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Meepagala KM, Anderson CM, Techen N, Duke SO. Pantoea ananatis, a plant growth stimulating bacterium, and its metabolites isolated from Hydrocotyle umbellata (dollarweed). PLANT SIGNALING & BEHAVIOR 2024; 19:2331894. [PMID: 38516998 PMCID: PMC10962587 DOI: 10.1080/15592324.2024.2331894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/22/2024] [Indexed: 03/23/2024]
Abstract
A bacterium growing on infected leaves of Hydrocotyle umbellata, commonly known as dollarweed, was isolated and identified as Pantoea ananatis. An ethyl acetate extract of tryptic soy broth (TSB) liquid culture filtrate of the bacterium was subjected to silica gel chromatography to isolate bioactive molecules. Indole was isolated as the major compound that gave a distinct, foul odor to the extract, together with phenethyl alcohol, phenol, tryptophol, N-acyl-homoserine lactone, 3-(methylthio)-1-propanol, cyclo(L-pro-L-tyr), and cyclo(dehydroAla-L-Leu). This is the first report of the isolation of cyclo(dehydroAla-L-Leu) from a Pantoea species. Even though tryptophol is an intermediate in the indoleacetic acid (IAA) pathway, we were unable to detect or isolate IAA. We investigated the effect of P. ananatis inoculum on the growth of plants. Treatment of Lemna paucicostata Hegelm plants with 4 × 109 colony forming units of P. ananatis stimulated their growth by ca. five-fold after 13 days. After 13 days of treatment, some control plants were browning, but treated plants were greener and no plants were browning. The growth of both Cucumis sativus (cucumber) and Sorghum bicolor (sorghum) plants was increased by ca. 20 to 40%, depending on the growth parameter and species, when the rhizosphere was treated with the bacterium after germination at the same concentration. Plant growth promotion by Pantoea ananatis could be due to the provision of the IAA precursor indole.
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Affiliation(s)
- Kumudini M. Meepagala
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, USA
| | - Caleb M. Anderson
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, USA
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Natascha Techen
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, USA
| | - Stephen O. Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, USA
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2
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Hu C, He G, Yang Y, Wang N, Zhang Y, Su Y, Zhao F, Wu J, Wang L, Lin Y, Shao L. Nanomaterials Regulate Bacterial Quorum Sensing: Applications, Mechanisms, and Optimization Strategies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306070. [PMID: 38350718 PMCID: PMC11022734 DOI: 10.1002/advs.202306070] [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] [Received: 08/28/2023] [Revised: 01/19/2024] [Indexed: 02/15/2024]
Abstract
Anti-virulence therapy that interferes with bacterial communication, known as "quorum sensing (QS)", is a promising strategy for circumventing bacterial resistance. Using nanomaterials to regulate bacterial QS in anti-virulence therapy has attracted much attention, which is mainly attributed to unique physicochemical properties and excellent designability of nanomaterials. However, bacterial QS is a dynamic and multistep process, and there are significant differences in the specific regulatory mechanisms and related influencing factors of nanomaterials in different steps of the QS process. An in-depth understanding of the specific regulatory mechanisms and related influencing factors of nanomaterials in each step can significantly optimize QS regulatory activity and enhance the development of novel nanomaterials with better comprehensive performance. Therefore, this review focuses on the mechanisms by which nanomaterials regulate bacterial QS in the signal supply (including signal synthesis, secretion, and accumulation) and signal transduction cascade (including signal perception and response) processes. Moreover, based on the two key influencing factors (i.e., the nanomaterial itself and the environment), optimization strategies to enhance the QS regulatory activity are comprehensively summarized. Collectively, applying nanomaterials to regulate bacterial QS is a promising strategy for anti-virulence therapy. This review provides reference and inspiration for further research on the anti-virulence application of nanomaterials.
