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Li C, Xu X, Geng Z, Zheng L, Song Q, Shen X, Wu J, Zhao J, Li H, He M, Tai X, Zhang L, Ma J, Dong Y, Ren A. Structure-based characterization and compound identification of the wild-type THF class-II riboswitch. Nucleic Acids Res 2024; 52:8454-8465. [PMID: 38769061 DOI: 10.1093/nar/gkae377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Riboswitches are conserved regulatory RNA elements participating in various metabolic pathways. Recently, a novel RNA motif known as the folE RNA motif was discovered upstream of folE genes. It specifically senses tetrahydrofolate (THF) and is therefore termed THF-II riboswitch. To unravel the ligand recognition mechanism of this newly discovered riboswitch and decipher the underlying principles governing its tertiary folding, we determined both the free-form and bound-form THF-II riboswitch in the wild-type sequences. Combining structural information and isothermal titration calorimetry (ITC) binding assays on structure-based mutants, we successfully elucidated the significant long-range interactions governing the function of THF-II riboswitch and identified additional compounds, including alternative natural metabolites and potential lead compounds for drug discovery, that interact with THF-II riboswitch. Our structural research on the ligand recognition mechanism of the THF-II riboswitch not only paves the way for identification of compounds targeting riboswitches, but also facilitates the exploration of THF analogs in diverse biological contexts or for therapeutic applications.
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Affiliation(s)
- Chunyan Li
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
| | - Xiaochen Xu
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Zhi Geng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Luqian Zheng
- College of Life Sciences, Anhui Normal University, Wuhu 241000 Anhui, China
| | - Qianqian Song
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
| | - Xin Shen
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
| | - Jingjing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jin Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hongcheng Li
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
| | - Mengqi He
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
| | - Xiaoqing Tai
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
| | - Long Zhang
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aiming Ren
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Biotherapy, Zhejiang University, Hangzhou 310058, China
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2
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Pham NP, Gingras H, Godin C, Feng J, Groppi A, Nikolski M, Leprohon P, Ouellette M. Holistic understanding of trimethoprim resistance in Streptococcus pneumoniae using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning. mBio 2024:e0136024. [PMID: 39120145 DOI: 10.1128/mbio.01360-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Antimicrobial resistance (AMR) is a public health threat worldwide. Next-generation sequencing (NGS) has opened unprecedented opportunities to accelerate AMR mechanism discovery and diagnostics. Here, we present an integrative approach to investigate trimethoprim (TMP) resistance in the key pathogen Streptococcus pneumoniae. We explored a collection of 662 S. pneumoniae genomes by conducting a genome-wide association study (GWAS), followed by functional validation using resistance reconstruction experiments, combined with machine learning (ML) approaches to predict TMP minimum inhibitory concentration (MIC). Our study showed that multiple additive mutations in the folA and sulA loci are responsible for TMP non-susceptibility in S. pneumoniae and can be used as key features to build ML models for digital MIC prediction, reaching an average accuracy within ±1 twofold dilution factor of 86.3%. Our roadmap of in silico analysis-wet-lab validation-diagnostic tool building could be adapted to explore AMR in other combinations of bacteria-antibiotic. IMPORTANCE In the age of next-generation sequencing (NGS), while data-driven methods such as genome-wide association study (GWAS) and machine learning (ML) excel at finding patterns, functional validation can be challenging due to the high numbers of candidate variants. We designed an integrative approach combining a GWAS on S. pneumoniae clinical isolates, followed by whole-genome transformation coupled with NGS to functionally characterize a large set of GWAS candidates. Our study validated several phenotypic folA mutations beyond the standard Ile100Leu mutation, and showed that the overexpression of the sulA locus produces trimethoprim (TMP) resistance in Streptococcus pneumoniae. These validated loci, when used to build ML models, were found to be the best inputs for predicting TMP minimal inhibitory concentrations. Integrative approaches can bridge the genotype-phenotype gap by biological insights that can be incorporated in ML models for accurate prediction of drug susceptibility.
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Affiliation(s)
- Nguyen-Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Chantal Godin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Alexis Groppi
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
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3
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Yu Y, Martins LM. Mitochondrial One-Carbon Metabolism and Alzheimer's Disease. Int J Mol Sci 2024; 25:6302. [PMID: 38928008 PMCID: PMC11203557 DOI: 10.3390/ijms25126302] [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: 03/12/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Mitochondrial one-carbon metabolism provides carbon units to several pathways, including nucleic acid synthesis, mitochondrial metabolism, amino acid metabolism, and methylation reactions. Late-onset Alzheimer's disease is the most common age-related neurodegenerative disease, characterised by impaired energy metabolism, and is potentially linked to mitochondrial bioenergetics. Here, we discuss the intersection between the molecular pathways linked to both mitochondrial one-carbon metabolism and Alzheimer's disease. We propose that enhancing one-carbon metabolism could promote the metabolic processes that help brain cells cope with Alzheimer's disease-related injuries. We also highlight potential therapeutic avenues to leverage one-carbon metabolism to delay Alzheimer's disease pathology.
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Affiliation(s)
- Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - L. Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
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Teng K, Liu Q, Zhang M, Naz H, Zheng P, Wu X, Chi YR. Design and Enantioselective Synthesis of Chiral Pyranone Fused Indole Derivatives with Antibacterial Activities against Xanthomonas oryzae pv oryzae for Protection of Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4622-4629. [PMID: 38386000 DOI: 10.1021/acs.jafc.3c07491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
A new class of chiral pyranone fused indole derivatives were prepared by means of N-heterocyclic carbene (NHC) organocatalysis and demonstrated notable antibacterial activity against Xanthomonas oryzae pv oryzae (Xoo). Bioassays showed that compounds (3S,4R)-5b, (3S,4R)-5d, and (3S,4R)-5l exhibited promising in vitro efficacy against Xoo, with EC50 values of 9.05, 9.71, and 5.84 mg/L, respectively, which were superior to that of the positive controls with commercial antibacterial agents, bismerthiazol (BT, EC50 = 27.8 mg/L) and thiodiazole copper (TC, EC50 = 70.1 mg/L). Furthermore, single enantiomer (3S,4R)-5l was identified as an optimal structure displaying 55.3% and 52.0% curative and protective activities against Xoo in vivo tests at a concentration of 200 mg/L, which slightly surpassed the positive control with TC (curative and protective activities of 47.2% and 48.8%, respectively). Mechanistic studies through molecular docking analysis revealed preliminary insights into the distinct anti-Xoo activity of the two single enantiomers (3S,4R)-5l and (3R,4S)-5l, wherein the (3S,4R)-configured stereoisomer could form a more stable interaction with XooDHPS (dihydropteroate synthase). These findings underscore the significant anti-Xoo potential of these chiral pyranone fused indole derivatives, and shall inspire further exploration as promising lead structures for a novel class of bactericides to combat bacterial infections and other plant diseases.
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Affiliation(s)
- Kunpeng Teng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Qian Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Meng Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Hira Naz
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Pengcheng Zheng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Xingxing Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Yonggui Robin Chi
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
- School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
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Yu JF, Xu JT, Feng A, Qi BL, Gu J, Deng JY, Zhang XE. Competition between H 4PteGlu and H 2PtePAS Confers para-Aminosalicylic Acid Resistance in Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 13:13. [PMID: 38275323 PMCID: PMC10812664 DOI: 10.3390/antibiotics13010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
Tuberculosis remains a serious challenge to human health worldwide. para-Aminosalicylic acid (PAS) is an important anti-tuberculosis drug, which requires sequential activation by Mycobacterium tuberculosis (M. tuberculosis) dihydropteroate synthase and dihydrofolate synthase (DHFS, FolC). Previous studies showed that loss of function mutations of a thymidylate synthase coding gene thyA caused PAS resistance in M. tuberculosis, but the mechanism is unclear. Here we showed that deleting thyA in M. tuberculosis resulted in increased content of tetrahydrofolate (H4PteGlu) in bacterial cells as they rely on the other thymidylate synthase ThyX to synthesize thymidylate, which produces H4PteGlu during the process. Subsequently, data of in vitro enzymatic activity experiments showed that H4PteGlu hinders PAS activation by competing with hydroxy dihydropteroate (H2PtePAS) for FolC catalysis. Meanwhile, over-expressing folC in ΔthyA strain and a PAS resistant clinical isolate with known thyA mutation partially restored PAS sensitivity, which relieved the competition between H4PteGlu and H2PtePAS. Thus, loss of function mutations in thyA led to increased H4PteGlu content in bacterial cells, which competed with H2PtePAS for catalysis by FolC and hence hindered the activation of PAS, leading to decreased production of hydroxyl dihydrofolate (H2PtePAS-Glu) and finally caused PAS resistance. On the other hand, functional deficiency of thyA in M. tuberculosis pushes the bacterium switch to an unidentified dihydrofolate reductase for H4PteGlu biosynthesis, which might also contribute to the PAS resistance phenotype. Our study revealed how thyA mutations confer PAS resistance in M. tuberculosis and provided new insights into studies on the folate metabolism of the bacterium.
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Affiliation(s)
- Ji-Fang Yu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin-Tian Xu
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ao Feng
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao-Ling Qi
- Shanghai Metabolome Institute-Wuhan (SMI), Wuhan 430000, China
| | - Jing Gu
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiao-Yu Deng
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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6
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Hervin V, Roy V, Agrofoglio LA. Antibiotics and Antibiotic Resistance-Mur Ligases as an Antibacterial Target. Molecules 2023; 28:8076. [PMID: 38138566 PMCID: PMC10745416 DOI: 10.3390/molecules28248076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of Multidrug Resistance (MDR) strains of bacteria has accelerated the search for new antibacterials. The specific bacterial peptidoglycan biosynthetic pathway represents opportunities for the development of novel antibacterial agents. Among the enzymes involved, Mur ligases, described herein, and especially the amide ligases MurC-F are key targets for the discovery of multi-inhibitors, as they share common active sites and structural features.
