1
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Zhang SG, Wan YQ, Zhang WH. Discovery of Dehydroabietylamine Derivatives as Antibacterial and Antifungal Agents. JOURNAL OF NATURAL PRODUCTS 2024; 87:924-934. [PMID: 38513270 DOI: 10.1021/acs.jnatprod.3c01213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
A diverse array of biologically active derivatives was derived by modifying the chemically active sites of dehydroabietylamine. Herein, we describe the synthesis of a new series of C-19-arylated dehydroabietylamine derivatives using a palladium-catalyzed C(sp3)-H activation reaction. Five analogues (3b, 3d, 3h, 3n, and 4a) exhibited antibacterial activity against Escherichia coli. Compound 4a exhibited strong inhibitory activity against DNA Topo II and Topo IV. Molecular docking modeling indicated that it can bind effectively to the target through interactions with amino acid residues. The synthesized compounds were tested in vitro for their antifungal activity against six common phytopathogenic fungi. The mechanism of action of compound 4c against Rhizoctorzia solani was investigated, revealing that it disrupts the morphology of the mycelium and enhances cell membrane permeability.
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Affiliation(s)
- Shu-Guang Zhang
- Jiangsu Key Laboratory of Pesticide, College of Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yu-Qiang Wan
- Jiangsu Key Laboratory of Pesticide, College of Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Wei-Hua Zhang
- Jiangsu Key Laboratory of Pesticide, College of Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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2
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Ajeigbe M, Childs S, Paget TA, Bingle LEH. Complete nucleotide sequence and comparative genomic analysis of microcin B17 plasmid pMccB17. Microbiologyopen 2024; 13:e1402. [PMID: 38440924 PMCID: PMC10912980 DOI: 10.1002/mbo3.1402] [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: 11/21/2023] [Revised: 02/11/2024] [Accepted: 02/16/2024] [Indexed: 03/06/2024] Open
Abstract
We present a comprehensive sequence and bioinformatic analysis of the prototypical microcin plasmid, pMccb17, which includes a definitive sequence for the microcin operon, mcb. Microcin B17 (MccB17) is a ribosomally synthesized and posttranslationally modified peptide produced by Escherichia coli. It inhibits bacterial DNA gyrase similarly to quinolone antibiotics. The mcb operon, which consists of seven genes encoding biosynthetic and immunity/export functions, was originally located on the low copy number IncFII plasmid pMccB17 in the Escherichia coli strain LP17. It was later transferred to E. coli K-12 through conjugation. In this study, the plasmid was extracted from the E. coli K-12 strain RYC1000 [pMccB17] and sequenced twice using an Illumina short-read method. The first sequencing was conducted with the host bacterial chromosome, and the plasmid DNA was then purified and sequenced separately. After assembly into a single contig, polymerase chain reaction primers were designed to close the single remaining gap via Sanger sequencing. The resulting complete circular DNA sequence is 69,190 bp long and includes 81 predicted genes. These genes were initially identified by Prokka and subsequently manually reannotated using BLAST. The plasmid was assigned to the F2:A-:B- replicon type with a MOBF12 group conjugation system. A comparison with other IncFII plasmids revealed a large proportion of shared genes, particularly in the conjugative plasmid backbone. However, unlike many contemporary IncFII plasmids, pMccB17 lacks transposable elements and antibiotic resistance genes. In addition to the mcb operon, this plasmid carries 25 genes of unknown function.
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Affiliation(s)
- Mayokun Ajeigbe
- School of Nursing and Health Sciences, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
| | - Stephen Childs
- School of Pharmacy & Pharmaceutical Sciences, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
| | - Timothy A. Paget
- School of Medicine, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
| | - Lewis E. H. Bingle
- School of Nursing and Health Sciences, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
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3
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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4
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Huo Y, Jiang Q, Zhao W. Meta-analysis of metagenomics reveals the signatures of vaginal microbiome in preterm birth. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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5
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Abstract
The two-component system CpxRA can sense environmental stresses and regulate transcription of a wide range of genes for the purpose of adaptation. Despite extensive research on this system, the identification of the CpxR regulon is not systematic or comprehensive. Herein, genome-wide screening was performed using a position-specific scoring matrix, resulting in the discovery of more than 10,000 putative CpxR binding sites, which provides an extensive and selective set of targets based on sequence. More than half of the candidate genes ultimately selected (73/97) were experimentally confirmed to be CpxR-regulated genes through experimental analysis. These genes are involved in various physiological functions, indicating that the CpxRA system regulates complex cellular processes. The study also found for the first time that the CpxR-regulated genes ydeE, xylE, alx, and galP contribute to Escherichia coli resistance to acid stress, whereas prlF, alx, casA, yacH, ydeE, sbmA, and ampH contribute to E. coli resistance to cationic antimicrobial peptide stress. Among these CpxR-regulated genes, ydeE and alx responded to both stressors. In a similar way, a cationic antimicrobial peptide is capable of directly activating the periplasmic domain of CpxA kinase in vitro, which is consistent with the CpxA response to acid stress. These results greatly expand our understanding of the CpxRA-dependent stress response network in E. coli. IMPORTANCE CpxRA system is found in many pathogens and plays an essential role in sensing environmental signals and transducing information inside cells for adaptation. It usually regulates expression of specific genes in response to different environmental stresses and is important for bacterial pathogenesis. However, systematically identifying CpxRA-regulated genes and elucidating the regulative role of CpxRA in bacteria responding to environmental stress remains challenging. This study discovered more than 10,000 putative CpxR binding sites based on sequence. This bioinformatics approach, combined with experimental assays, allowed the identification of many previously unknown CpxR-regulated genes. Among the novel 73 CpxRA-regulated genes identified in this study, the role of nine of them in contributing to E. coli resistance to acid or cationic antimicrobial peptide stress was studied. The potential correlation between these two environmental stress responses provides insight into the CpxRA-dependent stress response network. This also improves our understanding of environment-bacterium interaction and Gram-negative pathogenesis.
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6
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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7
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Telhig S, Ben Said L, Torres C, Rebuffat S, Zirah S, Fliss I. Evaluating the Potential and Synergetic Effects of Microcins against Multidrug-Resistant Enterobacteriaceae. Microbiol Spectr 2022; 10:e0275221. [PMID: 35543514 PMCID: PMC9241698 DOI: 10.1128/spectrum.02752-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/12/2022] [Indexed: 11/20/2022] Open
Abstract
The advent of multidrug-resistant bacteria has hampered the development of new antibiotics, exacerbating their morbidity and mortality. In this context, the gastrointestinal tract reveals a valuable source of novel antimicrobials. Microcins are bacteriocins produced by members of the family Enterobacteriaceae, which are endowed with a wide diversity of structures and mechanisms of action, and exert potent antibacterial activity against closely related bacteria. In this study, we investigated the antibacterial activities of four microcins against 54 Enterobacteriaceae isolates from three species (Escherichia coli, Klebsiella pneumoniae, and Salmonella enterica). The selected microcins, microcin C (McC, nucleotide peptide), microcin J25 (MccJ25, lasso peptide), microcin B17 (MccB17, linear azol(in)e-containing peptide), and microcin E492 (MccE492, siderophore peptide) carry different post-translational modifications and have distinct mechanisms of action. MICs and minimal bactericidal concentrations (MBC) of the microcins were measured and the efficacy of combinations of the microcins together or with antibiotics was assessed to identify potential synergies. Every isolate showed sensitivity to at least one microcin with MIC values ranging between 0.02 μM and 42.5 μM. Among the microcins tested, McC exhibited the broadest spectrum of inhibition with 46 strains inhibited, closely followed by MccE492 with 38 strains inhibited, while MccJ25 showed the highest activity. In general, microcin activity was observed to be independent of antibiotic resistance profile and strain genus. Of the 42 tested combinations, 20 provided enhanced activity (18 out of 20 being microcin-antibiotic combinations), with two being synergetic. IMPORTANCE With their wide range of structures and mechanisms of action, microcins are shown to exert antibacterial activities against Enterobacteriaceae resistant to antibiotics together with synergies with antibiotics and in particular colistin.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
| | - Carmen Torres
- Department of Food and Agriculture, University of La Rioja, Logrono, Spain
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Ismail Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Québec, Canada
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8
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Lewis JK, Jochimsen AS, Lefave SJ, Young AP, Kincannon WM, Roberts AG, Kieber-Emmons MT, Bandarian V. New Role for Radical SAM Enzymes in the Biosynthesis of Thio(seleno)oxazole RiPP Natural Products. Biochemistry 2021; 60:3347-3361. [PMID: 34730336 DOI: 10.1021/acs.biochem.1c00469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are ubiquitous and represent a structurally diverse class of natural products. The ribosomally encoded precursor polypeptides are often extensively modified post-translationally by enzymes that are encoded by coclustered genes. Radical S-adenosyl-l-methionine (SAM) enzymes catalyze numerous chemically challenging transformations. In RiPP biosynthetic pathways, these transformations include the formation of C-H, C-C, C-S, and C-O linkages. In this paper, we show that the Geobacter lovleyi sbtM gene encodes a radical SAM protein, SbtM, which catalyzes the cyclization of a Cys/SeCys residue in a minimal peptide substrate. Biochemical studies of this transformation support a mechanism involving H-atom abstraction at the C-3 of the substrate Cys to initiate the chemistry. Several possible cyclization products were considered. The collective biochemical, spectroscopic, mass spectral, and computational observations point to a thiooxazole as the product of the SbtM-catalyzed modification. To our knowledge, this is the first example of a radical SAM enzyme that catalyzes a transformation involving a SeCys-containing peptide and represents a new paradigm for formation of oxazole-containing RiPP natural products.
