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Jia J, Zheng M, Zhang C, Li B, Lu C, Bai Y, Tong Q, Hang X, Ge Y, Zeng L, Zhao M, Song F, Zhang H, Zhang L, Hong K, Bi H. Killing of Staphylococcus aureus persisters by a multitarget natural product chrysomycin A. SCIENCE ADVANCES 2023; 9:eadg5995. [PMID: 37540745 PMCID: PMC10403215 DOI: 10.1126/sciadv.adg5995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
Staphylococcus aureus poses a severe public health problem as one of the vital causative agents of healthcare- and community-acquired infections. There is a globally urgent need for new drugs with a novel mode of action (MoA) to combat S. aureus biofilms and persisters that tolerate antibiotic treatment. We demonstrate that a benzonaphthopyranone glycoside, chrysomycin A (ChryA), is a rapid bactericide that is highly active against S. aureus persisters, robustly eradicates biofilms in vitro, and shows a sustainable killing efficacy in vivo. ChryA was suggested to target multiple critical cellular processes. A wide range of genetic and biochemical approaches showed that ChryA directly binds to GlmU and DapD, involved in the biosynthetic pathways for the cell wall peptidoglycan and lysine precursors, respectively, and inhibits the acetyltransferase activities by competition with their mutual substrate acetyl-CoA. Our study provides an effective antimicrobial strategy combining multiple MoAs onto a single small molecule for treatments of S. aureus persistent infections.
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Affiliation(s)
- Jia Jia
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Mingxin Zheng
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Chongwen Zhang
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Binglei Li
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Cai Lu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuefan Bai
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Qian Tong
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Xudong Hang
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Yixin Ge
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Liping Zeng
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Ming Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Hongkai Bi
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
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Belete TM. Recent Progress in the Development of Novel Mycobacterium Cell Wall Inhibitor to Combat Drug-Resistant Tuberculosis. Microbiol Insights 2022; 15:11786361221099878. [PMID: 35645569 PMCID: PMC9131376 DOI: 10.1177/11786361221099878] [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: 11/26/2021] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Despite decades of research in drug development against TB, it is still the leading cause of death due to infectious diseases. The long treatment duration, patient noncompliance coupled with the ability of the tuberculosis bacilli to resist the current drugs increases multidrug-resistant tuberculosis that exacerbates the situation. Identification of novel drug targets is important for the advancement of drug development against Mycobacterium tuberculosis. The development of an effective treatment course that could help us eradicates TB. Hence, we require drugs that could eliminate the bacteria and shorten the treatment duration. This review briefly describes the available data on the peptidoglycan component structural characterization, identification of the metabolic pathway, and the key enzymes involved in the peptidoglycan synthesis, like N-Acetylglucosamine-1-phosphate uridyltransferase, mur enzyme, alanine racemase as well as their inhibition. Besides, this paper also provides studies on mycolic acid and arabinogalactan synthesis and the transport mechanisms that show considerable promise as new targets to develop a new product with their inhibiter.
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Affiliation(s)
- Tafere Mulaw Belete
- Department of Pharmacology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Whaley SG, Radka CD, Subramanian C, Frank MW, Rock CO. Malonyl-acyl carrier protein decarboxylase activity promotes fatty acid and cell envelope biosynthesis in Proteobacteria. J Biol Chem 2021; 297:101434. [PMID: 34801557 PMCID: PMC8666670 DOI: 10.1016/j.jbc.2021.101434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial fatty acid synthesis in Escherichia coli is initiated by the condensation of an acetyl-CoA with a malonyl-acyl carrier protein (ACP) by the β-ketoacyl-ACP synthase III enzyme, FabH. E. coli ΔfabH knockout strains are viable because of the yiiD gene that allows FabH-independent fatty acid synthesis initiation. However, the molecular function of the yiiD gene product is not known. Here, we show the yiiD gene product is a malonyl-ACP decarboxylase (MadA). MadA has two independently folded domains: an amino-terminal N-acetyl transferase (GNAT) domain (MadAN) and a carboxy-terminal hot dog dimerization domain (MadAC) that encodes the malonyl-ACP decarboxylase function. Members of the proteobacterial Mad protein family are either two domain MadA (GNAT-hot dog) or standalone MadB (hot dog) decarboxylases. Using structure-guided, site-directed mutagenesis of MadB from Shewanella oneidensis, we identified Asn45 on a conserved catalytic loop as critical for decarboxylase activity. We also found that MadA, MadAC, or MadB expression all restored normal cell size and growth rates to an E. coli ΔfabH strain, whereas the expression of MadAN did not. Finally, we verified that GlmU, a bifunctional glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase that synthesizes the key intermediate UDP-GlcNAc, is an ACP binding protein. Acetyl-ACP is the preferred glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase substrate, in addition to being the substrate for the elongation-condensing enzymes FabB and FabF. Thus, we conclude that the Mad family of malonyl-ACP decarboxylases supplies acetyl-ACP to support the initiation of fatty acid, lipopolysaccharide, peptidoglycan, and enterobacterial common antigen biosynthesis in Proteobacteria.