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Affiliation(s)
- Chen Hu
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
| | - Guixin He
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
| | - Yujun Yang
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
| | - Ning Wang
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
| | - Yanli Zhang
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
| | - Yuan Su
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
- Stomatology CenterShunde HospitalSouthern Medical University (The First People's Hospital of Shunde)Foshan528399China
| | - Fujian Zhao
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
| | - Junrong Wu
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
| | - Linlin Wang
- Hainan General Hospital·Hainan Affiliated Hospital of Hainan medical UniversityHaikou570311China
| | - Yuqing Lin
- Shenzhen Luohu People's HospitalShenzhen518000China
| | - Longquan Shao
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhou510280China
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3
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Singh S, Nwagwu E, Young L, Kumar P, Shinde PB, Edrada-Ebel R. Targeted Isolation of Antibiofilm Compounds from Halophytic Endophyte Bacillus velezensis 7NPB-3B Using LC-HR-MS-Based Metabolomics. Microorganisms 2024; 12:413. [PMID: 38399817 PMCID: PMC10891937 DOI: 10.3390/microorganisms12020413] [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: 01/15/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The discovery of new natural products has become more challenging because of the re-isolation of compounds and the lack of new sources. Microbes dwelling in extreme conditions of high salinity and temperature are huge prospects for interesting natural metabolites. In this study, the endophytic bacteria Bacillus velezensis 7NPB-3B isolated from the halophyte Salicornia brachiata was screened for its biofilm inhibition against methicillin-resistant Staphylococcus aureus (MRSA). The fractionation of the crude extract was guided by bioassay and LC-HRMS-based metabolomics using multivariate analysis. The 37 fractions obtained by high-throughput chromatography were dereplicated using an in-house MS-Excel macro coupled with the Dictionary of Natural Products database. Successive bioactivity-guided separation yielded one novel compound (1), a diketopiperazine (m/z 469.258 [M - H]-) with an attached saturated decanoic acid chain, and four known compounds (2-5). The compounds were identified based on 1D- and 2D-NMR and mass spectrometry. Compounds 1 and 5 exhibited excellent biofilm inhibition properties of >90% against the MRSA pathogen at minimum inhibition concentrations of 25 and 35 µg/mL, respectively. The investigation resulted in the isolation of a novel diketopiperazine from a bacterial endophyte of an untapped plant using an omics approach.
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Affiliation(s)
- Sanju Singh
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, India; (S.S.); (P.K.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, The John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (E.N.); (L.Y.)
| | - Elizabeth Nwagwu
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, The John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (E.N.); (L.Y.)
| | - Louise Young
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, The John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (E.N.); (L.Y.)
| | - Pankaj Kumar
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, India; (S.S.); (P.K.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pramod B. Shinde
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, India; (S.S.); (P.K.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, The John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (E.N.); (L.Y.)
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Yamchi A, Rahimi M, Akbari R, Ghobadi C, Aryapour H. Effects of Bacillus in Pectobacterium quorum quenching: A survey of two different acyl-homoserine lactonases. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01139-2. [PMID: 38305961 DOI: 10.1007/s12223-024-01139-2] [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: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Numerous functions in pathogenic Pectobacterium are regulated by quorum sensing (QS). Two different aiiA genes isolated from Bacillus sp. A24(aiiAA24) and Bacillus sp. DMS133(aiiADMS133) were used. Both genes encode acyl-homoserine lactonase (AiiA), which disrupts QS in Pectobacterium. To investigate the effect of different AiiAs on the inhibition of Pectobacterium carotovorum pathogenicity, two aiiA genes from different Bacillus strains were cloned and the resulting plasmids pME6863 (aiiAA24) and pME7080 (aiiADMS133) were transformed into P. carotovorum EMPCC cells. The effects of different lactonases on virulence features such as enzymatic activity, twitching and swimming motilities, and production of pellicle and biofilm formation were investigated. In EMPCC/pME6863, twitching and swimming motilities, and pellicle production were significantly reduced compared with EMPCC/pME7080. Quantitative real-time PCR (qRT-PCR) was used to measure virulence gene expression in transformed cells compared with expression levels in wild-type EMPCC. The expression of peh and hrpL genes was greatly reduced in EMPCC/pME6863 compared with EMPCC/pME7080. The sequence alignment and molecular dynamic modeling of two different AiiAA24 and AiiADMS133 proteins suggested that the replacement of proline 210 from AiiAA24 to serine in AiiADMS133 caused the reduction of enzyme activity in AiiADMS133.