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Affiliation(s)
- Julia K Lewis
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andrew S Jochimsen
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Sarah J Lefave
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony P Young
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - William M Kincannon
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Matthew T Kieber-Emmons
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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9
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Translocation of non-lytic antimicrobial peptides and bacteria penetrating peptides across the inner membrane of the bacterial envelope. Curr Genet 2021; 68:83-90. [PMID: 34750687 PMCID: PMC8801401 DOI: 10.1007/s00294-021-01217-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 11/02/2022]
Abstract
The increase in multidrug-resistant pathogenic bacteria has become a problem worldwide. Currently there is a strong focus on the development of novel antimicrobials, including antimicrobial peptides (AMP) and antimicrobial antisense agents. While the majority of AMP have membrane activity and kill bacteria through membrane disruption, non-lytic AMP are non-membrane active, internalize and have intracellular targets. Antimicrobial antisense agents such as peptide nucleic acids (PNA) and phosphorodiamidate morpholino oligomers (PMO), show great promise as novel antibacterial agents, killing bacteria by inhibiting translation of essential target gene transcripts. However, naked PNA and PMO are unable to translocate across the cell envelope of bacteria, to reach their target in the cytosol, and are conjugated to bacteria penetrating peptides (BPP) for cytosolic delivery. Here, we discuss how non-lytic AMP and BPP-PMO/PNA conjugates translocate across the cytoplasmic membrane via receptor-mediated transport, such as the cytoplasmic membrane transporters SbmA, MdtM/YjiL, and/or YgdD, or via a less well described autonomous process.
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10
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Ghilarov D, Inaba-Inoue S, Stepien P, Qu F, Michalczyk E, Pakosz Z, Nomura N, Ogasawara S, Walker GC, Rebuffat S, Iwata S, Heddle JG, Beis K. Molecular mechanism of SbmA, a promiscuous transporter exploited by antimicrobial peptides. SCIENCE ADVANCES 2021; 7:eabj5363. [PMID: 34516884 PMCID: PMC8442886 DOI: 10.1126/sciadv.abj5363] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/16/2021] [Indexed: 05/12/2023]
Abstract
Antibiotic metabolites and antimicrobial peptides mediate competition between bacterial species. Many of them hijack inner and outer membrane proteins to enter cells. Sensitivity of enteric bacteria to multiple peptide antibiotics is controlled by the single inner membrane protein SbmA. To establish the molecular mechanism of peptide transport by SbmA and related BacA, we determined their cryo–electron microscopy structures at 3.2 and 6 Å local resolution, respectively. The structures show a previously unknown fold, defining a new class of secondary transporters named SbmA-like peptide transporters. The core domain includes conserved glutamates, which provide a pathway for proton translocation, powering transport. The structures show an outward-open conformation with a large cavity that can accommodate diverse substrates. We propose a molecular mechanism for antibacterial peptide uptake paving the way for creation of narrow-targeted therapeutics.
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Affiliation(s)
- Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Satomi Inaba-Inoue
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
- Diffraction and Scattering Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1, Kouto, Sayo, Hyogo 679-5198, Japan
| | - Piotr Stepien
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Feng Qu
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | | | - Zuzanna Pakosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Satoshi Ogasawara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Graham Charles Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sylvie Rebuffat
- Molecules of Communication and Adaptation of Microorganisms Laboratory (MCAM, UMR 7245 CNRS-MNHN), Muséum National d’Histoire Naturelle, Sorbonne Universités, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, Paris 75005, France
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Research Acceleration Program, Membrane Protein Crystallography Project, Japan Science and Technology Agency, Kyoto, Japan
| | | | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
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11
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Mazurek Ł, Ghilarov D, Michalczyk E, Pakosz Z, Metelev M, Czyszczoń W, Wawro K, Behroz I, Dubiley S, Süssmuth RD, Heddle JG. Pentapeptide repeat protein QnrB1 requires ATP hydrolysis to rejuvenate poisoned gyrase complexes. Nucleic Acids Res 2021; 49:1581-1596. [PMID: 33434265 PMCID: PMC7897471 DOI: 10.1093/nar/gkaa1266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
DNA gyrase, a type II topoisomerase found predominantly in bacteria, is the target for a variety of 'poisons', namely natural product toxins (e.g. albicidin, microcin B17) and clinically important synthetic molecules (e.g. fluoroquinolones). Resistance to both groups can be mediated by pentapeptide repeat proteins (PRPs). Despite long-term studies, the mechanism of action of these protective PRPs is not known. We show that a PRP, QnrB1 provides specific protection against fluoroquinolones, which strictly requires ATP hydrolysis by gyrase. QnrB1 binds to the GyrB protein and stimulates ATPase activity of the isolated N-terminal ATPase domain of GyrB (GyrB43). We probed the QnrB1 binding site using site-specific incorporation of a photoreactive amino acid and mapped the crosslinks to the GyrB43 protein. We propose a model in which QnrB1 binding allosterically promotes dissociation of the fluoroquinolone molecule from the cleavage complex.
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Affiliation(s)
- Łukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Zuzanna Pakosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | | | - Wojciech Czyszczoń
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Karolina Wawro
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Iraj Behroz
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | | | - Roderich D Süssmuth
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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12
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Tsutsumi H, Kuroda T, Kimura H, Goto Y, Suga H. Posttranslational chemical installation of azoles into translated peptides. Nat Commun 2021; 12:696. [PMID: 33514734 PMCID: PMC7846737 DOI: 10.1038/s41467-021-20992-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Azoles are five-membered heterocycles often found in the backbones of peptidic natural products and synthetic peptidomimetics. Here, we report a method of ribosomal synthesis of azole-containing peptides involving specific ribosomal incorporation of a bromovinylglycine derivative into the nascent peptide chain and its chemoselective conversion to a unique azole structure. The chemoselective conversion was achieved by posttranslational dehydrobromination of the bromovinyl group and isomerization in aqueous media under fairly mild conditions. This method enables us to install exotic azole groups, oxazole and thiazole, at designated positions in the peptide chain with both linear and macrocyclic scaffolds and thereby expand the repertoire of building blocks in the mRNA-templated synthesis of designer peptides. Azoles are five-membered heterocycles found in peptidic natural products and synthetic peptiodomimetics. Here the authors demonstrate a posttranslational chemical modification method for in vitro ribosomal synthesis of peptides with exotic azole groups at specific positions.