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Affiliation(s)
- Sarah G Whaley
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher D Radka
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew W Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles O Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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Berges M, Michel AM, Lassek C, Nuss AM, Beckstette M, Dersch P, Riedel K, Sievers S, Becher D, Otto A, Maaß S, Rohde M, Eckweiler D, Borrero-de Acuña JM, Jahn M, Neumann-Schaal M, Jahn D. Iron Regulation in Clostridioides difficile. Front Microbiol 2018; 9:3183. [PMID: 30619231 PMCID: PMC6311696 DOI: 10.3389/fmicb.2018.03183] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/10/2018] [Indexed: 12/13/2022] Open
Abstract
The response to iron limitation of several bacteria is regulated by the ferric uptake regulator (Fur). The Fur-regulated transcriptional, translational and metabolic networks of the Gram-positive, pathogen Clostridioides difficile were investigated by a combined RNA sequencing, proteomic, metabolomic and electron microscopy approach. At high iron conditions (15 μM) the C. difficile fur mutant displayed a growth deficiency compared to wild type C. difficile cells. Several iron and siderophore transporter genes were induced by Fur during low iron (0.2 μM) conditions. The major adaptation to low iron conditions was observed for the central energy metabolism. Most ferredoxin-dependent amino acid fermentations were significantly down regulated (had, etf, acd, grd, trx, bdc, hbd). The substrates of these pathways phenylalanine, leucine, glycine and some intermediates (phenylpyruvate, 2-oxo-isocaproate, 3-hydroxy-butyryl-CoA, crotonyl-CoA) accumulated, while end products like isocaproate and butyrate were found reduced. Flavodoxin (fldX) formation and riboflavin biosynthesis (rib) were enhanced, most likely to replace the missing ferredoxins. Proline reductase (prd), the corresponding ion pumping RNF complex (rnf) and the reaction product 5-aminovalerate were significantly enhanced. An ATP forming ATPase (atpCDGAHFEB) of the F0F1-type was induced while the formation of a ATP-consuming, proton-pumping V-type ATPase (atpDBAFCEKI) was decreased. The [Fe-S] enzyme-dependent pyruvate formate lyase (pfl), formate dehydrogenase (fdh) and hydrogenase (hyd) branch of glucose utilization and glycogen biosynthesis (glg) were significantly reduced, leading to an accumulation of glucose and pyruvate. The formation of [Fe-S] enzyme carbon monoxide dehydrogenase (coo) was inhibited. The fur mutant showed an increased sensitivity to vancomycin and polymyxin B. An intensive remodeling of the cell wall was observed, Polyamine biosynthesis (spe) was induced leading to an accumulation of spermine, spermidine, and putrescine. The fur mutant lost most of its flagella and motility. Finally, the CRISPR/Cas and a prophage encoding operon were downregulated. Fur binding sites were found upstream of around 20 of the regulated genes. Overall, adaptation to low iron conditions in C. difficile focused on an increase of iron import, a significant replacement of iron requiring metabolic pathways and the restructuring of the cell surface for protection during the complex adaptation phase and was only partly directly regulated by Fur.
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Affiliation(s)
- Mareike Berges
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika-Marisa Michel
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Christian Lassek
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Aaron M Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Katharina Riedel
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Andreas Otto
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Sandra Maaß
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Denitsa Eckweiler
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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Hu S, Cao L, Wu Y, Zhou Y, Jiang T, Wang L, Wang Q, Ming D, Chen S, Wang M. Comparative genomic analysis of Myroides odoratimimus isolates. Microbiologyopen 2018; 8:e00634. [PMID: 29797432 PMCID: PMC6391281 DOI: 10.1002/mbo3.634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 12/13/2022] Open
Abstract
Myroides odoratimimus is an important nosocomial pathogen. Management of M. odoratimimus infection is difficult owing to the multidrug resistance and the unknown pathogenesis mechanisms. Based on our previous genomic sequencing data of M. odoratimimus PR63039 (isolated from a patient with the urinary tract infection), in this study, we further performed comparative genomic analysis for 10 selected Myroides strains. Our results showed that these Myroides genome contexts were very similar and phylogenetically related. Various prophages were identified in the four clinical isolate genomes, which possibly contributed to the genome evolution among the Myroides strains. CRISPR elements were only detected in the two clinical (PR63039 and CCUG10230) isolates and two environmental (CCUG12700 and H1bi) strains. With more stringent cutoff parameters in CARD analysis, the four clinical M. odoratimimus contained roughly equal antibiotic resistance genes, indicating their similar antibiotic resistance profiles. The three clinical (CCUG10230, CCUG12901, CIP101113) and three environmental (CCUG12700, L41, H1bi) M. odoratimimus strains were speculated to carry the indistinguishable virulent factors (VFs), which may involve in the similar pathogenesis mechanism. Moreover, some VFs might confer to the high capacity of dissemination, attacking tissue cells and induction of autoimmune complications. Our results facilitate the research of antibiotic resistance and the development of therapeutic regimens for the M. odoratimimus infections.
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Affiliation(s)
- Shaohua Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lin Cao
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Yiyin Wu
- College of Computer Science and Technology, Huaqiao University, Xiamen, Fujian, China
| | - Yajun Zhou
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Tao Jiang
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Liqiang Wang
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Qiujing Wang
- Department of Neurosurgery, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Desong Ming
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Fujian, China
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Mingxi Wang
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
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