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Affiliation(s)
- Ahad Yamchi
- Department of Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Maryam Rahimi
- Department of Horticulture, University of Zabol, Zabol, Iran
| | - Ramin Akbari
- Department of Agricultural Biotechnology, Isfahan University of Technology, Isfahan, Iran
| | - Cyrus Ghobadi
- Department of Horticulture Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
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Panchal J, Prajapati J, Dabhi M, Patel A, Patel S, Rawal R, Saraf M, Goswami D. Comprehensive computational investigation for ligand recognition and binding dynamics of SdiA: a degenerate LuxR -type receptor in Klebsiella pneumoniae. Mol Divers 2024:10.1007/s11030-023-10785-6. [PMID: 38212453 DOI: 10.1007/s11030-023-10785-6] [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: 07/24/2023] [Accepted: 11/26/2023] [Indexed: 01/13/2024]
Abstract
SdiA is a LuxR-type receptor that controls the virulence of Klebsiella pneumoniae, a Gram-negative bacterium that causes various infections in humans. SdiA senses exogenous acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2), two types of quorum sensing signals produced by other bacterial species. However, the molecular details of how SdiA recognizes and binds to different ligands and how this affects its function and regulation in K. pneumoniae still need to be better understood. This study uses computational methods to explore the protein-ligand binding dynamics of SdiA with 11 AHLs and 2 AI-2 ligands. The 3D structure of SdiA was predicted through homology modeling, followed by molecular docking with AHLs and AI-2 ligands. Binding affinities were quantified using MM-GBSA, and complex stability was assessed via Molecular Dynamics (MD) simulations. Results demonstrated that SdiA in Klebsiella pneumoniae exhibits a degenerate binding nature, capable of interacting with multiple AHLs and AI-2. Specific ligands, namely C10-HSL, C8-HSL, 3-oxo-C8-HSL, and 3-oxo-C10-HSL, were found to have high binding affinities and formed critical hydrogen bonds with key amino acid residues of SdiA. This finding aligns with the observed preference of SdiA for AHLs having 8 to 10 carbon-length acyl chains and lacking hydroxyl groups. In contrast, THMF and HMF demonstrated poor binding properties. Furthermore, AI-2 exhibited a low affinity, corroborating the inference that SdiA is not the primary receptor for AI-2 in K. pneumoniae. These findings provide insights into the protein-ligand binding dynamics of SdiA and its role in quorum sensing and virulence of K. pneumoniae.
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Affiliation(s)
- Janki Panchal
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Jignesh Prajapati
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Milan Dabhi
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Arun Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Kamdhenu University, Sardarkrushinagar 385505, Gujarat, India
| | - Sandip Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Kamdhenu University, Sardarkrushinagar 385505, Gujarat, India
| | - Rakesh Rawal
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Meenu Saraf
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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6
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Sukmarini L, Atikana A, Hertiani T. Antibiofilm activity of marine microbial natural products: potential peptide- and polyketide-derived molecules from marine microbes toward targeting biofilm-forming pathogens. J Nat Med 2024; 78:1-20. [PMID: 37930514 DOI: 10.1007/s11418-023-01754-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Controlling and treating biofilm-related infections is challenging because of the widespread presence of multidrug-resistant microbes. Biofilm, a naturally occurring matrix of microbial aggregates, has developed intricate and diverse resistance mechanisms against many currently used antibiotics. This poses a significant problem, especially for human health, including clinically chronic infectious diseases. Thus, there is an urgent need to search for and develop new and more effective antibiotics. As the marine environment is recognized as a promising reservoir of new biologically active molecules with potential pharmacological properties, marine natural products, particularly those of microbial origin, have emerged as a promising source of antibiofilm agents. Marine microbes represent an untapped source of secondary metabolites with antimicrobial activity. Furthermore, marine natural products, owing to their self-defense mechanisms and adaptation to harsh conditions, encompass a wide range of chemical compounds, including peptides and polyketides, which are primarily found in microbes. These molecules can be exploited to provide novel and unique structures for developing alternative antibiotics as effective antibiofilm agents. This review focuses on the possible antibiofilm mechanism of these marine microbial molecules against biofilm-forming pathogens. It provides an overview of biofilm development, its recalcitrant mode of action, strategies for the development of antibiofilm agents, and their assessments. The review also revisits some selected peptides and polyketides from marine microbes reported between 2016 and 2023, highlighting their moderate and considerable antibiofilm activities. Moreover, their antibiofilm mechanisms, such as adhesion modulation/inhibition targeting biofilm-forming pathogens, quorum sensing intervention and inhibition, and extracellular polymeric substance disruption, are highlighted herein.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), KST Soekarno, Jl. Raya Jakarta-Bogor Km. 46, Cibinong, West Java, 16911, Indonesia.