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Affiliation(s)
- Haruka Tsutsumi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomohiro Kuroda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroyuki Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
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13
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Isolation and structure determination of new linear azole-containing peptides spongiicolazolicins A and B from Streptomyces sp. CWH03. Appl Microbiol Biotechnol 2020; 105:93-104. [PMID: 33215256 DOI: 10.1007/s00253-020-11016-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
Linear azole-containing peptides are a class of ribosomally synthesized and post-translationally modified peptides. We performed a chemical investigation on marine actinomycetes, and new linear azole-containing peptides named spongiicolazolicins A and B were found in the MeOH extracts of a newly isolated strain Streptomyces sp. CWH03 (NBRC 114659) and two strains of S. spongiicola (strain HNM0071T: DSM 103383T and strain 531S: NBRC 113560). The strain Streptomyces sp. CWH03 was indicated to be a new species closely related to S. spongiicola by phylogenetic analysis using the genome sequence. The new peptides named spongiicolazolicins A and B were isolated from the cell of Streptomyces sp. CWH03. The partial structure of spongiicolazolicin A was determined by 2D NMR experiments. Based on data of MS/MS experiments, the chemical structures of spongiicolazolicins A and B were proposed using the amino acid sequence deduced from the precursor-encoding gene, which was found from whole-genome sequence data of Streptomyces sp. CWH03. The biosynthetic gene cluster of spongiicolazolicins was proposed based on comparative analysis with that of a known linear azole peptide goadsporin. KEY POINTS: • Streptomyces sp. CWH03 was a new species isolated from marine sediment. • New linear azole-containing peptides named spongiicolazolicins A and B were isolated. • Biosynthetic pathway of spongiicolazolicins was proposed.
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Slotboom DJ, Ettema TW, Nijland M, Thangaratnarajah C. Bacterial multi-solute transporters. FEBS Lett 2020; 594:3898-3907. [PMID: 32810294 DOI: 10.1002/1873-3468.13912] [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: 07/02/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022]
Abstract
Bacterial membrane proteins of the SbmA/BacA family are multi-solute transporters that mediate the uptake of structurally diverse hydrophilic molecules, including aminoglycoside antibiotics and antimicrobial peptides. Some family members are full-length ATP-binding cassette (ABC) transporters, whereas other members are truncated homologues that lack the nucleotide-binding domains and thus mediate ATP-independent transport. A recent cryo-EM structure of the ABC transporter Rv1819c from Mycobacterium tuberculosis has shed light on the structural basis for multi-solute transport and has provided insight into the mechanism of transport. Here, we discuss how the protein architecture makes SbmA/BacA family transporters prone to inadvertent import of antibiotics and speculate on the question which physiological processes may benefit from multi-solute transport.
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Affiliation(s)
- Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Thijs W Ettema
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Mark Nijland
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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15
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Jaswal S, Nehra B, Kumar S, Monga V. Recent advancements in the medicinal chemistry of bacterial type II topoisomerase inhibitors. Bioorg Chem 2020; 104:104266. [PMID: 33142421 DOI: 10.1016/j.bioorg.2020.104266] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
Replication proteins are sought as a potential targets for antimicrobial agents. Despite their promising target characteristics, only topoisomerase II inhibitors targeting DNA gyrase and/or topoisomerase IV have reached clinical use. Topoisomerases are the enzymes that are essential for cellular functions and various biological activities. A wide range of natural and synthetic compounds have been identified as potential topoisomerase inhibitors but the resistance is most commonly found in these drugs. The emergence of FQ resistance has increased the need for the development of novel topoisomerase inhibitors with efficacy and high potency against FQ-resistant strains. Besides structural modifications of existing FQ scaffolds, novel non-quinolone topoisomerase II inhibitors, known as novel bacterial topoisomerase inhibitors, have been developed which showed remarkable inhibitory activity against DNA gyrase/topoisomerase IV or both with an improved spectrum of antibacterial potency including drug-resistant strains. This review aims to summarize various recent advancements in the medicinal chemistry of topoisomerase inhibitors with the following objectives: (1) To represent inclusive data on types of topoisomerases and various marketed topoisomerase inhibitors as drugs; (2) To discuss the recent advances in the medicinal chemistry of various topoisomerase inhibitors (DNA gyrase and topo IV) belonging to different structural classes as potential antibacterial agents; (3) To summarizes the structure activity relationship (SAR) including in silico and mechanistic studies to afford ideas and to provide focused direction for the development of new chemical entities which are effective against drug-resistant bacterial pathogens and biofilms.
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Affiliation(s)
- Shalini Jaswal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Bhupender Nehra
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Shubham Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India.
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Russell AH, Truman AW. Genome mining strategies for ribosomally synthesised and post-translationally modified peptides. Comput Struct Biotechnol J 2020; 18:1838-1851. [PMID: 32728407 PMCID: PMC7369419 DOI: 10.1016/j.csbj.2020.06.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/14/2023] Open
Abstract
Genome mining is a computational method for the automatic detection and annotation of biosynthetic gene clusters (BGCs) from genomic data. This approach has been increasingly utilised in natural product (NP) discovery due to the large amount of sequencing data that is now available. Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a class of structurally complex NP with diverse bioactivities. RiPPs have recently been shown to occupy a much larger expanse of genomic and chemical space than previously appreciated, indicating that annotation of RiPP BGCs in genomes may have been overlooked in the past. This review provides an overview of the genome mining tools that have been specifically developed to aid in the discovery of RiPP BGCs, which have been built from an increasing knowledgebase of RiPP structures and biosynthesis. Given these recent advances, the application of targeted genome mining has great potential to accelerate the discovery of important molecules such as antimicrobial and anticancer agents whilst increasing our understanding about how these compounds are biosynthesised in nature.
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Affiliation(s)
- Alicia H Russell
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
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17
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Discovery of novel multi-substituted benzo-indole pyrazole schiff base derivatives with antibacterial activity targeting DNA gyrase. Bioorg Chem 2020; 99:103807. [DOI: 10.1016/j.bioorg.2020.103807] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 01/14/2023]
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18
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Liu H, Xia DG, Chu ZW, Hu R, Cheng X, Lv XH. Novel coumarin-thiazolyl ester derivatives as potential DNA gyrase Inhibitors: Design, synthesis, and antibacterial activity. Bioorg Chem 2020; 100:103907. [PMID: 32413631 DOI: 10.1016/j.bioorg.2020.103907] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/22/2020] [Accepted: 04/30/2020] [Indexed: 11/15/2022]
Abstract
The design and synthesis of novel coumarin-thiazolyl ester derivatives of potent DNA gyrase inhibitory activity were the main aims of this study. All the novel synthesized compounds were examined for their antibacterial activity against Staphylococcus aureus, Listeria monocytogenes, Escherichia coli and Salmonella. Compound 8p exhibited excellent antibacterial activity against four bacteria strains with MIC values of 0.05, 0.05, 8, and 0.05 μg/mL, respectively. In vitro drug-resistant bacterial inhibition experiments indicated that compound 8p exhibited the best bacteriostatic effect in the selected compounds and four positive control drugs with MIC values of 4 μg/mL. In vitro enzyme inhibitory assay showed that compound 8p exhibited potent inhibition against DNA gyrase with IC50 values of 0.13 μM. The molecular docking model indicated that compounds 8p can bind well to the DNA gyrase by interacting with amino acid residues. This study demonstrated that the compound 8p can act as the most potent DNA gyrase inhibitor in the reported series of compounds and provide valuable information for the commercial DNA gyrase inhibiting bactericides.
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Affiliation(s)
- Hao Liu
- School of Science, Anhui Agricultural University, 230036 Hefei, People's Republic of China
| | - Dong-Guo Xia
- School of Science, Anhui Agricultural University, 230036 Hefei, People's Republic of China
| | - Zhi-Wen Chu
- School of Science, Anhui Agricultural University, 230036 Hefei, People's Republic of China
| | - Rui Hu
- Central Iron & Steel Research Institute, 100081 Beijing, People's Republic of China
| | - Xiang Cheng
- School of Science, Anhui Agricultural University, 230036 Hefei, People's Republic of China
| | - Xian-Hai Lv
- School of Science, Anhui Agricultural University, 230036 Hefei, People's Republic of China.
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19
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Mhlongo JT, Brasil E, de la Torre BG, Albericio F. Naturally Occurring Oxazole-Containing Peptides. Mar Drugs 2020; 18:md18040203. [PMID: 32290087 PMCID: PMC7231064 DOI: 10.3390/md18040203] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/29/2022] Open
Abstract
Oxazole-containing peptides are mostly of marine origin and they form an intriguing family with a broad range of biological activities. Here we classify these peptides on the basis of their chemical structure and discuss a number of representatives of each class that reflect the extraordinary potential of this family as a source of new drugs.