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Affiliation(s)
| | - Vincent Roy
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| | - Luigi A. Agrofoglio
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
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7
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Júnior MA, Silva LC, Rocha OB, Oliveira AA, Portis IG, Alonso A, Alonso L, Silva KS, Gomes MN, Andrade CH, Soares CM, Pereira M. Proteomic identification of metabolic changes in Paracoccidioides brasiliensis induced by a nitroheteroarylchalcone. Future Microbiol 2023; 18:1077-1093. [PMID: 37424510 DOI: 10.2217/fmb-2022-0150] [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] [Indexed: 07/11/2023] Open
Abstract
Aim: To access the metabolic changes caused by a chalcone derivative (LabMol-75) through a proteomic approach. Methods: Proteomic analysis was performed after 9 h of Paracoccidioides brasiliensis yeast (Pb18) cell incubation with the LabMol-75 at MIC. The proteomic findings were validated through in vitro and in silico assays. Results: Exposure to the compound led to the downregulation of proteins associated with glycolysis and gluconeogenesis, β-oxidation, the citrate cycle and the electron transport chain. Conclusion: LabMol-75 caused an energetic imbalance in the fungus metabolism and deep oxidative stress. Additionally, the in silico molecular docking approach pointed to this molecule as a putative competitive inhibitor of DHPS.
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Affiliation(s)
- Marcos Abc Júnior
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lívia C Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Olivia B Rocha
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Amanda A Oliveira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Igor G Portis
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Antonio Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lais Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kleber Sf Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Marcelo N Gomes
- InsiChem, Goiás State University, Anápolis, Goiás, Brazil
- Faculdade Metropolitana de Anápolis, Anápolis, Goiás, Brazil
| | - Carolina H Andrade
- Laboratory for Molecular Modeling & Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Célia Ma Soares
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Maristela Pereira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
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8
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Feng Y, Chang SK, Portnoy DA. The major role of Listeria monocytogenes folic acid metabolism during infection is the generation of N-formylmethionine. mBio 2023; 14:e0107423. [PMID: 37695058 PMCID: PMC10653936 DOI: 10.1128/mbio.01074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 09/12/2023] Open
Abstract
IMPORTANCE Folic acid is an essential vitamin for bacteria, plants, and animals. The lack of folic acid leads to various consequences such as a shortage of amino acids and nucleotides that are fundamental building blocks for life. Though antifolate drugs are widely used for antimicrobial treatments, the underlying mechanism of bacterial folate deficiency during infection is unclear. This study compares the requirements of different folic acid end-products during the infection of Listeria monocytogenes, a facultative intracellular pathogen of animals and humans. The results reveal the critical importance of N-formylmethionine, the amino acid used by bacteria to initiate protein synthesis. This work extends the current understanding of folic acid metabolism in pathogens and potentially provides new insights into antifolate drug development in the future.
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Affiliation(s)
- Ying Feng
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Shannon K. Chang
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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9
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Duysak T, Jeong JH, Kim K, Kim JS, Choy HE. Analysis of random mutations in Salmonella Gallinarum dihydropteroate synthase conferring sulfonamide resistance. Arch Microbiol 2023; 205:363. [PMID: 37906281 DOI: 10.1007/s00203-023-03696-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
In bacteria and primitive eukaryotes, sulfonamide antibiotics block the folate pathway by inhibiting dihydropteroate synthase (FolP) that combines para-aminobenzoic acid (pABA) and dihydropterin pyrophosphate (DHPP) to form dihydropteroic acid (DHP), a precursor for tetrahydrofolate synthesis. However, the emergence of resistant strains has severely compromised the use of pABA mimetics as sulfonamide drugs. Salmonella enterica serovar Gallinarum (S. Gallinarum) is a significant source of antibiotic-resistant infections in poultry. Here, a sulfonamide-resistant FolP mutant library of S. Gallinarum was generated through random mutagenesis. Among resistant strains, substitution of amino acid Arginine 171 with Proline (R171P) in the FolP protein conferred the highest resistance against sulfonamide. Substitution of Phe28 with Leu or Ile (F28L/I) led to modest sulfonamide resistance. Structural modeling indicates that R171P and Phenylalanine 28 with leucine or isoleucine (F28L/I) substitution mutations are located far from the substrate-binding site and cause insignificant conformational changes in the FolP protein. Rather, in silico studies suggest that the mutations altered the stability of the protein, potentially resulting in sulfonamide resistance. Identification of specific mutations in FolP that confer resistance to sulfonamide would contribute to our understanding of the molecular mechanisms of antibiotic resistance.
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Affiliation(s)
- Taner Duysak
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea
| | - Kwangsoo Kim
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Korea.
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea.
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea.
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10
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Hershko Y, Levytskyi K, Rannon E, Assous MV, Ken-Dror S, Amit S, Ben-Zvi H, Sagi O, Schwartz O, Sorek N, Szwarcwort M, Barkan D, Burstein D, Adler A. Phenotypic and genotypic analysis of antimicrobial resistance in Nocardia species. J Antimicrob Chemother 2023; 78:2306-2314. [PMID: 37527397 DOI: 10.1093/jac/dkad236] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Antimicrobial resistance is common in Nocardia species but data regarding the molecular mechanisms beyond their resistance traits are limited. Our study aimed to determine the species distribution, the antimicrobial susceptibility profiles, and investigate the associations between the resistance traits and their genotypic determinants. METHODS The study included 138 clinical strains of Nocardia from nine Israeli microbiology laboratories. MIC values of 12 antimicrobial agents were determined using broth microdilution. WGS was performed on 129 isolates of the eight predominant species. Bioinformatic analysis included phylogeny and determination of antimicrobial resistance genes and mutations. RESULTS Among the isolates, Nocardia cyriacigeorgica was the most common species (36%), followed by Nocardia farcinica (16%), Nocardia wallacei (13%), Nocardia abscessus (9%) and Nocardia brasiliensis (8%). Linezolid was active against all isolates, followed by trimethoprim/sulfamethoxazole (93%) and amikacin (91%). Resistance to other antibiotics was species-specific, often associated with the presence of resistance genes or mutations: (1) aph(2″) in N. farcinica and N. wallacei (resistance to tobramycin); (ii) blaAST-1 in N. cyriacigeorgica and Nocardia neocaledoniensis (resistance to amoxicillin/clavulanate); (iii) blaFAR-1 in N. farcinica (resistance to ceftriaxone); (iv) Ser83Ala substitution in the gyrA gene in four species (resistance to ciprofloxacin); and (v) the 16S rRNA m1A1408 methyltransferase in N. wallacei isolates (correlating with amikacin resistance). CONCLUSIONS Our study provides a comprehensive understanding of Nocardia species diversity, antibiotic resistance patterns, and the molecular basis of antimicrobial resistance. Resistance appears to follow species-related patterns, suggesting a lesser role for de novo evolution or transmission of antimicrobial resistance.
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Affiliation(s)
- Yizhak Hershko
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
| | - Katia Levytskyi
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ella Rannon
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Marc V Assous
- Clinical Microbiology Laboratory, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shifra Ken-Dror
- Clalit Health Services, Haifa and Western Galilee District, Israel
| | - Sharon Amit
- Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Haim Ben-Zvi
- Microbiology Laboratory, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Orli Sagi
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva 84105, Israel
| | | | - Nadav Sorek
- Assuta Ashdod University Hospital, Ashdod, Israel
| | - Moran Szwarcwort
- Clinical Microbiology Laboratories, Laboratories Division, Rambam Health Care Campus, Haifa, Israel
| | - Daniel Barkan
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Amos Adler
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
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11
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Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. Empowering drug off-target discovery with metabolic and structural analysis. Nat Commun 2023; 14:3390. [PMID: 37296102 PMCID: PMC10256842 DOI: 10.1038/s41467-023-38859-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/15/2023] [Indexed: 06/12/2023] Open
Abstract
Elucidating intracellular drug targets is a difficult problem. While machine learning analysis of omics data has been a promising approach, going from large-scale trends to specific targets remains a challenge. Here, we develop a hierarchic workflow to focus on specific targets based on analysis of metabolomics data and growth rescue experiments. We deploy this framework to understand the intracellular molecular interactions of the multi-valent dihydrofolate reductase-targeting antibiotic compound CD15-3. We analyse global metabolomics data utilizing machine learning, metabolic modelling, and protein structural similarity to prioritize candidate drug targets. Overexpression and in vitro activity assays confirm one of the predicted candidates, HPPK (folK), as a CD15-3 off-target. This study demonstrates how established machine learning methods can be combined with mechanistic analyses to improve the resolution of drug target finding workflows for discovering off-targets of a metabolic inhibitor.
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Affiliation(s)
- Sourav Chowdhury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Joao V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens Lyngby, Denmark
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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12
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 218] [Impact Index Per Article: 218.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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13
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Urdaneta-Páez V, Hamchand R, Anthony K, Crawford J, Sutherland AG, Kazmierczak BI. Identification of Efflux Substrates Using a Riboswitch-Based Reporter in Pseudomonas aeruginosa. mSphere 2023; 8:e0006923. [PMID: 36946743 PMCID: PMC10117056 DOI: 10.1128/msphere.00069-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Pseudomonas aeruginosa is intrinsically resistant to many classes of antibiotics, reflecting the restrictive nature of its outer membrane and the action of its numerous efflux systems. However, the dynamics of compound uptake, retention, and efflux in this bacterium remain incompletely understood. Here, we exploited the sensor capabilities of a Z-nucleotide-sensing riboswitch to create an experimental system able to identify physicochemical and structural properties of compounds that permeate the bacterial cell, avoid efflux, and perturb the folate cycle or de novo purine synthesis. In the first step, a collection of structurally diverse compounds enriched in antifolate drugs was screened for ZTP (5-aminoimidazole-4-carboxamide riboside 5'-triphosphate) riboswitch reporter activity in efflux-deficient P. aeruginosa, allowing us to identify compounds that entered the cell and disrupted the folate pathway. These initial hits were then rescreened using isogenic efflux-proficient bacteria, allowing us to separate efflux substrates from efflux avoiders. We confirmed this categorization by measuring intracellular levels of select compounds in the efflux-deficient and -proficient strain using high-resolution liquid chromatography-mass spectrometry (LC-MS). This simple yet powerful method, optimized for high-throughput screening, enables the discovery of numerous permeable compounds that avoid efflux and paves the way for further refinement of the physicochemical and structural rules governing efflux in this multidrug-resistant Gram-negative pathogen. IMPORTANCE Treatment of Pseudomonas aeruginosa infections has become increasingly challenging. The development of novel antibiotics against this multidrug-resistant bacterium is a priority, but many drug candidates never achieve effective concentrations in the bacterial cell due to its highly restrictive outer membrane and the action of multiple efflux pumps. Here, we develop a robust and simple reporter system in P. aeruginosa to screen chemical libraries and identify compounds that either enter the cell and remain inside or enter the cell and are exported by efflux systems. This approach enables the development of rules of compound uptake and retention in P. aeruginosa that will lead to more rational design of novel antibiotics.