- Indonesian Biofilm Research Collaboration Center, Jl. Farmako Sekip Utara, Yogyakarta, 55281, Indonesia.
| | - Akhirta Atikana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), KST Soekarno, Jl. Raya Jakarta-Bogor Km. 46, Cibinong, West Java, 16911, Indonesia
- Indonesian Biofilm Research Collaboration Center, Jl. Farmako Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Triana Hertiani
- Indonesian Biofilm Research Collaboration Center, Jl. Farmako Sekip Utara, Yogyakarta, 55281, Indonesia.
- Pharmaceutical Biology Department, Faculty of Pharmacy, Gadjah Mada University, Jl. Sekip Utara, Yogyakarta, 55281, Indonesia.
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7
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Kauser A, Parisini E, Suarato G, Castagna R. Light-Based Anti-Biofilm and Antibacterial Strategies. Pharmaceutics 2023; 15:2106. [PMID: 37631320 PMCID: PMC10457815 DOI: 10.3390/pharmaceutics15082106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Biofilm formation and antimicrobial resistance pose significant challenges not only in clinical settings (i.e., implant-associated infections, endocarditis, and urinary tract infections) but also in industrial settings and in the environment, where the spreading of antibiotic-resistant bacteria is on the rise. Indeed, developing effective strategies to prevent biofilm formation and treat infections will be one of the major global challenges in the next few years. As traditional pharmacological treatments are becoming inadequate to curb this problem, a constant commitment to the exploration of novel therapeutic strategies is necessary. Light-triggered therapies have emerged as promising alternatives to traditional approaches due to their non-invasive nature, precise spatial and temporal control, and potential multifunctional properties. Here, we provide a comprehensive overview of the different biofilm formation stages and the molecular mechanism of biofilm disruption, with a major focus on the quorum sensing machinery. Moreover, we highlight the principal guidelines for the development of light-responsive materials and photosensitive compounds. The synergistic effects of combining light-triggered therapies with conventional treatments are also discussed. Through elegant molecular and material design solutions, remarkable results have been achieved in the fight against biofilm formation and antibacterial resistance. However, further research and development in this field are essential to optimize therapeutic strategies and translate them into clinical and industrial applications, ultimately addressing the global challenges posed by biofilm and antimicrobial resistance.
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Affiliation(s)
- Ambreen Kauser
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (A.K.); (E.P.)
- Faculty of Materials Science and Applied Chemistry, Riga Technical University, Paula Valdena 3, LV-1048 Riga, Latvia
| | - Emilio Parisini
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (A.K.); (E.P.)
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Giulia Suarato
- Istituto di Elettronica e di Ingegneria dell’Informazione e delle Telecomunicazioni, Consiglio Nazionale delle Ricerche, CNR-IEIIT, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Rossella Castagna
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (A.K.); (E.P.)
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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8
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Cui B, Guo Q, Li X, Song S, Wang M, Wang G, Yan A, Zhou J, Deng Y. A response regulator controls Acinetobacter baumannii virulence by acting as an indole receptor. PNAS NEXUS 2023; 2:pgad274. [PMID: 37649583 PMCID: PMC10465187 DOI: 10.1093/pnasnexus/pgad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
Indole is an important signal employed by many bacteria to modulate intraspecies signaling and interspecies or interkingdom communication. Our recent study revealed that indole plays a key role in regulating the physiology and virulence of Acinetobacter baumannii. However, it is not clear how A. baumannii perceives and responds to the indole signal in modulating biological functions. Here, we report that indole controls the physiology and virulence of A. baumannii through a previously uncharacterized response regulator designated as AbiR (A1S_1394), which contains a cheY-homologous receiver (REC) domain and a helix-turn-helix (HTH) DNA-binding domain. AbiR controls the same biological functions as the indole signal, and indole-deficient mutant phenotypes were rescued by in trans expression of AbiR. Intriguingly, unlike other response regulators that commonly interact with signal ligands through the REC domain, AbiR binds to indole with a high affinity via an unusual binding region, which is located between its REC and HTH domains. This interaction substantially enhances the activity of AbiR in promoter binding and in modulation of target gene expression. Taken together, our results present a widely conserved regulator that controls bacterial physiology and virulence by sensing the indole signal in a unique mechanism.