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Affiliation(s)
- Jessica T. Mhlongo
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Edikarlos Brasil
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Beatriz G. de la Torre
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Correspondence: (B.G.d.l.T.); (F.A.); Tel.: +27-614009144 (F.A.)
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- CIBER-BBN (Networking Centre on Bioengineering, Biomaterials and Nanomedicine) and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: (B.G.d.l.T.); (F.A.); Tel.: +27-614009144 (F.A.)
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20
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Li Y, Rebuffat S. The manifold roles of microbial ribosomal peptide-based natural products in physiology and ecology. J Biol Chem 2020; 295:34-54. [PMID: 31784450 PMCID: PMC6952617 DOI: 10.1074/jbc.rev119.006545] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ribosomally synthesized and posttranslationally modified peptides (RiPPs), also called ribosomal peptide natural products (RPNPs), form a growing superfamily of natural products that are produced by many different organisms and particularly by bacteria. They are derived from precursor polypeptides whose modification by various dedicated enzymes helps to establish a vast array of chemical motifs. RiPPs have attracted much interest as a source of potential therapeutic agents, and in particular as alternatives to conventional antibiotics to address the bacterial resistance crisis. However, their ecological roles in nature are poorly understood and explored. The present review describes major RiPP actors in competition within microbial communities, the main ecological and physiological functions currently evidenced for RiPPs, and the microbial ecosystems that are the sites for these functions. We envision that the study of RiPPs may lead to discoveries of new biological functions and highlight that a better knowledge of how bacterial RiPPs mediate inter-/intraspecies and interkingdom interactions will hold promise for devising alternative strategies in antibiotic development.
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Affiliation(s)
- Yanyan Li
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
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21
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A Putative Microcin Amplifies Shiga Toxin 2a Production of Escherichia coli O157:H7. J Bacteriol 2019; 202:JB.00353-19. [PMID: 31611289 DOI: 10.1128/jb.00353-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/01/2019] [Indexed: 01/15/2023] Open
Abstract
Escherichia coli O157:H7 is a foodborne pathogen implicated in various multistate outbreaks. It encodes Shiga toxin on a prophage, and Shiga toxin production is linked to phage induction. An E. coli strain, designated 0.1229, that amplified Stx2a production when cocultured with E. coli O157:H7 strain PA2 was identified. Growth of PA2 in 0.1229 cell-free supernatants had a similar effect, even when supernatants were heated to 100°C for 10 min, but not after treatment with proteinase K. The secreted molecule was shown to use TolC for export and the TonB system for import. The genes sufficient for production of this molecule were localized to a 5.2-kb region of a 12.8-kb plasmid. This region was annotated, identifying hypothetical proteins, a predicted ABC transporter, and a cupin superfamily protein. These genes were identified and shown to be functional in two other E. coli strains, and bioinformatic analyses identified related gene clusters in similar and distinct bacterial species. These data collectively suggest that E. coli 0.1229 and other E. coli strains produce a microcin that induces the SOS response in target bacteria. Besides adding to the limited number of microcins known to be produced by E. coli, this study provides an additional mechanism by which stx 2a expression is increased in response to the gut microflora.IMPORTANCE How the gut microflora influences the progression of bacterial infections is only beginning to be understood. Antibiotics are counterindicated for E. coli O157:H7 infections, limiting treatment options. An increased understanding of how the gut microflora directs O157:H7 virulence gene expression may lead to additional treatment options. This work identified E. coli strains that enhance the production of Shiga toxin by O157:H7 through the secretion of a proposed microcin. Microcins are natural antimicrobial peptides that target specific species, can act as alternatives to antibiotics, and mediate microbial competition. This work demonstrates another mechanism by which non-O157 E. coli strains may increase Shiga toxin production and adds to our understanding of microcins, a group of antimicrobials less well understood than colicins.
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Baquero F, Lanza VF, Baquero MR, Del Campo R, Bravo-Vázquez DA. Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere. Front Microbiol 2019; 10:2261. [PMID: 31649628 PMCID: PMC6795089 DOI: 10.3389/fmicb.2019.02261] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/17/2019] [Indexed: 12/31/2022] Open
Abstract
Microcins are low-molecular-weight, ribosomally produced, highly stable, bacterial-inhibitory molecules involved in competitive, and amensalistic interactions between Enterobacteriaceae in the intestine. These interactions take place in a highly complex chemical landscape, the intestinal eco-active chemosphere, composed of chemical substances that positively or negatively influence bacterial growth, including those originated from nutrient uptake, and those produced by the action of the human or animal host and the intestinal microbiome. The contribution of bacteria results from their effect on the host generated molecules, on food and digested food, and organic substances from microbial origin, including from bacterial degradation. Here, we comprehensively review the main chemical substances present in the human intestinal chemosphere, particularly of those having inhibitory effects on microorganisms. With this background, and focusing on Enterobacteriaceae, the most relevant human pathogens from the intestinal microbiota, the microcin’s history and classification, mechanisms of action, and mechanisms involved in microcin’s immunity (in microcin producers) and resistance (non-producers) are reviewed. Products from the chemosphere likely modulate the ecological effects of microcin activity. Several cross-resistance mechanisms are shared by microcins, colicins, bacteriophages, and some conventional antibiotics, which are expected to produce cross-effects. Double-microcin-producing strains (such as microcins MccM and MccH47) have been successfully used for decades in the control of pathogenic gut organisms. Microcins are associated with successful gut colonization, facilitating translocation and invasion, leading to bacteremia, and urinary tract infections. In fact, Escherichia coli strains from the more invasive phylogroups (e.g., B2) are frequently microcinogenic. A publicly accessible APD3 database http://aps.unmc.edu/AP/ shows particular genes encoding microcins in 34.1% of E. coli strains (mostly MccV, MccM, MccH47, and MccI47), and much less in Shigella and Salmonella (<2%). Some 4.65% of Klebsiella pneumoniae are microcinogenic (mostly with MccE492), and even less in Enterobacter or Citrobacter (mostly MccS). The high frequency and variety of microcins in some Enterobacteriaceae indicate key ecological functions, a notion supported by their dominance in the intestinal microbiota of biosynthetic gene clusters involved in the synthesis of post-translationally modified peptide microcins.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Maria-Rosario Baquero
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
| | - Rosa Del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Daniel A Bravo-Vázquez
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
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Takuma M, Kuroha M, Nagano Y, Kaweewan I, Hemmi H, Oyoshi T, Kodani S. Heterologous production of coryneazolicin in Escherichia coli. J Antibiot (Tokyo) 2019; 72:800-806. [PMID: 31366953 DOI: 10.1038/s41429-019-0212-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/04/2019] [Accepted: 06/21/2019] [Indexed: 11/09/2022]
Abstract
Coryneazolicin is a plantazolicin family peptide, belonging to linear azole-containing peptides (LAPs). Although coryneazolicin was previously synthesized by in vitro experiments, its biological activity has not been evaluated. In this report, the heterologous production of coryneazolicin was accomplished to obtain enough coryneazolicin for biological activity tests. The structure of coryneazolicin was confirmed by ESI-MS and NMR analyses. The biological activity tests indicated that coryneazolicin possessed potent antibacterial activity and cytotoxicity. Although antibacterial activity of plantazolicin was previously reported, cytotoxicity was newly found in coryneazolicin among plantazolicin type peptides. In addition, we revealed that coryneazolicin induced apoptosis on HCT116 and HOS cancer cell lines.