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Affiliation(s)
- Verónica Urdaneta-Páez
- Department of Medicine, Section of Infectious Diseases, Yale University, New Haven, Connecticut, USA
| | - Randy Hamchand
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | | | - Jason Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | | | - Barbara I Kazmierczak
- Department of Medicine, Section of Infectious Diseases, Yale University, New Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
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14
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Xie J, Long ZQ, Chen AQ, Ding YG, Liu ST, Zhou X, Liu LW, Yang S. Novel Sulfonamide Derivatives Containing a Piperidine Moiety as New Bactericide Leads for Managing Plant Bacterial Diseases. Int J Mol Sci 2023; 24:ijms24065861. [PMID: 36982936 PMCID: PMC10054644 DOI: 10.3390/ijms24065861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Plant bacterial diseases are an intractable problem due to the fact that phytopathogens have acquired strong resistances for traditional pesticides, resulting in restricting the quality and yield of agricultural products around the world. To develop new agrochemical alternatives, we prepared a novel series of sulfanilamide derivatives containing piperidine fragments and assessed their antibacterial potency. The bioassay results revealed that most molecules displayed excellent in vitro antibacterial potency towards Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas axonopodis pv. citri (Xac). In particular, molecule C4 exhibited outstanding inhibitory activity toward Xoo with EC50 value of 2.02 µg mL-1, which was significantly better than those of the commercial agents bismerthiazol (EC50 = 42.38 µg mL-1) and thiodiazole copper (EC50 = 64.50 µg mL-1). A series of biochemical assays confirmed that compound C4 interacted with dihydropteroate synthase, and irreversibly damaged the cell membrane. In vivo assays showed that the molecule C4 presented acceptable curative and protection activities of 34.78% and 39.83%, respectively, at 200 µg mL-1, which were greater than those of thiodiazole and bismerthiazol. This study highlights the valuable insights for the excavation and development of new bactericides that can concurrently target dihydropteroate synthase and bacterial cell membranes.
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Affiliation(s)
- Jiao Xie
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhou-Qing Long
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Ai-Qun Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Ying-Guo Ding
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Shi-Tao Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Li-Wei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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15
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Identification of efflux substrates using a riboswitch-based reporter in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530370. [PMID: 36909469 PMCID: PMC10002626 DOI: 10.1101/2023.02.27.530370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Pseudomonas aeruginosa is intrinsically resistant to many classes of antibiotics, reflecting the restrictive nature of its outer membrane and the action of its numerous efflux systems. However, the dynamics of compound uptake, retention and efflux in this bacterium remain incompletely understood. Here, we exploited the sensor capabilities of a Z-nucleotide sensing riboswitch to create an experimental system able to identify physicochemical and structural properties of compounds that permeate the bacterial cell, avoid efflux, and perturb the folate cycle or de novo purine synthesis. In a first step, a collection of structurally diverse compounds enriched in antifolate drugs was screened for ZTP riboswitch reporter activity in efflux-deficient P. aeruginosa , allowing us to identify compounds that entered the cell and disrupted the folate pathway. These initial hits were then rescreened using isogenic efflux-proficient bacteria, allowing us to separate efflux substrates from efflux avoiders. We confirmed this categorization by measuring intracellular levels of select compounds in the efflux-deficient and - proficient strain using high resolution LC-MS. This simple yet powerful method, optimized for high throughput screening, enables the discovery of numerous permeable compounds that avoid efflux and paves the way for further refinement of the physicochemical and structural rules governing efflux in this multi-drug resistant Gram-negative pathogen. Importance Treatment of Pseudomonas aeruginosa infections has become increasingly challenging. The development of novel antibiotics against this multi-drug resistant bacterium is a priority, but many drug candidates never achieve effective concentrations in the bacterial cell due due to its highly restrictive outer membrane and the action of multiple efflux pumps. Here, we develop a robust and simple reporter system in P. aeruginosa to screen chemical libraries and identify compounds that either enter the cell and remain inside, or enter the cell and are exported by efflux systems. This approach enables developing rules of compound uptake and retention in P. aeruginosa that will lead to more rational design of novel antibiotics.
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16
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Ugalde-Arbizu M, Aguilera-Correa JJ, García-Almodóvar V, Ovejero-Paredes K, Díaz-García D, Esteban J, Páez PL, Prashar S, San Sebastian E, Filice M, Gómez-Ruiz S. Dual Anticancer and Antibacterial Properties of Silica-Based Theranostic Nanomaterials Functionalized with Coumarin343, Folic Acid and a Cytotoxic Organotin(IV) Metallodrug. Pharmaceutics 2023; 15:pharmaceutics15020560. [PMID: 36839883 PMCID: PMC9962538 DOI: 10.3390/pharmaceutics15020560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
Five different silica nanoparticles functionalized with vitamin B12, a derivative of coumarin found in green plants and a minimum content of an organotin(IV) fragment (1-MSN-Sn, 2-MSN-Sn, 2-SBA-Sn, 2-FSPm-Sn and 2-FSPs-Sn), were identified as excellent anticancer agents against triple negative breast cancer, one of the most diagnosed and aggressive cancerous tumors, with very poor prognosis. Notably, compound 2-MSN-Sn shows selectivity for cancer cells and excellent luminescent properties detectable by imaging techniques once internalized. The same compound is also able to interact with and nearly eradicate biofilms of Staphylococcus aureus, the most common bacteria isolated from chronic wounds and burns, whose treatment is a clinical challenge. 2-MSN-Sn is efficiently internalized by bacteria in a biofilm state and destroys the latter through reactive oxygen species (ROS) generation. Its internalization by bacteria was also efficiently monitored by fluorescence imaging. Since silica nanoparticles are particularly suitable for oral or topical administration, and considering both its anticancer and antibacterial activity, 2-MSN-Sn represents a new dual-condition theranostic agent, based primarily on natural products or their derivatives and with only a minimum amount of a novel metallodrug.
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Affiliation(s)
- Maider Ugalde-Arbizu
- Departamento de Química Aplicada, Facultad de Química, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel Lardizabal 3, 20018 Donostia San Sebastián, Spain
- Clinical Microbiology Department, IIS-Fundación Jiménez Diaz, UAM, Avenida Reyes 15 Católicos 2, 28037 Madrid, Spain
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, C/Tulipán s/n, 28933 Móstoles, Spain
| | - John Jairo Aguilera-Correa
- Clinical Microbiology Department, IIS-Fundación Jiménez Diaz, UAM, Avenida Reyes 15 Católicos 2, 28037 Madrid, Spain
- CIBERINFEC-CIBER de Enfermedades Infecciosas, 28029 Madrid, Spain
- Correspondence: (J.J.A.-C.); (M.F.); (S.G.-R.)
| | - Victoria García-Almodóvar
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, C/Tulipán s/n, 28933 Móstoles, Spain
| | - Karina Ovejero-Paredes
- Nanobiotechnology for Life Sciences Group, Department of Chemistry in Pharmaceutical Sciences, Faculty of Pharmacy, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- Microscopy and Dynamic Imaging Unit, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Calle Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Diana Díaz-García
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, C/Tulipán s/n, 28933 Móstoles, Spain
| | - Jaime Esteban
- Clinical Microbiology Department, IIS-Fundación Jiménez Diaz, UAM, Avenida Reyes 15 Católicos 2, 28037 Madrid, Spain
- CIBERINFEC-CIBER de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Paulina L. Páez
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Sanjiv Prashar
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, C/Tulipán s/n, 28933 Móstoles, Spain
| | - Eider San Sebastian
- Departamento de Química Aplicada, Facultad de Química, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel Lardizabal 3, 20018 Donostia San Sebastián, Spain
| | - Marco Filice
- Nanobiotechnology for Life Sciences Group, Department of Chemistry in Pharmaceutical Sciences, Faculty of Pharmacy, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- Microscopy and Dynamic Imaging Unit, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Calle Melchor Fernandez Almagro 3, 28029 Madrid, Spain
- Correspondence: (J.J.A.-C.); (M.F.); (S.G.-R.)
| | - Santiago Gómez-Ruiz
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, C/Tulipán s/n, 28933 Móstoles, Spain
- Correspondence: (J.J.A.-C.); (M.F.); (S.G.-R.)