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Affiliation(s)
- Binbin Cui
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Quan Guo
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Xia Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Shihao Song
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
- School of Pharmaceutical Sciences, Hainan University, Renmin Avenue, Meilan District, Haikou 570228, China
| | - Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Gerun Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, University Road, Pok Fu Lam Estate, Central and Western District, Hong Kong 999077, China
| | - Jianuan Zhou
- Integrative Microbiology Research Center, South China Agricultural University, Wushan Road, Wushan Street, Tianhe District Guangzhou 510642, China
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
- School of Pharmaceutical Sciences, Hainan University, Renmin Avenue, Meilan District, Haikou 570228, China
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9
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Thompson TP, Busetti A, Gilmore BF. Quorum Sensing in Halorubrum saccharovorum Facilitates Cross-Domain Signaling between Archaea and Bacteria. Microorganisms 2023; 11:1271. [PMID: 37317245 DOI: 10.3390/microorganisms11051271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
Quorum Sensing (QS) is a well-studied intercellular communication mechanism in bacteria, regulating collective behaviors such as biofilm formation, virulence, and antibiotic resistance. However, cell-cell signaling in haloarchaea remains largely unexplored. The coexistence of bacteria and archaea in various environments, coupled with the known cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms and the presence of cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms, suggests a possibility for haloarchaea to possess analogous cell-cell signaling or QS systems. Recently, N-acylhomoserine lactone (AHL)-like compounds were identified in haloarchaea; yet, their precise role-for example, persister cell formation-remains ambiguous. This study investigated the capacity of crude supernatant extract from the haloarchaeon Halorubrum saccharovorum CSM52 to stimulate bacterial AHL-dependent QS phenotypes using bioreporter strains. Our findings reveal that these crude extracts induced several AHL-dependent bioreporters and modulated pyocyanin and pyoverdine production in Pseudomonas aeruginosa. Importantly, our study suggests cross-domain communication between archaea and bacterial pathogens, providing evidence for archaea potentially influencing bacterial virulence. Using Thin Layer Chromatography overlay assays, lactonolysis, and colorimetric quantification, the bioactive compound was inferred to be a chemically modified AHL-like compound or a diketopiperazine-like molecule, potentially involved in biofilm formation in H. saccharovorum CSM52. This study offers new insights into putative QS mechanisms in haloarchaea and their potential role in interspecies communication and coordination, thereby enriching our understanding of microbial interactions in diverse environments.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Alessandro Busetti
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
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10
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Dhillon J, Newman JW, Fiehn O, Ortiz RM. Almond Consumption for 8 Weeks Altered Host and Microbial Metabolism in Comparison to a Control Snack in Young Adults. JOURNAL OF THE AMERICAN NUTRITION ASSOCIATION 2023; 42:242-254. [PMID: 35512761 PMCID: PMC9396742 DOI: 10.1080/07315724.2021.2025168] [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] [Received: 10/12/2021] [Revised: 12/10/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Almond consumption can improve cardiometabolic (CM) health. However, the mechanisms underlying those benefits are not well characterized. This study explored the effects of consuming a snack of almonds vs. crackers for 8 weeks on changes in metabolomic profiles in young adults (clinicaltrials.gov ID: NCT03084003). Participants (n = 73, age: 18-19 years, BMI: 18-41 kg/m2) were randomly assigned to consume either almonds (2 oz/d, n = 38) or an isocaloric control snack of graham crackers (325 kcal/d, n = 35) daily for 8 weeks. Blood samples were collected at baseline prior to and at 4 and 8 weeks after the intervention. Metabolite abundances in the serum were quantified by hydrophilic interaction chromatography quadrupole (Q) time-of-flight (TOF) mass spectrometry (MS/MS), gas chromatography (GC) TOF MS, CSH-ESI (electrospray) QTOF MS/MS, and targeted analyses for free PUFAs, total fatty acids, oxylipins and endocannabinoids. Linear mixed model analyses with baseline-adjustment were conducted, and those results were used for enrichment and network analyses. Microbial community pathway predictions from 16S rRNA sequencing of fecal samples was done using PICRUST2. Almond consumption enriched unsaturated triglycerides, unsaturated phosphatidylcholines, saturated and unsaturated lysophosphatidylcholines, tricarboxylic acids, and tocopherol clusters (p < 0.05). Targeted analyses reveal lower levels of omega-3 total fatty acids (TFAs) overall in the almond group compared to the cracker group (p < 0.05). Microbial amino acid biosynthesis, and amino sugar and nucleotide sugar metabolism pathways were also differentially enriched at the end of the intervention (p < 0.05). The study demonstrates the differential effects of almonds on host tocopherol, lipid, and TCA cycle metabolism with potential changes in microbial metabolism, which may interact with host metabolism to facilitate the CM benefits.