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Affiliation(s)
- Momoko Takuma
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Mai Kuroha
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yuki Nagano
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Issara Kaweewan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hikaru Hemmi
- Food Research Institute, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Takanori Oyoshi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.,Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan. .,Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan. .,Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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24
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The Microbial Toxin Microcin B17: Prospects for the Development of New Antibacterial Agents. J Mol Biol 2019; 431:3400-3426. [PMID: 31181289 PMCID: PMC6722960 DOI: 10.1016/j.jmb.2019.05.050] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 01/03/2023]
Abstract
Microcin B17 (MccB17) is an antibacterial peptide produced by strains of Escherichia coli harboring the plasmid-borne mccB17 operon. MccB17 possesses many notable features. It is able to stabilize the transient DNA gyrase–DNA cleavage complex, a very efficient mode of action shared with the highly successful fluoroquinolone drugs. MccB17 stabilizes this complex by a distinct mechanism making it potentially valuable in the fight against bacterial antibiotic resistance. MccB17 was the first compound discovered from the thiazole/oxazole-modified microcins family and the linear azole-containing peptides; these ribosomal peptides are post-translationally modified to convert serine and cysteine residues into oxazole and thiazole rings. These chemical moieties are found in many other bioactive compounds like the vitamin thiamine, the anti-cancer drug bleomycin, the antibacterial sulfathiazole and the antiviral nitazoxanide. Therefore, the biosynthetic machinery that produces these azole rings is noteworthy as a general method to create bioactive compounds. Our knowledge of MccB17 now extends to many aspects of antibacterial–bacteria interactions: production, transport, interaction with its target, and resistance mechanisms; this knowledge has wide potential applicability. After a long time with limited progress on MccB17, recent publications have addressed critical aspects of MccB17 biosynthesis as well as an explosion in the discovery of new related compounds in the thiazole/oxazole-modified microcins/linear azole-containing peptides family. It is therefore timely to summarize the evidence gathered over more than 40 years about this still enigmatic molecule and place it in the wider context of antibacterials. Microcin B17 (MccB17) is a microbial toxin with a unique mode of action. MccB17 stabilizes the gyrase–DNA cleavage complex; it is a potential substitute for fluoroquinolones. The structures of microcin synthase and TldD/E have given key insight into its biosynthesis. A variety of modified McB17s have been generated and characterized. MccB17 has been implicated in IBD.
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25
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Dong SH, Liu A, Mahanta N, Mitchell DA, Nair SK. Mechanistic Basis for Ribosomal Peptide Backbone Modifications. ACS CENTRAL SCIENCE 2019; 5:842-851. [PMID: 31139720 PMCID: PMC6535971 DOI: 10.1021/acscentsci.9b00124] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/16/2023]
Abstract
YcaO enzymes are known to catalyze the ATP-dependent formation of azoline heterocycles, thioamides, and (macro)lactamidines on peptide substrates. These enzymes are found in multiple biosynthetic pathways, including those for several different classes of ribosomally synthesized and post-translationally modified peptides (RiPPs). However, there are major knowledge gaps in the mechanistic and structural underpinnings that govern each of the known YcaO-mediated modifications. Here, we present the first structure of any YcaO enzyme bound to its peptide substrate in the active site, specifically that from Methanocaldococcus jannaschii which is involved in the thioamidation of the α-subunit of methyl-coenzyme M reductase (McrA). The structural data are leveraged to identify and test the residues involved in substrate binding and catalysis by site-directed mutagenesis. We also show that thioamide-forming YcaOs can carry out the cyclodehydration of a related peptide substrate, which underscores the mechanistic conservation across the YcaO family and allows for the extrapolation of mechanistic details to azoline-forming YcaOs involved in RiPP biosynthesis. A bioinformatic survey of all YcaOs highlights the diverse sequence space in azoline-forming YcaOs and suggests their early divergence from a common ancestor. The data presented within provide a detailed molecular framework for understanding this family of enzymes, which reconcile several decades of prior data on RiPP cyclodehydratases. These studies also provide the foundational knowledge to impact our mechanistic understanding of additional RiPP biosynthetic classes.
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Affiliation(s)
- Shi-Hui Dong
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Andi Liu
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Nilkamal Mahanta
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Satish K. Nair
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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Ghilarov D, Stevenson CEM, Travin DY, Piskunova J, Serebryakova M, Maxwell A, Lawson DM, Severinov K. Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol Cell 2019; 73:749-762.e5. [PMID: 30661981 PMCID: PMC6395948 DOI: 10.1016/j.molcel.2018.11.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/24/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
Abstract
The introduction of azole heterocycles into a peptide backbone is the principal step in the biosynthesis of numerous compounds with therapeutic potential. One of them is microcin B17, a bacterial topoisomerase inhibitor whose activity depends on the conversion of selected serine and cysteine residues of the precursor peptide to oxazoles and thiazoles by the McbBCD synthetase complex. Crystal structures of McbBCD reveal an octameric B4C2D2 complex with two bound substrate peptides. Each McbB dimer clamps the N-terminal recognition sequence, while the C-terminal heterocycle of the modified peptide is trapped in the active site of McbC. The McbD and McbC active sites are distant from each other, which necessitates alternate shuttling of the peptide substrate between them, while remaining tethered to the McbB dimer. An atomic-level view of the azole synthetase is a starting point for deeper understanding and control of biosynthesis of a large group of ribosomally synthesized natural products. Azole synthetase McbBCD is co-crystallized with its product, microcin B17 Crystal structure of McbBCD reveals an octameric assembly of B4C2D2 Two McbB subunits within each asymmetric unit interact to recognize a peptide Formation of each azole ring requires shuttling of peptide between two active centers
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Affiliation(s)
- Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | | | - Dmitrii Y Travin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Julia Piskunova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina Serebryakova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK.
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Hudson GA, Mitchell DA. RiPP antibiotics: biosynthesis and engineering potential. Curr Opin Microbiol 2018; 45:61-69. [PMID: 29533845 PMCID: PMC6131089 DOI: 10.1016/j.mib.2018.02.010] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/23/2018] [Indexed: 01/14/2023]
Abstract
The threat of antibiotic resistant bacterial infections continues to underscore the need for new treatment options. Historically, small molecule metabolites from microbes have provided a rich source of antibiotic compounds, and as a result, significant effort has been invested in engineering the responsible biosynthetic pathways to generate novel analogs with attractive pharmacological properties. Unfortunately, biosynthetic stringency has limited the capacity of non-ribosomal peptide synthetases and polyketide synthases from producing substantially different analogs in large numbers. Another class of natural products, the ribosomally synthesized and post-translationally modified peptides (RiPPs), have rapidly expanded in recent years with many natively displaying potent antibiotic activity. RiPP biosynthetic pathways are modular and intrinsically tolerant to alternative substrates. Several prominent RiPPs with antibiotic activity will be covered in this review with a focus on their biosynthetic plasticity. While only a few RiPP enzymes have been thoroughly investigated mechanistically, this knowledge has already been harnessed to generate new-to-nature compounds. Through the use of synthetic biology approaches, on-going efforts in RiPP engineering hold great promise in unlocking the potential of this natural product class.
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Affiliation(s)
- Graham A Hudson
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Department of Microbiology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States.
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28
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Liu H, Ren ZL, Wang W, Gong JX, Chu MJ, Ma QW, Wang JC, Lv XH. Novel coumarin-pyrazole carboxamide derivatives as potential topoisomerase II inhibitors: Design, synthesis and antibacterial activity. Eur J Med Chem 2018; 157:81-87. [PMID: 30075404 DOI: 10.1016/j.ejmech.2018.07.059] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 11/18/2022]
Abstract
The identification of novel Topoisomerase II (Topo II) inhibitors is one of the most attractive directions in the field of bactericide research and development. In our ongoing efforts to pursue the class of inhibitors, six series of 70 novel coumarin-pyrazole carboxamide derivatives were designed and synthesized. As a result of the evaluation against four destructive bacteria, including Staphylococcus aureus, Listeria monocytogenes, Escherichia coli and Salmonella. Compound 8III-k (MIC = 0.25 mg/L) showed considerable inhibitory activity than ciprofloxacin (MIC = 0.5 mg/L) against Escherichia coli and 8V-c (MIC = 0.05 mg/L) exhibited excellent antibacterial activity than ciprofloxacin (MIC = 0.25 mg/L) against Salmonella. The selected compounds (8III-k, 8V-c and 8V-k) exhibit potent inhibition against Topo II and Topo IV with IC50 values (9.4-25 mg/L). Molecular docking model showed that the compounds 8V-c and 8V-k can bind well to the target by interacting with amino acid residues. It will provide some valuable information for the commercial Topo II inhibiting bactericides.