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17
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Shaw M, Petzer A, Petzer JP, Cloete TT. The pterin binding site of dihydropteroate synthase (DHPS): in silico screening and in vitro antibacterial activity of existing drugs. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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18
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Shaw GX, Fan L, Cherry S, Shi G, Tropea JE, Ji X. Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design. Curr Res Struct Biol 2023; 5:100095. [PMID: 36820301 PMCID: PMC9937910 DOI: 10.1016/j.crstbi.2023.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/27/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Dihydroneopterin aldolase (DHNA) is essential for folate biosynthesis in microorganisms. Without a counterpart in mammals, DHNA is an attractive target for antimicrobial agents. Helicobacter pylori infection occurs in human stomach of over 50% of the world population, but first-line therapies for the infection are facing rapidly increasing resistance. Novel antibiotics are urgently needed, toward which structural information on potential targets is critical. We have determined the crystal structure of H. pylori DHNA (HpDHNA) in complex with a pterin molecule (HpDHNA:Pterin) at 1.49-Å resolution. The HpDHNA:Pterin complex forms a tetramer in crystal. The tetramer is also observed in solution by dynamic light scattering and confirmed by small-angle X-ray scattering. To date, all but one reported DHNA structures are octameric complexes. As the only exception, ligand-free Mycobacterium tuberculosis DHNA (apo-MtDHNA) forms a tetramer in crystal, but its active sites are only partially formed. In contrast, the tetrameric HpDHNA:Pterin complex has well-formed active sites. Each active site accommodates one pterin molecule, but the exit of active site is blocked by two amino acid residues exhibiting a contact distance of 5.2 Å. In contrast, the corresponding contact distance in Staphylococcus aureus DHNA (SaDHNA) is twice the size, ranging from 9.8 to 10.5 Å, for ligand-free enzyme, the substrate complex, the product complex, and an inhibitor complex. This large contact distance indicates that the active site of SaDHNA is wide open. We propose that this isozyme-specific contact distance (ISCD) is a characteristic feature of DHNA active site. Comparative analysis of HpDHNA and SaDHNA structures suggests a fragment-based strategy for the development of isozyme-specific inhibitors.
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Key Words
- ANL, Argonne National Laboratory
- APS, Advanced Photon Source
- Antibiotic
- DHFS, dihydrofolate synthase
- DHNA, dihydroneopterin aldolase
- DHNP, 7,8-dihydroneopterin
- DHPS, dihydropteroate synthase
- DLS, dynamic light scattering
- Dihydroneopterin aldolase
- Dmax, maximum dimension
- EcDHNA, Escherichia coli DHNA
- FBDD, fragment-based drug discovery
- Folate biosynthesis
- Fragment-based drug discovery
- GA, glycoaldehyde
- HP, 6-hydroxymethyl-7,8-dihydropterin
- HPPK, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
- Helicobacter pylori
- HpDHNA, Helicobacter pylori DHNA
- ISCD, isozyme-specific contact distance
- MW, molecular weight
- MtDHNA, Mycobacterium tuberculosis DHNA
- NP, neopterin
- P(r), pair-distance distribution function
- PCR, polymerase chain reaction
- Rg, radius of gyration
- SAXS, small-angle X-ray scattering
- SER-CAT, Southeast Regional Collaborative Access Team
- SaDHNA, Staphylococcus aureus DHNA
- SpDHNA, Streptococcus pneumoniae DHNA
- TCEP, tris(2-carboxyethyl)phosphine
- TEV, tobacco etch virus
- wwPDB, Worldwide Protein Data Bank
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Affiliation(s)
- Gary X. Shaw
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Lixin Fan
- Basic Research Program, Frederick National Laboratory for Cancer Research, Small-angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Genbin Shi
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Joseph E. Tropea
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Xinhua Ji
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
- Corresponding author. 1050 Boyles Street, Frederick, MD, 21702, USA.
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19
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Rua M, Simón JA, Collantes M, Ecay M, Leiva J, Carmona-Torre F, Ramos R, Pareja F, Pulagam KR, Llop J, Del Pozo JL, Peñuelas I. Infection-specific PET imaging with 18F-fluorodeoxysorbitol and 2-[ 18F]F-ρ-aminobenzoic acid: An extended diagnostic tool for bacterial and fungal diseases. Front Microbiol 2023; 14:1094929. [PMID: 36760503 PMCID: PMC9905739 DOI: 10.3389/fmicb.2023.1094929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Suspected infectious diseases located in difficult-to-access sites can be challenging due to the need for invasive procedures to isolate the etiological agent. Positron emission tomography (PET) is a non-invasive imaging technology that can help locate the infection site. The most widely used radiotracer for PET imaging (2-deoxy-2[18F] fluoro-D-glucose: [18F]FDG) shows uptake in both infected and sterile inflammation. Therefore, there is a need to develop new radiotracers able to specifically detect microorganisms. Methods We tested two specific radiotracers: 2-deoxy-2-[18F]-fluoro-D-sorbitol ([18F]FDS) and 2-[18F]F-ρ-aminobenzoic acid ([18F]FPABA), and also developed a simplified alternative of the latter for automated synthesis. Clinical and reference isolates of bacterial and yeast species (19 different strains in all) were tested in vitro and in an experimental mouse model of myositis infection. Results and discussion Non-lactose fermenters (Pseudomonas aeruginosa and Stenotrophomonas maltophilia) were unable to take up [18F]FDG in vitro. [18F]FDS PET was able to visualize Enterobacterales myositis infection (i.e., Escherichia coli) and to differentiate between yeasts with differential assimilation of sorbitol (i.e., Candida albicans vs. Candida glabrata). All bacteria and yeasts tested were detected in vitro by [18F]FPABA. Furthermore, [18F]FPABA was able to distinguish between inflammation and infection in the myositis mouse model (E. coli and Staphylococcus aureus) and could be used as a probe for a wide variety of bacterial and fungal species.
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Affiliation(s)
- Marta Rua
- Clinical Microbiology Laboratory, Clínica Universidad de Navarra, Pamplona, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Jon Ander Simón
- Radiopharmacy Unit, Department of Nuclear Medicine, Clinica Universidad de Navarra, Pamplona, Spain
| | - María Collantes
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain,Translational Molecular Imaging Unit, Department of Nuclear Medicine, Clinica Universidad de Navarra, Pamplona, Spain,*Correspondence: María Collantes, ✉
| | - Margarita Ecay
- Translational Molecular Imaging Unit, Department of Nuclear Medicine, Clinica Universidad de Navarra, Pamplona, Spain
| | - José Leiva
- Clinical Microbiology Laboratory, Clínica Universidad de Navarra, Pamplona, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Francisco Carmona-Torre
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain,Infectious Diseases Division, Clínica Universidad de Navarra, Pamplona, Spain
| | - Rocío Ramos
- Radiopharmacy Unit, Department of Nuclear Medicine, Clinica Universidad de Navarra, Pamplona, Spain
| | - Félix Pareja
- Radiopharmacy Unit, Department of Nuclear Medicine, Clinica Universidad de Navarra, Pamplona, Spain
| | - Krishna R. Pulagam
- Basque Research and Technology Alliance (BRTA), CIC BiomaGUNE, San Sebastián, Spain
| | - Jordi Llop
- Basque Research and Technology Alliance (BRTA), CIC BiomaGUNE, San Sebastián, Spain
| | - José Luis Del Pozo
- Clinical Microbiology Laboratory, Clínica Universidad de Navarra, Pamplona, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain,Infectious Diseases Division, Clínica Universidad de Navarra, Pamplona, Spain
| | - Iván Peñuelas
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain,Radiopharmacy Unit, Department of Nuclear Medicine, Clinica Universidad de Navarra, Pamplona, Spain,Translational Molecular Imaging Unit, Department of Nuclear Medicine, Clinica Universidad de Navarra, Pamplona, Spain
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Xu L, Xiao Y, Zhang J, Fang X. Structural insights into translation regulation by the THF-II riboswitch. Nucleic Acids Res 2023; 51:952-965. [PMID: 36620887 PMCID: PMC9881143 DOI: 10.1093/nar/gkac1257] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
In bacteria, expression of folate-related genes is controlled by the tetrahydrofolate (THF) riboswitch in response to specific binding of THF and its derivatives. Recently, a second class of THF riboswitches, named THF-II, was identified in Gram-negative bacteria, which exhibit distinct architecture from the previously characterized THF-I riboswitches found in Gram-positive bacteria. Here, we present the crystal structures of the ligand-bound THF-II riboswitch from Mesorhizobium loti. These structures exhibit a long rod-like fold stabilized by continuous base pair and base triplet stacking across two helices of P1 and P2 and their interconnecting ligand-bound binding pocket. The pterin moiety of the ligand docks into the binding pocket by forming hydrogen bonds with two highly conserved pyrimidines in J12 and J21, which resembles the hydrogen-bonding pattern at the ligand-binding site FAPK in the THF-I riboswitch. Using small-angle X-ray scattering and isothermal titration calorimetry, we further characterized the riboswitch in solution and reveal that Mg2+ is essential for pre-organization of the binding pocket for efficient ligand binding. RNase H cleavage assay indicates that ligand binding reduces accessibility of the ribosome binding site in the right arm of P1, thus down-regulating the expression of downstream genes. Together, these results provide mechanistic insights into translation regulation by the THF-II riboswitch.
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Affiliation(s)
| | | | - Jie Zhang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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Das BK, Chakraborty D. Deciphering the competitive inhibition of dihydropteroate synthase by 8 marcaptoguanine analogs: enhanced potency in phenylsulfonyl fragments. J Biomol Struct Dyn 2022; 40:13083-13102. [PMID: 34581241 DOI: 10.1080/07391102.2021.1981452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of sulfa-drug resistance and reduced efficacy of pterin-based analogs towards Dihydropteroate synthase (DHPS) inhibition dictate a pressing need of developing novel antimicrobial agents for immune-compromised patients. Recently, a series of 8-Marcaptoguanin (8-MG) derivatives synthesized for 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (experimental KD ∼ 100-.0.36) showed remarkable homology with the pteroic-acid and serve as a template for product antagonism in DHPS. The present work integrates ligand-based drug discovery techniques with structure-based docking, enhanced MD simulation, and MM/PBSA techniques to demonstrate the essential features of 8-MG analogs which make it a potent inhibitor for DHPS. The delicate balance in hydrophilic, hydrophobic substitutions on the 8-MG core is the crucial signature for DHPS inhibition. It is found that the dynamic interactions of active compounds are mainly dominated by consistent hydrogen bonding network with Asp 96, Asn 115, Asp 185, Ser 222, Arg 255 and π-π stacking, π-cation interactions with Phe 190, Lys 221. Further, two new 8-MG compounds containing N-phenylacetamide (compound S1, ΔGbind-eff = -62.03 kJ/mol) and phenylsulfonyl (compound S3, ΔGbind-eff = -71.29 kJ/mol) fragments were found to be the most potent inhibitor of DHPS, which stabilize the flexible pABA binding loop, thereby increasing their binding affinity. MM/PBSA calculation shows electrostatic energy contribution to be the principal component in stabilizing the inhibitors in the binding pocket. This fact is further confirmed by the higher energy barrier obtained in umbrella sampling for this class of inhibitors.
