubility and different binding mode of the C(3) arm of antibiotic at RNAP binding pocket (molecular target) leading to different antibacterial potency. The highest antibacterial potency against S. aureus (including MRSA and MLSB strains) and S. epidermidis strains, even higher than reference rifampicin (Rif) and rifaximin (Rifx) antibiotics, was found for rifamycin congeners bearing at the C(3) arm relatively rigid and basic substituents (bipiperidine and guanidine groups). These modifications provide favorable docking mode and excellent water solubility resulting in high potency (MICs 0.0078 μg/mL what gives ∼ 8.5 nM), irrespective whether rifamycin congener is a tertiary amine (15) or hydrazone (29). In turn, for a higher antibacterial potency of rifamycin congeners against E. faecalis strain (MICs 0.5 μg/mL that is 0.6 μM) as compared to Rif and Rifx, the most crucial factors are: bulkiness and the lipophilic character of the end of the C(3) rebuilt arm.
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Affiliation(s)
- Krystian Pyta
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Anna Janas
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Monika Szukowska
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Paulina Pecyna
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland
| | - Marcelina Jaworska
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland
| | - Marzena Gajecka
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland; Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Franz Bartl
- Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, Institut für Biologie, Biophysikalische Chemie, Invalidenstr. 42, 10099, Berlin, Germany
| | - Piotr Przybylski
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland.
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26
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Taylor ZW, Chamberlain AR, Raushel FM. Substrate Specificity and Chemical Mechanism for the Reaction Catalyzed by Glutamine Kinase. Biochemistry 2018; 57:5447-5455. [PMID: 30142271 DOI: 10.1021/acs.biochem.8b00811] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni, a leading cause of gastroenteritis worldwide, has a unique O-methyl phosphoramidate (MeOPN) moiety attached to its capsular polysaccharide. Investigations into the biological role of MeOPN have revealed that it contributes to the pathogenicity of C. jejuni, and this modification is important for the colonization of C. jejuni. Previously, the reactions catalyzed by four enzymes (Cj1418-Cj1415) from C. jejuni that are required for the biosynthesis of the phosphoramidate modification have been elucidated. Cj1418 (l-glutamine kinase) catalyzes the formation of the initial phosphoramidate bond with the ATP-dependent phosphorylation of the amide nitrogen of l-glutamine. Here we show that Cj1418 catalyzes the phosphorylation of l-glutamine through a three-step reaction mechanism via the formation of covalent pyrophosphorylated ( Enz-X-Pβ-Pγ) and phosphorylated ( Enz-X-Pβ) intermediates. In the absence of l-glutamine, the enzyme was shown to catalyze a positional isotope exchange (PIX) reaction within β-[18O4]-ATP in support of the formation of the Enz-X-Pβ-Pγintermediate. In the absence of ATP, the enzyme was shown to catalyze a molecular isotope exchange (MIX) reaction between l-glutamine phosphate and [15N-amide]-l-glutamine in direct support of the Enz-X-Pβintermediate. The active site nucleophile has been identified as His-737 based on the lack of activity of the H737N mutant and amino acid sequence comparisons. The enzyme was shown to also catalyze the phosphorylation of d-glutamine, γ-l-glutamyl hydroxamate, γ-l-glutamyl hydrazide, and β-l-aspartyl hydroxamate, in addition to l-glutamine.
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Affiliation(s)
- Zane W Taylor
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States
| | - Alexandra R Chamberlain
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States.,Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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27
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Shin JH, Eom H, Song WJ, Rho M. Integrative metagenomic and biochemical studies on rifamycin ADP-ribosyltransferases discovered in the sediment microbiome. Sci Rep 2018; 8:12143. [PMID: 30108275 PMCID: PMC6092378 DOI: 10.1038/s41598-018-30547-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/30/2018] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance is a serious and growing threat to human health. The environmental microbiome is a rich reservoir of resistomes, offering opportunities to discover new antibiotic resistance genes. Here we demonstrate an integrative approach of utilizing gene sequence and protein structural information to characterize unidentified genes that are responsible for the resistance to the action of rifamycin antibiotic rifampin, a first-line antimicrobial agent to treat tuberculosis. Biochemical characterization of four environmental metagenomic proteins indicates that they are adenosine diphosphate (ADP)-ribosyltransferases and effective in the development of resistance to FDA-approved rifamycins. Our analysis suggests that even a single residue with low sequence conservation plays an important role in regulating the degrees of antibiotic resistance. In addition to advancing our understanding of antibiotic resistomes, this work demonstrates the importance of an integrative approach to discover new metagenomic genes and decipher their biochemical functions.