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Affiliation(s)
- Hao Liu
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China
| | - Zi-Li Ren
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China
| | - Wei Wang
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China
| | - Jie-Xiu Gong
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China
| | - Ming-Jie Chu
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China
| | - Quan-Wei Ma
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China
| | - Jie-Chun Wang
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China
| | - Xian-Hai Lv
- School of Science, Anhui Agricultural University, 230036, Hefei, People's Republic of China; State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, 210093, Nanjing, People's Republic of China.
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29
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Khan T, Sankhe K, Suvarna V, Sherje A, Patel K, Dravyakar B. DNA gyrase inhibitors: Progress and synthesis of potent compounds as antibacterial agents. Biomed Pharmacother 2018; 103:923-938. [DOI: 10.1016/j.biopha.2018.04.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/24/2018] [Accepted: 04/03/2018] [Indexed: 12/22/2022] Open
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30
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Xiaoli L, Figler HM, Goswami Banerjee K, Hayes CS, Dudley EG. Non-pathogenic Escherichia coli Enhance Stx2a Production of E. coli O157:H7 Through Both bamA-Dependent and Independent Mechanisms. Front Microbiol 2018; 9:1325. [PMID: 29973923 PMCID: PMC6020778 DOI: 10.3389/fmicb.2018.01325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/30/2018] [Indexed: 01/14/2023] Open
Abstract
Intestinal colonization by the foodborne pathogen Escherichia coli O157:H7 leads to serious disease symptoms, including hemolytic uremic syndrome (HUS) and hemorrhagic colitis (HC). Synthesis of one or more Shiga toxins (Stx) is essential for HUS and HC development. The genes encoding Stx, including Stx2a, are found within a lambdoid prophage integrated in the E. coli O157:H7 chromosome. Enhanced Stx2a expression was reported when specific non-pathogenic E. coli strains were co-cultured with E. coli O157:H7, and it was hypothesized that this phenotype required the non-pathogenic E. coli to be sensitive to stx-converting phage infection. We tested this hypothesis by generating phage resistant non-pathogenic E. coli strains where bamA (an essential gene and Stx phage receptor) was replaced with an ortholog from other species. Such heterologous gene replacement abolished the ability of the laboratory strain E. coli C600 to enhance toxin production when co-cultured with E. coli O157:H7 strain PA2, which belongs to the hypervirulent clade 8. The extracellular loops of BamA (loop 4, 6, 7) were further shown to be important for infection by stx2a-converting phages. However, similar gene replacement in another commensal E. coli, designated 1.1954, revealed a bamA-independent mechanism for toxin amplification. Toxin enhancement by 1.1954 was not the result of phage infection through an alternative receptor (LamB or FadL), lysogen formation by stx2a-converting phages, or the production of a secreted molecule. Collectively, these data suggest that non-pathogenic E. coli can enhance toxin production through at least two mechanisms.
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Affiliation(s)
- Lingzi Xiaoli
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Hillary M Figler
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Kakolie Goswami Banerjee
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Christopher S Hayes
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States.,Center for Immunology and Infectious Disease, The Pennsylvania State University, University Park, PA, United States
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Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli. G3-GENES GENOMES GENETICS 2017; 7:3955-3966. [PMID: 29046437 PMCID: PMC5714492 DOI: 10.1534/g3.117.300284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we used short-term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that Escherichia coli develops low cost resistance to kanamycin via different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD/cpxA/topA/cyaA Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance. In this work, we expand our understanding of these second site mutations, the goal being to understand how these mutations affect the activities of the mutated gene products to confer resistance. We show that the mutation in cpxA most likely results in an active Cpx stress response. Further evolution of an EF-G mutant in a higher concentration of kanamycin than what was used in our previous experiments identified the cpxA locus as a primary target for a significant increase in resistance. The mutation in cyaA results in a loss of catalytic activity and probably results in resistance via altered CRP function. Despite a reduction in cAMP levels, the CyaAN600Y mutant has a transcriptome indicative of increased CRP activity, pointing to an unknown role for CyaA and / or cAMP in gene expression. From the transcriptomes of double and single mutants, we describe the epistasis between the mutation in EF-G and these second site mutations. We show that the large scale transcriptomic changes in the topoisomerase I (FusAA608E-TopAS180L) mutant likely result from increased negative supercoiling in the cell. Finally, genes with known roles in aminoglycoside resistance were present among the misregulated genes in the mutants.
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32
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Barrière Q, Guefrachi I, Gully D, Lamouche F, Pierre O, Fardoux J, Chaintreuil C, Alunni B, Timchenko T, Giraud E, Mergaert P. Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules. Sci Rep 2017; 7:9063. [PMID: 28831061 PMCID: PMC5567381 DOI: 10.1038/s41598-017-08830-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022] Open
Abstract
Legumes harbor in their symbiotic nodule organs nitrogen fixing rhizobium bacteria called bacteroids. Some legumes produce Nodule-specific Cysteine-Rich (NCR) peptides in the nodule cells to control the intracellular bacterial population. NCR peptides have antimicrobial activity and drive bacteroids toward terminal differentiation. Other legumes do not produce NCR peptides and their bacteroids are not differentiated. Bradyrhizobia, infecting NCR-producing Aeschynomene plants, require the peptide uptake transporter BclA to cope with the NCR peptides as well as a specific peptidoglycan-modifying DD-carboxypeptidase, DD-CPase1. We show that Bradyrhizobium diazoefficiens strain USDA110 forms undifferentiated bacteroids in NCR-lacking soybean nodules. Unexpectedly, in Aeschynomene afraspera nodules the nitrogen fixing USDA110 bacteroids are hardly differentiated despite the fact that this host produces NCR peptides, suggesting that USDA110 is insensitive to the host peptide effectors and that nitrogen fixation can be uncoupled from differentiation. In agreement with the absence of bacteroid differentiation, USDA110 does not require its bclA gene for nitrogen fixing symbiosis with these two host plants. Furthermore, we show that the BclA and DD-CPase1 act independently in the NCR-induced morphological differentiation of bacteroids. Our results suggest that BclA is required to protect the rhizobia against the NCR stress but not to induce the terminal differentiation pathway.
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Affiliation(s)
- Quentin Barrière
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Ibtissem Guefrachi
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, 6072, Gabès, Tunisia.,Université de Pau et des Pays de l'Adour, Pau, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Florian Lamouche
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Olivier Pierre
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Institut Sophia AgroBiotech, Sophia-Antipolis, France
| | - Joël Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Benoît Alunni
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.
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33
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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34
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Quereda JJ, Meza-Torres J, Cossart P, Pizarro-Cerdá J. Listeriolysin S: A bacteriocin from epidemic Listeria monocytogenes strains that targets the gut microbiota. Gut Microbes 2017; 8:384-391. [PMID: 28156183 PMCID: PMC5570420 DOI: 10.1080/19490976.2017.1290759] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Listeria monocytogenes is a Gram-positive food-borne pathogen that in humans may traverse the intestinal, placental and blood/brain barriers, causing gastroenteritis, abortions and meningitis. Crossing of these barriers is dependent on the bacterial ability to enter host cells, and several L. monocytogenes surface and secreted virulence factors are known to facilitate entry and the intracellular lifecycle. The study of L. monocytogenes strains associated to human listeriosis epidemics has revealed the presence of novel virulence factors. One such factor is Listeriolysin S, a thiazole/oxazole modified microcin that displays bactericidal activity and modifies the host microbiota during infection. Our recent results therefore highlight the interaction of L. monocytogenes with gut microbes as a crucial step in epidemic listeriosis. In this article, we will discuss novel implications for this family of toxins in the pathogenesis of diverse medically relevant microorganisms.
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Affiliation(s)
- Juan J. Quereda
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France
| | - Jazmín Meza-Torres
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France,CONTACT Javier Pizarro-Cerda Unité des Interactions Bactéries-Cellules, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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35
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Graf M, Mardirossian M, Nguyen F, Seefeldt AC, Guichard G, Scocchi M, Innis CA, Wilson DN. Proline-rich antimicrobial peptides targeting protein synthesis. Nat Prod Rep 2017; 34:702-711. [DOI: 10.1039/c7np00020k] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) bind within the exit tunnel of the ribosome and inhibit translation elongation. Structures of ribosome-bound PrAMPs reveal the interactions with ribosomal components and could pave the way for the development of novel peptide-based antimicrobial agents.