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Affiliation(s)
- Bratin Kumar Das
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
| | - Debashree Chakraborty
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
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22
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Sikdar R, Elias MH. Evidence for Complex Interplay between Quorum Sensing and Antibiotic Resistance in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0126922. [PMID: 36314960 PMCID: PMC9769976 DOI: 10.1128/spectrum.01269-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
Quorum sensing (QS) is a cell-density-dependent, intercellular communication system mediated by small diffusible signaling molecules. QS regulates a range of bacterial behaviors, including biofilm formation, virulence, drug resistance mechanisms, and antibiotic tolerance. Enzymes capable of degrading signaling molecules can interfere in QS-a process termed as quorum quenching (QQ). Remarkably, previous work reported some cases where enzymatic interference in QS was synergistic to antibiotics against Pseudomonas aeruginosa. The premise of combination therapy is attractive to fight against multidrug-resistant bacteria, yet comprehensive studies are lacking. Here, we evaluate the effects of QS signal disruption on the antibiotic resistance profile of P. aeruginosa by testing 222 antibiotics and antibacterial compounds from 15 different classes. We found compelling evidence that QS signal disruption does indeed affect antibiotic resistance (40% of all tested compounds; 89/222), albeit not always synergistically (not synergistic for 19% of compounds; 43/222). For some tested antibiotics, such as sulfathiazole and trimethoprim, we were able to relate the changes in resistance caused by QS signal disruption to the modulation of the expression of key genes of the folate biosynthetic pathway. Moreover, using a P. aeruginosa-based Caenorhabditis elegans killing model, we confirmed that enzymatic QQ modulates the effects of antibiotics on P. aeruginosa's pathogenicity in vivo. Altogether, these results show that signal disruption has profound and complex effects on the antibiotic resistance profile of P. aeruginosa. This work suggests that combination therapy including QQ and antibiotics should be discussed not globally but, rather, in case-by-case studies. IMPORTANCE Quorum sensing (QS) is a cell-density-dependent communication system used by a wide range of bacteria to coordinate behaviors. Strategies pertaining to the interference in QS are appealing approaches to control microbial behaviors that depend on QS, including virulence and biofilms. Interference in QS was previously reported to be synergistic with antibiotics, yet no systematic assessment exists. Here, we evaluate the potential of combination treatments using the model opportunistic human pathogen Pseudomonas aeruginosa PA14. In this model, collected data demonstrate that QS largely modulates the antibiotic resistance profile of PA14 (for more than 40% of the tested drugs). However, the outcome of combination treatments is synergistic for only 19% of them. This research demonstrates the complex relationship between QS and antibiotic resistance and suggests that combination therapy including QS inhibitors and antibiotics should be discussed not globally but, rather, in case-by-case studies.
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Affiliation(s)
- Rakesh Sikdar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Mikael H. Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
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Matshwele JTP, Odisitse S, Mazimba O, Julius LG, Mogatwe T, Nareetsile F. Synthesis and Crystal Structure of Pyridin-4-ylmethyl 4-Aminobenzoate, C13H12N2O2. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522070094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Dey H, Vasudevan K, KR D, Majji R, CN P, C GPD. An integrated gene network analysis to decode the multi-drug resistance mechanism in Klebsiella pneumoniae. Microb Pathog 2022; 173:105878. [DOI: 10.1016/j.micpath.2022.105878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
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25
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Singh H, Saini V. Development, synthesis, computational and in silico investigations of Pd(II)-catalyzed aryl fluorinated and hydroxylated sulfonamides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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Lazenby JJ, Li ES, Whitchurch CB. Cell wall deficiency - an alternate bacterial lifestyle? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925044 DOI: 10.1099/mic.0.001218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Historically, many species of bacteria have been reported to produce viable, cell wall deficient (CWD) variants. A variety of terms have been used to refer to CWD bacteria and a plethora of methods described in which to induce, cultivate and propagate them. In this review, we will examine the long history of scientific research on CWD bacteria examining the methods by which CWD bacteria are generated; the requirements for survival in a CWD state; the replicative processes within a CWD state; and the reversion of CWD bacteria into a walled state, or lack thereof. In doing so, we will present evidence that not all CWD variants are alike and that, at least in some cases, CWD variants arise through an adaptive lifestyle switch that enables them to live and thrive without a cell wall, often to avoid antimicrobial activity. Finally, the implications of CWD bacteria in recurring infections, tolerance to antibiotic therapy and antimicrobial resistance will be examined to illustrate the importance of greater understanding of the CWD bacteria in human health and disease.
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Affiliation(s)
- James J Lazenby
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Erica S Li
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Cynthia B Whitchurch
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TK, UK
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Bauman JS, Pizzey R, Beckmann M, Villarreal-Ramos B, King J, Hopkins B, Rooke D, Hewinson G, Mur LAJ. Untargeted metabolomic analysis of thoracic blood from badgers indicate changes linked to infection with bovine tuberculosis (Mycobacterium bovis): a pilot study. Metabolomics 2022; 18:61. [PMID: 35896834 PMCID: PMC9329164 DOI: 10.1007/s11306-022-01915-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB) in cattle, represents a major disease burden to UK cattle farming, with considerable costs associated with its control. The European badger (Meles meles) is a known wildlife reservoir for bTB and better knowledge of the epidemiology of bTB through testing wildlife is required for disease control. Current tests available for the diagnosis of bTB in badgers are limited by cost, processing time or sensitivities. MATERIALS AND METHODS We assessed the ability of flow infusion electrospray-high-resolution mass spectrometry (FIE-HRMS) to determine potential differences between infected and non-infected badgers based on thoracic blood samples obtained from badgers found dead in Wales. Thoracic blood samples were autoclaved for handling in a containment level 2 (CL2) hazard laboratory. RESULTS Here we show the major differences associated with with M. bovis infection were changes to folate, pyrimidine, histidine, glycerophospholipid and phosphonate metabolism. CONCLUSIONS Our studies have indicated differences in the metabolomic signature of badgers found dead in relation to their infection status, suggesting metabolomics could hold potential for developing novel diagnostics for bTB in badgers. As well as highlighting a potential way to handle samples containing a highly pathogenic agent at CL2 for metabolomics studies.
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Affiliation(s)
- James Scott Bauman
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA, Ceredigion, UK
| | - Richard Pizzey
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA, Ceredigion, UK
| | - Manfred Beckmann
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA, Ceredigion, UK
| | - Bernardo Villarreal-Ramos
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA, Ceredigion, UK
- Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Aberystwyth, SY23 3AR, Ceredigion, UK
- TB Research Group, Animal and Plant Health Agency, New Haw, Addlestone, KT15 3NB, Surrey, UK
| | - Jonathan King
- Wales Veterinary Science Centre, Y Buarth, Aberystwyth, SY23 1ND, Ceredigion, UK
| | - Beverley Hopkins
- Wales Veterinary Science Centre, Y Buarth, Aberystwyth, SY23 1ND, Ceredigion, UK
| | | | - Glyn Hewinson
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA, Ceredigion, UK
- Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Aberystwyth, SY23 3AR, Ceredigion, UK
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA, Ceredigion, UK.
- Aberystwyth University, B2.03 Edward Llwyd, Penglais, Aberystwyth, SY23 3FL, UK.
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Owusu-Kwarteng J, Agyei D, Akabanda F, Atuna RA, Amagloh FK. Plant-Based Alkaline Fermented Foods as Sustainable Sources of Nutrients and Health-Promoting Bioactive Compounds. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.885328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Traditional food fermentation is a practice that precedes human history. Acidic products such as yogurts and sourdoughs or alcoholic beverages produced through lactic acid or yeast fermentations, respectively, are widely described and documented. However, a relatively less popular group of fermented products known as alkaline fermented foods are common traditional products in Africa and Asia. These products are so called “alkaline” because the pH tends to increase during fermentation due to the formation of ammonia resulting from protein degradation by Bacillus species. Plant-based alkaline fermented foods (AFFs) are generally produced from legumes including soybean, non-soybean leguminous seeds, and other non-legume plant raw materials. Alkaline fermented food products such as natto, douchi, kinema, doenjang, chongkukjang, thua nao, meitauza, yandou, dawadawa/iru, ugba, kawal, okpehe, otiru, oso, ogiri, bikalga, maari/tayohounta, ntoba mbodi, cabuk, and owoh are produced at small industrial scale or household levels and widely consumed in Asia and Africa where they provide essential nutrients and health-promoting bioactive compounds for the population. Alkaline food fermentation is important for sustainable food security as it contributes to traditional dietary diversity, significantly reduces antinutritional components in raw plant materials thereby improving digestibility, improves health via the production of vitamins, and may confer probiotic and post-biotic effects onto consumers. In this review, we present currently available scientific information on plant-based AFFs and their role as sustainable sources of nutrients and bioactive compounds for improved health. Finally, we provide perspectives on research needs required to harness the full potential of AFFs in contributing to nutrition and health.
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B Vitamins and Their Roles in Gut Health. Microorganisms 2022; 10:microorganisms10061168. [PMID: 35744686 PMCID: PMC9227236 DOI: 10.3390/microorganisms10061168] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host’s metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed.
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31
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Zhao Y, Min H, Luo K, Zhang R, Chen Q, Chen Z. Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153169. [PMID: 35051480 DOI: 10.1016/j.scitotenv.2022.153169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.
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Affiliation(s)
- Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Hongchao Min
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Ruijie Zhang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China.
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China.