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Affiliation(s)
- Jae Hong Shin
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
| | - Hyunuk Eom
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Woon Ju Song
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea.
- Department of Biomedical Informatics, Hanyang University, Seoul, Korea.
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28
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You Z, Liu X, Zhang S, Wang Y. Characterization of a prodigiosin synthetase PigC from Serratia marcescens jx-1 and its application in prodigiosin analogue synthesis. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.01.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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29
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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: 83] [Impact Index Per Article: 13.8] [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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30
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Koteva K, Cox G, Kelso JK, Surette MD, Zubyk HL, Ejim L, Stogios P, Savchenko A, Sørensen D, Wright GD. Rox, a Rifamycin Resistance Enzyme with an Unprecedented Mechanism of Action. Cell Chem Biol 2018; 25:403-412.e5. [PMID: 29398560 DOI: 10.1016/j.chembiol.2018.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/07/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
Abstract
Rifamycin monooxygenases (Rox) are present in a variety of environmental bacteria and are associated with decomposition of the clinically utilized antibiotic rifampin. Here we report the structure and function of a drug-inducible rox gene from Streptomyces venezuelae, which encodes a class A flavoprotein monooxygenase that inactivates a broad range of rifamycin antibiotics. Our findings describe a mechanism of rifamycin inactivation initiated by monooxygenation of the 2-position of the naphthyl group, which subsequently results in ring opening and linearization of the antibiotic. The result is an antibiotic that no longer adopts the basket-like structure essential for binding to the RNA exit tunnel of the target RpoB, thereby providing the molecular logic of resistance. This unique mechanism of enzymatic inactivation underpins the broad spectrum of rifamycin resistance mediated by Rox enzymes and presents a new antibiotic resistance mechanism not yet seen in microbial antibiotic detoxification.
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Affiliation(s)
- Kalinka Koteva
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Georgina Cox
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Jayne K Kelso
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Matthew D Surette
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Haley L Zubyk
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Linda Ejim
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5G 1L6, Canada; Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Dan Sørensen
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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31
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The complex resistomes of Paenibacillaceae reflect diverse antibiotic chemical ecologies. ISME JOURNAL 2017; 12:885-897. [PMID: 29259290 DOI: 10.1038/s41396-017-0017-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/17/2017] [Accepted: 11/05/2017] [Indexed: 12/31/2022]
Abstract
The ecology of antibiotic resistance involves the interplay of a long natural history of antibiotic production in the environment, and the modern selection of resistance in pathogens through human use of these drugs. Important components of the resistome are intrinsic resistance genes of environmental bacteria, evolved and acquired over millennia, and their mobilization, which drives dissemination in pathogens. Understanding the dynamics and evolution of resistance across bacterial taxa is essential to address the current crisis in drug-resistant infections. Here we report the exploration of antibiotic resistance in the Paenibacillaceae prompted by our discovery of an ancient intrinsic resistome in Paenibacillus sp. LC231, recovered from the isolated Lechuguilla cave environment. Using biochemical and gene expression analysis, we have mined the resistome of the second member of the Paenibacillaceae family, Brevibacillus brevis VM4, which produces several antimicrobial secondary metabolites. Using phylogenomics, we show that Paenibacillaceae resistomes are in flux, evolve mostly independent of secondary metabolite biosynthetic diversity, and are characterized by cryptic, redundant, pseudoparalogous, and orthologous genes. We find that in contrast to pathogens, mobile genetic elements are not significantly responsible for resistome remodeling. This offers divergent modes of resistome development in pathogens and environmental bacteria.
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32
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Complementary uses of small angle X-ray scattering and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1623-1630. [PMID: 28743534 DOI: 10.1016/j.bbapap.2017.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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33
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Taylor ZW, Brown HA, Narindoshvili T, Wenzel CQ, Szymanski CM, Holden HM, Raushel FM. Discovery of a Glutamine Kinase Required for the Biosynthesis of the O-Methyl Phosphoramidate Modifications Found in the Capsular Polysaccharides of Campylobacter jejuni. J Am Chem Soc 2017; 139:9463-9466. [PMID: 28650156 PMCID: PMC5629633 DOI: 10.1021/jacs.7b04824] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial capsular polysaccharides (CPS) are complex carbohydrate structures that play a role in the overall fitness of the organism. Campylobacter jejuni, known for being a major cause of bacterial gastroenteritis worldwide, produces a CPS with a unique O-methyl phosphoramidate (MeOPN) modification on specific sugar residues. The formation of P-N bonds in nature is relatively rare, and the pathway for the assembly of the phosphoramidate moiety in the CPS of C. jejuni is unknown. In this investigation we discovered that the initial transformation in the biosynthetic pathway for the MeOPN modification of the CPS involves the direct phosphorylation of the amide nitrogen of l-glutamine with ATP by the catalytic activity of Cj1418. The other two products are AMP and inorganic phosphate. The l-glutamine-phosphate product was characterized using 31P NMR spectroscopy and mass spectrometry. We suggest that this newly discovered enzyme be named l-glutamine kinase.