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Affiliation(s)
- Michael Graf
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
| | - Mario Mardirossian
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
| | - Fabian Nguyen
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
| | | | - Gilles Guichard
- Université de Bordeaux
- CNRS
- Institut Polytechnique de Bordeaux
- UMR 5248
- Institut de Chimie et Biologie des Membranes et des Nano-objets (CBMN)
| | - Marco Scocchi
- Department of Life Sciences
- University of Trieste
- Trieste
- Italy
| | - C. Axel Innis
- Univ. Bordeaux
- ARNA Laboratory
- Inserm U1212
- CNRS UMR 5320
- IECB
| | - Daniel N. Wilson
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
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36
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Balandin SV, Ovchinnikova TV. Antimicrobial peptides of invertebrates. Part 2. biological functions and mechanisms of action. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s106816201604004x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Higashi DL, Biais N, Donahue DL, Mayfield JA, Tessier CR, Rodriguez K, Ashfeld BL, Luchetti J, Ploplis VA, Castellino FJ, Lee SW. Activation of band 3 mediates group A Streptococcus streptolysin S-based beta-haemolysis. Nat Microbiol 2016; 1:15004. [PMID: 27571972 DOI: 10.1038/nmicrobiol.2015.4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/18/2015] [Indexed: 11/09/2022]
Abstract
Streptococcus pyogenes, or group A Streptococcus (GAS), is a human bacterial pathogen that can manifest as a range of diseases from pharyngitis and impetigo to severe outcomes such as necrotizing fasciitis and toxic shock syndrome. GAS disease remains a global health burden with cases estimated at over 700 million annually and over half a million deaths due to severe infections(1). For over 100 years, a clinical hallmark of diagnosis has been the appearance of complete (beta) haemolysis when grown in the presence of blood. This activity is due to the production of a small peptide toxin by GAS known as streptolysin S. Although it has been widely held that streptolysin S exerts its lytic activity through membrane disruption, its exact mode of action has remained unknown. Here, we show, using high-resolution live cell imaging, that streptolysin S induces a dramatic osmotic change in red blood cells, leading to cell lysis. This osmotic change was characterized by the rapid influx of Cl(-) ions into the red blood cells through SLS-mediated disruption of the major erythrocyte anion exchange protein, band 3. Chemical inhibition of band 3 function significantly reduced the haemolytic activity of streptolysin S, and dramatically reduced the pathology in an in vivo skin model of GAS infection. These results provide key insights into the mechanism of streptolysin S-mediated haemolysis and have implications for the development of treatments against GAS.
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Affiliation(s)
- Dustin L Higashi
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences Center, Notre Dame, Indiana 46556, USA
| | - Nicolas Biais
- Biology Department, Brooklyn College CUNY, New York 11210, USA
| | - Deborah L Donahue
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jeffrey A Mayfield
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Charles R Tessier
- Indiana University School of Medicine, South Bend, Indiana 46617, USA
| | - Kevin Rodriguez
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Brandon L Ashfeld
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jeffrey Luchetti
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences Center, Notre Dame, Indiana 46556, USA
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, USA.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, USA.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences Center, Notre Dame, Indiana 46556, USA.,W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, USA
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38
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Guefrachi I, Pierre O, Timchenko T, Alunni B, Barrière Q, Czernic P, Villaécija-Aguilar JA, Verly C, Bourge M, Fardoux J, Mars M, Kondorosi E, Giraud E, Mergaert P. Bradyrhizobium BclA Is a Peptide Transporter Required for Bacterial Differentiation in Symbiosis with Aeschynomene Legumes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1155-66. [PMID: 26106901 DOI: 10.1094/mpmi-04-15-0094-r] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nodules of legume plants are highly integrated symbiotic systems shaped by millions of years of evolution. They harbor nitrogen-fixing rhizobium bacteria called bacteroids. Several legume species produce peptides called nodule-specific cysteine-rich (NCR) peptides in the symbiotic nodule cells which house the bacteroids. NCR peptides are related to antimicrobial peptides of innate immunity. They induce the endosymbionts into a differentiated, enlarged, and polyploid state. The bacterial symbionts, on their side, evolved functions for the response to the NCR peptides. Here, we identified the bclA gene of Bradyrhizobium sp. strains ORS278 and ORS285, which is required for the formation of differentiated and functional bacteroids in the nodules of the NCR peptide-producing Aeschynomene legumes. The BclA ABC transporter promotes the import of NCR peptides and provides protection against the antimicrobial activity of these peptides. Moreover, BclA can complement the role of the related BacA transporter of Sinorhizobium meliloti, which has a similar symbiotic function in the interaction with Medicago legumes.
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Affiliation(s)
- Ibtissem Guefrachi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Olivier Pierre
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Benoît Alunni
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Quentin Barrière
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Pierre Czernic
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Camille Verly
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Mickaël Bourge
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Joël Fardoux
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Mohamed Mars
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Eva Kondorosi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 4 Institute of Biochemistry, Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary
| | - Eric Giraud
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Peter Mergaert
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
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39
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Piscotta FJ, Tharp JM, Liu WR, Link AJ. Expanding the chemical diversity of lasso peptide MccJ25 with genetically encoded noncanonical amino acids. Chem Commun (Camb) 2014; 51:409-12. [PMID: 25407838 DOI: 10.1039/c4cc07778d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using the amber suppression approach, four noncanonical amino acids (ncAAs) were used to replace existing amino acids at four positions in lasso peptide microcin J25 (MccJ25). The lasso peptide biosynthesis enzymes tolerated all four ncAAs and produced antibiotics with efficacy equivalent to wild-type in some cases. Given the rapid expansion of the genetically encoded ncAA pool, this study is the first to demonstrate an expedient method to significantly increase the chemical diversity of lasso peptides.
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Affiliation(s)
- Frank J Piscotta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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40
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Affiliation(s)
- Rebecca A. Flaherty
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Stefan D. Freed
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Shaun W. Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
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41
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Goto Y, Ito Y, Kato Y, Tsunoda S, Suga H. One-pot synthesis of azoline-containing peptides in a cell-free translation system integrated with a posttranslational cyclodehydratase. ACTA ACUST UNITED AC 2014; 21:766-74. [PMID: 24856821 DOI: 10.1016/j.chembiol.2014.04.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 03/26/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
Abstract
Azoline moieties in the backbones of peptidic natural products are important structural motifs that contribute to diverse bioactivities. Some azoline-containing peptides (Az-peptides) are produced from ribosomally synthesized precursor peptides, in which cysteine, serine, and threonine residues are converted to their corresponding azolines by posttranslational modification through a cyclodehydratase. We have devised an in vitro biosynthesis system of Az-peptides, referred to as the FIT-PatD (flexible in vitro translation) system, by the integration of a cell-free translation system with the posttranslational cyclodehydratase PatD. This system enabled the "one-pot" synthesis of a wide variety of Az-peptide derivatives expressed from synthetic DNA templates. The FIT-PatD system also facilitated mutagenesis studies on a wide array of precursor peptide sequences, unveiling unique in vitro substrate tolerance of PatD.
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Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; JST, PRESTO, Tokyo 113-0033, Japan.
| | - Yumi Ito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yasuharu Kato
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shotaro Tsunoda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; JST, CREST, Tokyo 113-0033, Japan.
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42
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Narayanan S, Modak JK, Ryan CS, Garcia-Bustos J, Davies JK, Roujeinikova A. Mechanism of Escherichia coli resistance to Pyrrhocoricin. Antimicrob Agents Chemother 2014; 58:2754-62. [PMID: 24590485 PMCID: PMC3993218 DOI: 10.1128/aac.02565-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 02/23/2014] [Indexed: 01/07/2023] Open
Abstract
Due to their lack of toxicity to mammalian cells and good serum stability, proline-rich antimicrobial peptides (PR-AMPs) have been proposed as promising candidates for the treatment of infections caused by antimicrobial-resistant bacterial pathogens. It has been hypothesized that these peptides act on multiple targets within bacterial cells, and therefore the likelihood of the emergence of resistance was considered to be low. Here, we show that spontaneous Escherichia coli mutants resistant to pyrrhocoricin arise at a frequency of approximately 6 × 10(-7). Multiple independently derived mutants all contained a deletion in a nonessential gene that encodes the putative peptide uptake permease SbmA. Sensitivity could be restored to the mutants by complementation with an intact copy of the sbmA gene. These findings question the viability of the development of insect PR-AMPs as antimicrobials.