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Host cell targeting of novel antimycobacterial 4-aminosalicylic acid derivatives with tuftsin carrier peptides. Eur J Pharm Biopharm 2022; 174:111-130. [DOI: 10.1016/j.ejpb.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 11/23/2022]
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Hegde PV, Howe MD, Zimmerman MD, Boshoff HIM, Sharma S, Remache B, Jia Z, Pan Y, Baughn AD, Dartois V, Aldrich CC. Synthesis and biological evaluation of orally active prodrugs and analogs of para-aminosalicylic acid (PAS). Eur J Med Chem 2022; 232:114201. [PMID: 35219151 PMCID: PMC8941652 DOI: 10.1016/j.ejmech.2022.114201] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
Tuberculosis (TB) is one of the world's most deadly infectious diseases resulting in nearly 1.3 million deaths annually and infecting nearly one-quarter of the population. para-Aminosalicylic acid (PAS), an important second-line agent for treating drug-resistant Mycobacterium tuberculosis, has moderate bioavailability and rapid clearance that necessitate high daily doses of up to 12 g per day, which in turn causes severe gastrointestinal disturbances presumably by disruption of gut microbiota and host epithelial cells. We first synthesized a series of alkyl, acyloxy and alkyloxycarbonyloxyalkyl ester prodrugs to increase the oral bioavailability and thereby prevent intestinal accumulation as well as undesirable bioactivation by the gut microbiome to non-natural folate species that exhibit cytotoxicity. The pivoxyl prodrug of PAS was superior to all of the prodrugs examined and showed nearly quantitative absorption. While the conceptually simple prodrug approach improved the oral bioavailability of PAS, it did not address the intrinsic rapid clearance of PAS mediated by N-acetyltransferase-1 (NAT-1). Thus, we next modified the PAS scaffold to reduce NAT-1 catalyzed inactivation by introduction of groups to sterically block N-acetylation and fluorination of the aryl ring of PAS to attenuate N-acetylation by electronically deactivating the para-amino group. Among the mono-fluorinated analogs prepared, 5-fluoro-PAS, exhibited the best activity and an 11-fold decreased rate of inactivation by NAT-1 that translated to a 5-fold improved exposure as measured by area-under-the-curve (AUC) following oral dosing to CD-1 mice. The pivoxyl prodrug and fluorination at the 5-position of PAS address the primary limitations of PAS and have the potential to revitalize this second-line TB drug.
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Affiliation(s)
- Pooja V Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Michael D Howe
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Brianna Remache
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Ziyi Jia
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Yan Pan
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Anthony D Baughn
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Veronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
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Dharuman S, Wallace MJ, Reeve SM, Bulitta JB, Lee RE. Synthesis and Structure–Activity Relationship of Thioacetamide-Triazoles against Escherichia coli. Molecules 2022; 27:molecules27051518. [PMID: 35268619 PMCID: PMC8911640 DOI: 10.3390/molecules27051518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Infections due to Gram-negative bacteria are increasingly dangerous due to the spread of multi-drug resistant strains, emphasizing the urgent need for new antibiotics with alternative modes of action. We have previously identified a novel class of antibacterial agents, thioacetamide-triazoles, using an antifolate targeted screen and determined their mode of action which is dependent on activation by cysteine synthase A. Herein, we report a detailed examination of the anti-E. coli structure–activity relationship of the thioacetamide-triazoles. Analogs of the initial hit compounds were synthesized to study the contribution of the aryl, thioacetamide, and triazole sections. A clear structure–activity relationship was observed generating compounds with excellent inhibition values. Substitutions to the aryl ring were generally best tolerated, including the introduction of thiazole and pyridine heteroaryl systems. Substitutions to the central thioacetamide linker section were more nuanced; the introduction of a methyl branch to the thioacetamide linker substantially decreased antibacterial activity, but the isomeric propionamide and N-benzamide systems retained activity. Changes to the triazole portion of the molecule dramatically decreased the antibacterial activity, further indicating that 1,2,3-triazole is critical for potency. From these studies, we have identified new lead compounds with desirable in-vitro ADME properties and in-vivo pharmacokinetic properties.
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Affiliation(s)
- Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie M. Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
| | - Jürgen B. Bulitta
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, FL 31836, USA;
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
- Correspondence:
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35
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Affiliation(s)
- Bernhard Kräutler
- Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria.
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Lionaki E, Ploumi C, Tavernarakis N. One-Carbon Metabolism: Pulling the Strings behind Aging and Neurodegeneration. Cells 2022; 11:cells11020214. [PMID: 35053330 PMCID: PMC8773781 DOI: 10.3390/cells11020214] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 01/27/2023] Open
Abstract
One-carbon metabolism (OCM) is a network of biochemical reactions delivering one-carbon units to various biosynthetic pathways. The folate cycle and methionine cycle are the two key modules of this network that regulate purine and thymidine synthesis, amino acid homeostasis, and epigenetic mechanisms. Intersection with the transsulfuration pathway supports glutathione production and regulation of the cellular redox state. Dietary intake of micronutrients, such as folates and amino acids, directly contributes to OCM, thereby adapting the cellular metabolic state to environmental inputs. The contribution of OCM to cellular proliferation during development and in adult proliferative tissues is well established. Nevertheless, accumulating evidence reveals the pivotal role of OCM in cellular homeostasis of non-proliferative tissues and in coordination of signaling cascades that regulate energy homeostasis and longevity. In this review, we summarize the current knowledge on OCM and related pathways and discuss how this metabolic network may impact longevity and neurodegeneration across species.
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Affiliation(s)
- Eirini Lionaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Crete, Greece; (E.L.); (C.P.)
| | - Christina Ploumi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Crete, Greece; (E.L.); (C.P.)
- Department of Basic Sciences, Faculty of Medicine, University of Crete, 70013 Heraklion, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Crete, Greece; (E.L.); (C.P.)
- Department of Basic Sciences, Faculty of Medicine, University of Crete, 70013 Heraklion, Crete, Greece
- Correspondence: ; Tel.: +30-2810-391069
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Shahrear S, Afroj Zinnia M, Sany MRU, Islam ABMMK. Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential. Bioinform Biol Insights 2022; 16:11779322221136002. [PMID: 36386863 PMCID: PMC9661560 DOI: 10.1177/11779322221136002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
Vibrio parahaemolyticus, an aquatic pathogen, is a major concern in the shrimp aquaculture industry. Several strains of this pathogen are responsible for causing acute hepatopancreatic necrosis disease as well as other serious illness, both of which result in severe economic losses. The genome sequence of two pathogenic strains of V. parahaemolyticus, MSR16 and MSR17, isolated from Bangladesh, have been reported to gain a better understanding of their diversity and virulence. However, the prevalence of hypothetical proteins (HPs) makes it challenging to obtain a comprehensive understanding of the pathogenesis of V. parahaemolyticus. The aim of the present study is to provide a functional annotation of the HPs to elucidate their role in pathogenesis employing several in silico tools. The exploration of protein domains and families, similarity searches against proteins with known function, gene ontology enrichment, along with protein-protein interaction analysis of the HPs led to the functional assignment with a high level of confidence for 656 proteins out of a pool of 2631 proteins. The in silico approach used in this study was important for accurately assigning function to HPs and inferring interactions with proteins with previously described functions. The HPs with function predicted were categorized into various groups such as enzymes involved in small-compound biosynthesis pathway, iron binding proteins, antibiotics resistance proteins, and other proteins. Several proteins with potential druggability were identified among them. In addition, the HPs were investigated in search of virulent factors, which led to the identification of proteins that have the potential to be exploited as vaccine candidate. The findings of the study will be effective in gaining a better understanding of the molecular mechanisms of bacterial pathogenesis. They may also provide an insight into the process of evaluating promising targets for the development of drugs and vaccines against V. parahaemolyticus.
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Affiliation(s)
- Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md. Rabi Us Sany
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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Synthesis, characterization of nitro or amino substituted pyridyl ligands bridged by an ester or ether bond, and their antibacterial assessment against drug resistant bacteria. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Reducing the Periplasmic Glutathione Content Makes Escherichia coli Resistant to Trimethoprim and Other Antimicrobial Drugs. Microbiol Spectr 2021; 9:e0074321. [PMID: 34908461 PMCID: PMC8672908 DOI: 10.1128/spectrum.00743-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Although glutathione (GSH) has been shown to influence the antimicrobial effects of many kinds of antibiotics, little is known about its role in relation to trimethoprim (TMP), a widely used antifolate. In this study, several genes related to glutathione metabolism were deleted in different Escherichia coli strains (i.e., O157:H7 and ATCC 25922), and their effects on susceptibility to TMP were tested. The results showed that deleting gshA, gshB, grxA, and cydD caused TMP resistance, and deleting cydD also caused resistance to other drugs. Meanwhile, deleting gshA, grxA, and cydD resulted in a significant decrease of the periplasmic glutathione content. Supplementing exogenous GSH or further deleting glutathione importer genes (gsiB and ggt) restored TMP sensitivity to ΔcydD. Subsequently, the results of quantitative-reverse transcription PCR experiments showed that expression levels of acrA, acrB, and tolC were significantly upregulated in both ΔgrxA and ΔcydD. Correspondingly, deleting cydD led to a decreased accumulation of TMP within bacterial cells, and further deleting acrA, acrB, or tolC restored TMP sensitivity to ΔcydD. Inactivation of CpxR and SoxS, two transcriptional factors that modulate the transcription of acrAB-tolC, restored TMP sensitivity to ΔcydD. Furthermore, mutations of gshA, gshB, grxA, cydC, and cydD are highly prevalent in E. coli clinical strains. Collectively, these data suggest that reducing the periplasmic glutathione content of E. coli leads to increased expression of acrAB-tolC with the involvement of CpxR and SoxS, ultimately causing drug resistance. To the best of our knowledge, this is the first report showing a linkage between periplasmic GSH and drug resistance in bacteria. IMPORTANCE After being used extensively for decades, trimethoprim still remains one of the key accessible antimicrobials recommended by the World Health Organization. A better understanding of the mechanisms of resistance would be beneficial for the future utilization of this drug. It has been shown that the AcrAB-TolC efflux pump is associated with trimethoprim resistance in E. coli clinical strains. In this study, we show that E. coli can sense the periplasmic glutathione content with the involvement of the CpxAR two-component system. As a result, reducing the periplasmic glutathione content leads to increased expression of acrA, acrB, and tolC via CpxR and SoxS, causing resistance to antimicrobials, including trimethoprim. Meanwhile, mutations in the genes responsible for periplasmic glutathione content maintenance are highly prevalent in E. coli clinical isolates, indicating a potential correlation of the periplasmic glutathione content and clinical antimicrobial resistance, which merits further investigation.