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Affiliation(s)
- Zane W. Taylor
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, 77843
| | - Haley A. Brown
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | | | - Cory Q. Wenzel
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
| | - Christine M. Szymanski
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30602
| | - Hazel M. Holden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Frank M. Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, 77843
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843
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34
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Liu LK, Abdelwahab H, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. The Structure of the Antibiotic Deactivating, N-hydroxylating Rifampicin Monooxygenase. J Biol Chem 2016; 291:21553-21562. [PMID: 27557658 PMCID: PMC5076826 DOI: 10.1074/jbc.m116.745315] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Indexed: 11/06/2022] Open
Abstract
Rifampicin monooxygenase (RIFMO) catalyzes the N-hydroxylation of the natural product antibiotic rifampicin (RIF) to 2'-N-hydroxy-4-oxo-rifampicin, a metabolite with much lower antimicrobial activity. RIFMO shares moderate sequence similarity with well characterized flavoprotein monooxygenases, but the protein has not been isolated and characterized at the molecular level. Herein, we report crystal structures of RIFMO from Nocardia farcinica, the determination of the oligomeric state in solution with small angle x-ray scattering, and the spectrophotometric characterization of substrate binding. The structure identifies RIFMO as a class A flavoprotein monooxygenase and is similar in fold and quaternary structure to MtmOIV and OxyS, which are enzymes in the mithramycin and oxytetracycline biosynthetic pathways, respectively. RIFMO is distinguished from other class A flavoprotein monooxygenases by its unique middle domain, which is involved in binding RIF. Small angle x-ray scattering analysis shows that RIFMO dimerizes via the FAD-binding domain to form a bell-shaped homodimer in solution with a maximal dimension of 110 Å. RIF binding was monitored using absorbance at 525 nm to determine a dissociation constant of 13 μm Steady-state oxygen consumption assays show that NADPH efficiently reduces the FAD only when RIF is present, implying that RIF binds before NADPH in the catalytic scheme. The 1.8 Å resolution structure of RIFMO complexed with RIF represents the precatalytic conformation that occurs before formation of the ternary E-RIF-NADPH complex. The RIF naphthoquinone blocks access to the FAD N5 atom, implying that large conformational changes are required for NADPH to reduce the FAD. A model for these conformational changes is proposed.
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Affiliation(s)
- Li-Kai Liu
- From the Departments of Biochemistry and
| | - Heba Abdelwahab
- the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
- the Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
| | | | | | - Pablo Sobrado
- the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
| | - John J Tanner
- From the Departments of Biochemistry and
- Chemistry and
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35
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Mechanism of Rifampicin Inactivation in Nocardia farcinica. PLoS One 2016; 11:e0162578. [PMID: 27706151 PMCID: PMC5051949 DOI: 10.1371/journal.pone.0162578] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/24/2016] [Indexed: 12/26/2022] Open
Abstract
A novel mechanism of rifampicin (Rif) resistance has recently been reported in Nocardia farcinica. This new mechanism involves the activity of rifampicin monooxygenase (RifMO), a flavin-dependent monooxygenase that catalyzes the hydroxylation of Rif, which is the first step in the degradation pathway. Recombinant RifMO was overexpressed and purified for biochemical analysis. Kinetic characterization revealed that Rif binding is necessary for effective FAD reduction. RifMO exhibits only a 3-fold coenzyme preference for NADPH over NADH. RifMO catalyzes the incorporation of a single oxygen atom forming an unstable intermediate that eventually is converted to 2'-N-hydroxy-4-oxo-Rif. Stable C4a-hydroperoxyflavin was not detected by rapid kinetics methods, which is consistent with only 30% of the activated oxygen leading to product formation. These findings represent the first reported detailed biochemical characterization of a flavin-monooxygenase involved in antibiotic resistance.
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