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Affiliation(s)
- Shalini Narayanan
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Joyanta K. Modak
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Catherine S. Ryan
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Jose Garcia-Bustos
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - John K. Davies
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Anna Roujeinikova
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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43
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Nigam A, Gupta D, Sharma A. Treatment of infectious disease: beyond antibiotics. Microbiol Res 2014; 169:643-51. [PMID: 24661689 DOI: 10.1016/j.micres.2014.02.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 12/09/2013] [Accepted: 02/23/2014] [Indexed: 11/29/2022]
Abstract
Several antibiotics have been discovered following the discovery of penicillin. These antibiotics had been helpful in treatment of infectious diseases considered dread for centuries. The advent of multiple drug resistance in microbes has posed new challenge to researchers. The scientists are now evaluating alternatives for combating infectious diseases. This review focuses on major alternatives to antibiotics on which preliminary work had been carried out. These promising anti-microbial include: phages, bacteriocins, killing factors, antibacterial activities of non-antibiotic drugs and quorum quenching.
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Affiliation(s)
- Anshul Nigam
- IPLS Building, School of Life Science, Pondicherry University, Puducherry 605014, India.
| | - Divya Gupta
- Department of Biotechnology, Mangalayatan University, Beswan, Aligarh, Uttar Pradesh 202145, India
| | - Ashwani Sharma
- Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
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Metelev MV, Ghilarov DA. Structure, function, and biosynthesis of thiazole/oxazole-modified microcins. Mol Biol 2014. [DOI: 10.1134/s0026893314010105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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The C-terminal part of microcin B is crucial for DNA gyrase inhibition and antibiotic uptake by sensitive cells. J Bacteriol 2014; 196:1759-67. [PMID: 24563033 DOI: 10.1128/jb.00015-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcin B (McB) is a ribosomally synthesized antibacterial peptide. It contains up to nine oxazole and thiazole heterocycles that are introduced posttranslationally and are required for activity. McB inhibits the DNA gyrase, a validated drug target. Previous structure-activity analyses indicated that two fused heterocycles located in the central part of McB are important for antibacterial action and gyrase inhibition. Here, we used site-specific mutagenesis of the McB precursor gene to assess the functional significance of the C-terminal part of McB that is located past the second fused heterocycle and contains two single heterocycles as well as an unmodified four-amino-acid C-terminal tail. We found that removal of unmodified C-terminal amino acids of McB, while having no effect on fused heterocycles, has a very strong negative effect on activity in vivo and in vitro. In fact, even nonconservative point substitutions in the last McB amino acid have a very strong effect by simultaneously decreasing uptake and ability to inhibit the gyrase. The results highlight the importance of unmodified McB amino acids for function and open the way for creation of recombinant McB derivatives with an altered or expanded spectrum of antibacterial action.
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46
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Murru S, Nefzi A. Combinatorial synthesis of oxazol-thiazole bis-heterocyclic compounds. ACS COMBINATORIAL SCIENCE 2014; 16:39-45. [PMID: 24295491 DOI: 10.1021/co400133a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A combinatorial library of novel oxazol-thiazole bis-heterocycles was synthesized in good to excellent overall yields with high purity using a solution and solid-phase parallel synthesis approach. Oxazole amino acids, prepared from serine methyl ester and amino acids via coupling and cyclodehydration, were treated with Fmoc-NCS and α-haloketones for the parallel synthesis of diverse bis-heterocycles. Fmoc-isothiocyanate is used as a traceless reagent for thiazole formation. Oxazole diversity can be achieved by using variety of amino acids, whereas thiazole diversity is produced with various haloketones.
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Affiliation(s)
- Siva Murru
- Torrey Pines Institute for Molecular Studies, 11350
SW Village Parkway, Port St Lucie, Florida 34987, United States
| | - Adel Nefzi
- Torrey Pines Institute for Molecular Studies, 11350
SW Village Parkway, Port St Lucie, Florida 34987, United States
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47
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Majumdar KC, Sinha B. Coinage metals (Cu, Ag and Au) in the synthesis of natural products. RSC Adv 2014. [DOI: 10.1039/c3ra44336a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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48
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Thompson RE, Collin F, Maxwell A, Jolliffe KA, Payne RJ. Synthesis of full length and truncated microcin B17 analogues as DNA gyrase poisons. Org Biomol Chem 2014; 12:1570-8. [DOI: 10.1039/c3ob42516a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a combination of solid-phase peptide synthesis and fragment assembly strategies a library of full-length and truncated analogues of the antibacterial post-translationally modified peptide microcin B17 have been synthesised. Both antibacterial and DNA gyrase poisoning activities are also described for the synthetic analogues.
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Affiliation(s)
| | - Frédéric Collin
- Department of Biological Chemistry
- John Innes Centre
- Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry
- John Innes Centre
- Norwich NR4 7UH, UK
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49
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Functional characterization of SbmA, a bacterial inner membrane transporter required for importing the antimicrobial peptide Bac7(1-35). J Bacteriol 2013; 195:5343-51. [PMID: 24078610 DOI: 10.1128/jb.00818-13] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SbmA is an inner membrane protein of Gram-negative bacteria that is involved in the internalization of glycopeptides and prokaryotic and eukaryotic antimicrobial peptides, as well as of peptide nucleic acid (PNA) oligomers. The SbmA homolog BacA is required for the development of Sinorhizobium meliloti bacteroids within plant cells and favors chronic infections with Brucella abortus and Mycobacterium tuberculosis in mice. Here, we investigated functional features of SbmA/BacA using the proline-rich antimicrobial peptide Bac7(1-35) as a substrate. Circular dichroism and affinity chromatography studies were used to investigate the ability of SbmA to bind the peptide, and a whole-cell transport assay with fluorescently labeled peptide allowed the determination of transport kinetic parameters with a calculated Km value of 6.95 ± 0.89 μM peptide and a Vmax of 53.91 ± 3.17 nmol/min/mg SbmA. Use of a bacterial two-hybrid system coupled to SEC-MALLS (size exclusion chromatography coupled with multiangle laser light scattering) analyses established that SbmA is a homodimer in the membrane, and treatment of the cells with arsenate or ionophores indicated that the peptide transport mediated by SbmA is driven by the electrochemical gradient. Overall, these results shed light on the SbmA-mediated internalization of peptide substrates and suggest that the transport of an unknown substrate(s) represents the function of this protein.
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50
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Abstract
SbmA protein has been proposed as a dimeric secondary transporter. The protein is involved in the transport of microcins B17 and J25, bleomycin, proline-rich antimicrobial peptides, antisense peptide phosphorodiamidate morpholino oligomers, and peptide nucleic acids into the Escherichia coli cytoplasm. The sbmA homologue is found in a variety of bacteria, though the physiological role of the protein is hitherto unknown. In this work, we carried out a functional and structural analysis to determine which amino acids are critical for the transport properties of SbmA. We created a set of 15 site-directed sbmA mutants in which single conserved amino acids were replaced by glycine residues. Our work demonstrated that strains carrying the site-directed mutants V102G, F219G, and E276G had a null phenotype for SbmA transport functions. In contrast, strains carrying the single point mutants W19G, W53G, F60G, S69G, N155G, R190, L233G, A344G, T255G, N308G, and R385G showed transport capacities indistinguishable from those of strains harboring a wild-type sbmA. The strain carrying the Y116G mutant exhibited mixed phenotypic characteristics. We also demonstrated that those sbmA mutants with severely impaired transport capacity showed a dominant negative phenotype. Electron microscopy data and in silico three-dimensional (3D) homology modeling support the idea that SbmA forms a homodimeric complex, closely resembling the membrane-spanning region of the ATP-binding cassette transporter family. Direct mapping of the sbmA single point mutants on the protein surface allowed us to explain the observed phenotypic differences in transport ability.
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