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Chen Q, Yang X, Meng Q, Zhao L, Yuan Y, Chi W, He L, Shi K, Liu S. Integrative multiomics analysis of the acid stress response of Oenococcus oeni mutants at different growth stages. Food Microbiol 2021; 102:103905. [PMID: 34809937 DOI: 10.1016/j.fm.2021.103905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acid stress is one of the most important environmental stresses that adversely affect the growth of lactic acid bacteria (LAB), such as Oenococcus oeni which was isolated from grape-berries and mainly used in wine fermentation. The aim of this paper is to comprehensively characterize the mechanisms of acid stress regulation in O. oeni and to provide a viable theoretical basis for breed and improvement of existing LAB. METHOD First, six O. oeni mutants with acid-sensitive (strains b2, a1, c2) and acid-tolerant (strains b1, a3, c1) phenotypes were screened from three wild-type O. oeni, and then their genome (sequencing), transcriptome and metabolome (LC-MS/MS) were examined. RESULTS A total of 459 genes were identified with one or more intragenic single nucleotide polymorphisms (SNPs) in these mutants, and were extensively involved in metabolism and cellular functions with a high mutation rates in purine (46%) and pyrimidine (48%) metabolic pathways. There were 210 mutated genes that cause significant changes in expression levels. In addition, 446 differentially accumulated metabolites were detected, and they were consistently detected at relatively high levels in the acid-tolerant O. oeni mutant. The levels of intracellular differentially expressed genes and differential metabolites changed with increasing culture time. CONCLUSION The integrative pathways analysis showed that the intracellular response associated with acid regulation differed significantly between acid-sensitive and acid-tolerant O. oeni mutants, and also changed at different growth stages.
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Affiliation(s)
- Qiling Chen
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xiangke Yang
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Henan University of Animal Husbandry and Economy, Zhenzhou, Henan, China
| | - Qiang Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhao
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Yuan
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wei Chi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ling He
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Kan Shi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
| | - Shuwen Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
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41
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Shome S, Sankar K, Jernigan RL. Simulated Drug Efflux for the AbgT Family of Membrane Transporters. J Chem Inf Model 2021; 61:5673-5681. [PMID: 34714659 DOI: 10.1021/acs.jcim.1c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug extrusion through molecular efflux pumps is an important mechanism for the survival of many pathogenic bacteria by removing drugs, providing multidrug resistance (MDR). Understanding molecular mechanisms for drug extrusion in multidrug efflux pumps is important for the development of new antiresistance drugs. The AbgT family of transporters involved in the folic acid biosynthesis pathway represents one such important efflux pump system. In addition to the transport of the folic acid precursor p-amino benzoic acid (PABA), members of this family are involved in the efflux of several sulfa drugs, conferring drug resistance to the bacteria. With the availability of structures for two members of this family (YdaH and MtrF), we investigate molecular pathways for transport of PABA and a sulfa drug (sulfamethazine) particularly for the YdaH transporter using steered molecular dynamics. Our analyses reveal the probable ligand migration pathways through the transporter, which also identifies key residues along the transport pathway. In addition, simulations using both PABA and sulfamethazine show how the protein is able to transport ligands of different shapes and sizes out of the pathogen. Our observations confirm previously reported functional residues for transport along the pathways by which YdaH transporters achieve antibiotic resistance to shuttle drugs out of the cells.
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Affiliation(s)
- Sayane Shome
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Kannan Sankar
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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Müller R, Gerwel TM, Kimuda MP, Bishop ÖT, Veale CGL, Hoppe HC. Virtual screening and in vitro validation identifies the first reported inhibitors of Salmonella enterica HPPK. RSC Med Chem 2021; 12:1750-1756. [PMID: 34778775 PMCID: PMC8528203 DOI: 10.1039/d1md00237f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 11/21/2022] Open
Abstract
HPPK, which directly precedes DHPS in the folate biosynthetic pathway, is a promising but chronically under-exploited anti-microbial target. Here we report the identification of new S. enterica HPPK inhibitors, offering potential for new resistance circumventing S. enterica therapies as well as avenues for diversifying the current HPPK inhibitor space.
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Affiliation(s)
- Ronel Müller
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal Private Bag X01 Scottsville 3209 South Africa
| | - Tiaan M Gerwel
- Faculty of Pharmacy, Rhodes University Makhanda 6140 South Africa
| | - Magambo Phillip Kimuda
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University Makhanda 6140 South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University Makhanda 6140 South Africa
| | - Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal Private Bag X01 Scottsville 3209 South Africa
| | - Heinrich C Hoppe
- Department of Biochemistry and Microbiology, Rhodes University Makhanda 6140 South Africa
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Si L, Gu J, Wen M, Wang R, Fleming J, Li J, Xu J, Bi L, Deng J. relA Inactivation Converts Sulfonamides Into Bactericidal Compounds. Front Microbiol 2021; 12:698468. [PMID: 34646242 PMCID: PMC8503649 DOI: 10.3389/fmicb.2021.698468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Folates are required for the de novo biosynthesis of purines, thymine, methionine, glycine, and pantothenic acid, key metabolites that bacterial cells cannot survive without. Sulfonamides, which inhibit bacterial folate biosynthesis and are generally considered as bacteriostats, have been extensively used as broad-spectrum antimicrobials for decades. Here we show that, deleting relA in Escherichia coli and other bacterial species converted sulfamethoxazole from a bacteriostat into a bactericide. Not as previously assumed, the bactericidal effect of SMX was not caused by thymine deficiency. When E. coli ∆relA was treated with SMX, reactive oxygen species and ferrous ion accumulated inside the bacterial cells, which caused extensive DNA double-strand breaks without the involvement of incomplete base excision repair. In addition, sulfamethoxazole showed bactericidal effect against E. coli O157 ∆relA in mice, suggesting the possibility of designing new potentiators for sulfonamides targeting RelA. Thus, our study uncovered the previously unknown bactericidal effects of sulfonamides, which advances our understanding of their mechanisms of action, and will facilitate the designing of new potentiators for them.
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Affiliation(s)
- Lizhen Si
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Gu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Mi Wen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruiqi Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jinyue Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jintian Xu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lijun Bi
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Stomatology and Medicine, Foshan University, Foshan, China
- Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China
| | - Jiaoyu Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China
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Rashdan HRM, Shehadi IA, Abdelrahman MT, Hemdan BA. Antibacterial Activities and Molecular Docking of Novel Sulfone Biscompound Containing Bioactive 1,2,3-Triazole Moiety. Molecules 2021; 26:molecules26164817. [PMID: 34443405 PMCID: PMC8399954 DOI: 10.3390/molecules26164817] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, a new synthetic 1,2,3-triazole-containing disulfone compound was derived from dapsone. Its chemical structure was confirmed using microchemical and analytical data, and it was tested for its in vitro antibacterial potential. Six different pathogenic bacteria were selected. MICs values and ATP levels were determined. Further, toxicity performance was measured using MicroTox Analyzer. In addition, a molecular docking study was performed against two vital enzymes: DNA gyrase and Dihydropteroate synthase. The results of antibacterial abilities showed that the studied synthetic compound had a strong bactericidal effect against all tested bacterial strains, as Gram-negative species were more susceptible to the compound than Gram-positive species. Toxicity results showed that the compound is biocompatible and safe without toxic impact. The molecular docking of the compound showed interactions within the pocket of two enzymes, which are able to stabilize the compound and reveal its antimicrobial activity. Hence, from these results, this study recommends that the established compound could be an outstanding candidate for fighting a broad spectrum of pathogenic bacterial strains, and it might therefore be used for biomedical and pharmaceutical applications.
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Affiliation(s)
- Huda R. M. Rashdan
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, Cairo 12622, Egypt
- Correspondence:
| | - Ihsan A. Shehadi
- Chemistry Department, College of Science, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Mohamad T. Abdelrahman
- Radioisotopes Department, Nuclear Research Centre, Egyptian Atomic Energy Authority, Cairo 12311, Egypt;
| | - Bahaa A. Hemdan
- Water Pollution Research Department, Environmental Research Division, National Research Centre, 33 El Buhouth Street, Cairo 12622, Egypt;
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Shi H, Li T, Xu J, Yu J, Yang S, Zhang XE, Tao S, Gu J, Deng JY. MgrB Inactivation Confers Trimethoprim Resistance in Escherichia coli. Front Microbiol 2021; 12:682205. [PMID: 34394028 PMCID: PMC8355897 DOI: 10.3389/fmicb.2021.682205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/30/2021] [Indexed: 11/22/2022] Open
Abstract
After several decades of use, trimethoprim (TMP) remains one of the key access antimicrobial drugs listed by the World Health Organization. To circumvent the problem of trimethoprim resistance worldwide, a better understanding of drug-resistance mechanisms is required. In this study, we screened the single-gene knockout library of Escherichia coli, and identified mgrB and other several genes involved in trimethoprim resistance. Subsequent comparative transcriptional analysis between ΔmgrB and the wild-type strain showed that expression levels of phoP, phoQ, and folA were significantly upregulated in ΔmgrB. Further deleting phoP or phoQ could partially restore trimethoprim sensitivity to ΔmgrB, and co-overexpression of phoP/Q caused TMP resistance, suggesting the involvement of PhoP/Q in trimethoprim resistance. Correspondingly, MgrB and PhoP were shown to be able to modulated folA expression in vivo. After that, efforts were made to test if PhoP could directly modulate the expression of folA. Though phosphorylated PhoP could bind to the promotor region of folA in vitro, the former only provided a weak protection on the latter as shown by the DNA footprinting assay. In addition, deleting the deduced PhoP box in ΔmgrB could only slightly reverse the TMP resistance phenotype, suggesting that it is less likely for PhoP to directly modulate the transcription of folA. Taken together, our data suggested that, in E. coli, MgrB affects susceptibility to trimethoprim by modulating the expression of folA with the involvement of PhoP/Q. This work broadens our understanding of the regulation of folate metabolism and the mechanisms of TMP resistance in bacteria.
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Affiliation(s)
- Hongmei Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ting Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jintian Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jifang Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jing Gu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jiao-Yu Deng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China
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Caffaratti C, Plazy C, Mery G, Tidjani AR, Fiorini F, Thiroux S, Toussaint B, Hannani D, Le Gouellec A. What We Know So Far about the Metabolite-Mediated Microbiota-Intestinal Immunity Dialogue and How to Hear the Sound of This Crosstalk. Metabolites 2021; 11:406. [PMID: 34205653 PMCID: PMC8234899 DOI: 10.3390/metabo11060406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/25/2022] Open
Abstract
Trillions of microorganisms, termed the "microbiota", reside in the mammalian gastrointestinal tract, and collectively participate in regulating the host phenotype. It is now clear that the gut microbiota, metabolites, and intestinal immune function are correlated, and that alterations of the complex and dynamic host-microbiota interactions can have deep consequences for host health. However, the mechanisms by which the immune system regulates the microbiota and by which the microbiota shapes host immunity are still not fully understood. This article discusses the contribution of metabolites in the crosstalk between gut microbiota and immune cells. The identification of key metabolites having a causal effect on immune responses and of the mechanisms involved can contribute to a deeper insight into host-microorganism relationships. This will allow a better understanding of the correlation between dysbiosis, microbial-based dysmetabolism, and pathogenesis, thus creating opportunities to develop microbiota-based therapeutics to improve human health. In particular, we systematically review the role of soluble and membrane-bound microbial metabolites in modulating host immunity in the gut, and of immune cells-derived metabolites affecting the microbiota, while discussing evidence of the bidirectional impact of this crosstalk. Furthermore, we discuss the potential strategies to hear the sound of such metabolite-mediated crosstalk.
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Affiliation(s)
- Clément Caffaratti
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
| | - Caroline Plazy
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
- Service de Biochimie Biologie Moléculaire Toxicologie Environnementale, UM Biochimie des Enzymes et des Protéines, Institut de Biologie et Pathologie, CHU Grenoble-Alpes, 38000 Grenoble, France
- Plateforme de Métabolomique GEMELI-GExiM, Institut de Biologie et Pathologie, CHU Grenoble-Alpes, 38000 Grenoble, France;
| | - Geoffroy Mery
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
- Department of Infectiology-Pneumology, CHU Grenoble-Alpes, 38000 Grenoble, France
| | - Abdoul-Razak Tidjani
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
| | - Federica Fiorini
- Plateforme de Métabolomique GEMELI-GExiM, Institut de Biologie et Pathologie, CHU Grenoble-Alpes, 38000 Grenoble, France;
| | - Sarah Thiroux
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
| | - Bertrand Toussaint
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
- Service de Biochimie Biologie Moléculaire Toxicologie Environnementale, UM Biochimie des Enzymes et des Protéines, Institut de Biologie et Pathologie, CHU Grenoble-Alpes, 38000 Grenoble, France
- Plateforme de Métabolomique GEMELI-GExiM, Institut de Biologie et Pathologie, CHU Grenoble-Alpes, 38000 Grenoble, France;
| | - Dalil Hannani
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
| | - Audrey Le Gouellec
- Faculty of Medicine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble Alpes, TIMC (UMR5525), 38000 Grenoble, France; (C.C.); (C.P.); (G.M.); (A.-R.T.); (S.T.); (B.T.)
- Service de Biochimie Biologie Moléculaire Toxicologie Environnementale, UM Biochimie des Enzymes et des Protéines, Institut de Biologie et Pathologie, CHU Grenoble-Alpes, 38000 Grenoble, France
- Plateforme de Métabolomique GEMELI-GExiM, Institut de Biologie et Pathologie, CHU Grenoble-Alpes, 38000 Grenoble, France;
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47
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Yu M, Zhang G, Li P, Lu H, Tang W, Yang X, Huang R, Yu F, Wu W, Xiao Y, Xing X. Acid-activated ROS generator with folic acid targeting for bacterial biofilm elimination. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 127:112225. [PMID: 34225870 DOI: 10.1016/j.msec.2021.112225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Many medical and chemical applications require the precise supply of antimicrobial components in a controlled manner at the location of mature biofilm deposits. This work reports a facile strategy to fabricate nanoscale metal-organic frameworks (NMOFs) coencapsulating the antibacterial ligand (lysine carbon dots, Lys-CDs) and targeted drug (folic acid, FA) in one pot to improve antibiofilm efficiency against established biofilms. The resulting products are characterized by transmission electron microscopy, field-emission scanning electron microscopy, powder x-ray diffraction, and ultraviolet-visible spectroscopy. The results show that Lys-CDs could coordinate with Zn2+ and the adding of FA inhibits the coordination of Lys-CDs with central ions of Zn. The Lys-CDs and FA are successfully exposed with the NMOFs disintegrating in the acid environment of bacterial metabolites. We are surprised to find a sharp increase of reactive oxygen species (ROS) inside the bacterial cells by FA functionalizing NMOFs, which undoubtedly enhance the antibacterial and antibiofilm activity. The as-synthesized ZIF-8-based nanocomposites also show the peroxidase-like activity in an acid environment, and produce extremely active hydroxyl radicals resulting in the improved antibacterial and antibiofilm activity. The possible mechanisms of antibacterial activities indicate that the presence of FA is significant in the sense of targeting bacteria. This study shows a novel approach to construct acid stimulation supply system which may be helpful for the research of antibiofilms.
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Affiliation(s)
- Meizhe Yu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Gaoke Zhang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Peili Li
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Haojie Lu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Wentao Tang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xu Yang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Ruobing Huang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Fan Yu
- Department of Oral Surgery, 920th Hospital of Joint Logistics Support Force, Kunming 650032, China
| | - Wenzhen Wu
- Department of Oral Surgery, 920th Hospital of Joint Logistics Support Force, Kunming 650032, China
| | - Yuhong Xiao
- Department of Oral Surgery, 920th Hospital of Joint Logistics Support Force, Kunming 650032, China
| | - Xiaodong Xing
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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Wei N, Song L, Gan N. Quantitative Proteomic and Microcystin Production Response of Microcystis aeruginosa to Phosphorus Depletion. Microorganisms 2021; 9:microorganisms9061183. [PMID: 34072711 PMCID: PMC8227402 DOI: 10.3390/microorganisms9061183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/20/2022] Open
Abstract
Microcystis blooms are the most widely distributed and frequently occurring cyanobacterial blooms in freshwater. Reducing phosphorus is suggested to be effective in mitigating cyanobacterial blooms, while the underlying molecular mechanisms are yet to be elucidated. In the present study, isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics was employed to study the effects of phosphorus depletion on Microcystis aeruginosa FACHB-905. The production of microcystins (MCs), a severe hazard of Microcystis blooms, was also analyzed. In total, 230 proteins were found to be differentially abundant, with 136 downregulated proteins. The results revealed that, upon phosphorus limitation stress, Microcystis aeruginosa FACHB-905 raised the availability of phosphorus primarily by upregulating the expression of orthophosphate transport system proteins, with no alkaline phosphatase producing ability. Phosphorus depletion remarkably inhibited cell growth and the primary metabolic processes of Microcystis, including transcription, translation and photosynthesis, with structures of photosystems remaining intact. Moreover, expression of nitrogen assimilation proteins was downregulated, while proteins involved in carbon catabolism were significantly upregulated, which was considered beneficial for the intracellular balance among carbon, nitrogen and phosphorus. The expression of MC synthetase was not significantly different upon phosphorus depletion, while MC content was significantly suppressed. It is assumed that phosphorus depletion indirectly regulates the production of MC by the inhibition of metabolic processes and energy production. These results contribute to further understanding of the influence mechanisms of phosphorus depletion on both biological processes and MC production in Microcystis cells.
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Affiliation(s)
- Nian Wei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430072, China
| | - Lirong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
- Correspondence: (L.S.); (N.G.)
| | - Nanqin Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
- Correspondence: (L.S.); (N.G.)
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Navarrete-Euan H, Rodríguez-Escamilla Z, Pérez-Rueda E, Escalante-Herrera K, Martínez-Núñez MA. Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan. Microorganisms 2021; 9:877. [PMID: 33923859 PMCID: PMC8073884 DOI: 10.3390/microorganisms9040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.
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Affiliation(s)
- Herón Navarrete-Euan
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Unidad Académica Yucatán, Mérida, Yucatán 97302, Mexico;
| | - Karla Escalante-Herrera
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
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50
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Lade H, Kim JS. Bacterial Targets of Antibiotics in Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2021; 10:398. [PMID: 33917043 PMCID: PMC8067735 DOI: 10.3390/antibiotics10040398] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/17/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent bacterial pathogens and continues to be a leading cause of morbidity and mortality worldwide. MRSA is a commensal bacterium in humans and is transmitted in both community and healthcare settings. Successful treatment remains a challenge, and a search for new targets of antibiotics is required to ensure that MRSA infections can be effectively treated in the future. Most antibiotics in clinical use selectively target one or more biochemical processes essential for S. aureus viability, e.g., cell wall synthesis, protein synthesis (translation), DNA replication, RNA synthesis (transcription), or metabolic processes, such as folic acid synthesis. In this review, we briefly describe the mechanism of action of antibiotics from different classes and discuss insights into the well-established primary targets in S. aureus. Further, several components of bacterial cellular processes, such as teichoic acid, aminoacyl-tRNA synthetases, the lipid II cycle, auxiliary factors of β-lactam resistance, two-component systems, and the accessory gene regulator quorum sensing system, are discussed as promising targets for novel antibiotics. A greater molecular understanding of the bacterial targets of antibiotics has the potential to reveal novel therapeutic strategies or identify agents against antibiotic-resistant pathogens.
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Affiliation(s)
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea;
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