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Affiliation(s)
- Jaapna Dhillon
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia
- Department of Molecular and Cell Biology, University of California, Merced
| | - John W. Newman
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis CA, USA
- Department of Nutrition, University of California, Davis
- Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, University of California, Davis
| | - Oliver Fiehn
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis CA, USA
| | - Rudy M. Ortiz
- Department of Molecular and Cell Biology, University of California, Merced
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11
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Alwali AY, Parkinson EI. Small molecule inducers of actinobacteria natural product biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad019. [PMID: 37587009 PMCID: PMC10549211 DOI: 10.1093/jimb/kuad019] [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: 05/22/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Actinobacteria are a large and diverse group of bacteria that are known to produce a wide range of secondary metabolites, many of which have important biological activities, including antibiotics, anti-cancer agents, and immunosuppressants. The biosynthesis of these compounds is often highly regulated with many natural products (NPs) being produced at very low levels in laboratory settings. Environmental factors, such as small molecule elicitors, can induce the production of secondary metabolites. Specifically, they can increase titers of known NPs as well as enabling discovery of novel NPs typically produced at undetectable levels. These elicitors can be NPs, including antibiotics or hormones, or synthetic compounds. In recent years, there has been a growing interest in the use of small molecule elicitors to induce the production of secondary metabolites from actinobacteria, especially for the discovery of NPs from "silent" biosynthetic gene clusters. This review aims to highlight classes of molecules that induce secondary metabolite production in actinobacteria and to describe the potential mechanisms of induction. ONE-SENTENCE SUMMARY This review describes chemical elicitors of actinobacteria natural products described to date and the proposed mechanisms of induction.
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Affiliation(s)
- Amir Y Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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12
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De Kesel J, Bonneure E, Frei M, De Meyer T, Mangelinckx S, Kyndt T. Diproline-induced resistance to parasitic nematodes in the same and subsequent rice generations: Roles of iron, nitric oxide and ethylene. FRONTIERS IN PLANT SCIENCE 2023; 14:1112007. [PMID: 36824193 PMCID: PMC9941634 DOI: 10.3389/fpls.2023.1112007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Induced resistance (IR) is a plant phenotype characterized by lower susceptibility to biotic challenges upon elicitation by so-called IR stimuli. Earlier, we identified diproline (cyclo(l-Pro-l-Pro)) as IR stimulus that protects rice (Oryza sativa) against the root-knot nematode Meloidogyne graminicola (Mg). In the current study, detailed transcriptome analyses at different time points, and under uninfected and nematode-infected conditions revealed that this rice IR phenotype is correlated with induction of genes related to iron (Fe), ethylene (ET) and reactive oxygen species (ROS)/reactive nitrogen species (RNS) metabolism. An infection experiment under Fe limiting conditions confirmed that diproline-IR is only effective under optimal Fe supply. Although total root Fe levels were not affected in diproline-treated plants, phytosiderophore secretion was found to be induced by this treatment. Experiments on mutant and transgenic rice lines impaired in ET or ROS/RNS metabolism confirmed that these metabolites are involved in diproline-IR. Finally, we provide evidence for transgenerational inheritance of diproline-IR (diproline-TIR), as two successive generations of diproline-treated ancestors exhibited an IR phenotype while themselves never being exposed to diproline. Transcriptome analyses on the offspring plants revealed extensive overlap between the pathways underpinning diproline-IR and diproline-TIR. Although diproline induces significant systemic changes in global DNA methylation levels early after treatment, such changes in DNA methylation were not detected in the descendants of these plants. To our knowledge, this is the first report of TIR in rice and the first transcriptional assessment of TIR in monocots.
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Affiliation(s)
- Jonas De Kesel
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Eli Bonneure
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Michael Frei
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sven Mangelinckx
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tina Kyndt
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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13
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Rodrigues MV, Kis P, Xavier KB, Ventura MR. Synthesis and potential of Autoinducer‐2 and analogs to manipulate inter‐species Quorum Sensing. Isr J Chem 2023. [DOI: 10.1002/ijch.202200091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Miguel V. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Peter Kis
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
- Institute of Chemistry Slovak Academy of Sciences 845 38 Bratislava Slovakia
| | | | - M. Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
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14
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Starr AM, Zabet-Moghaddam M, San Francisco M. Identification of a novel secreted metabolite cyclo(phenylalanyl-prolyl) from Batrachochytrium dendrobatidis and its effect on Galleria mellonella. BMC Microbiol 2022; 22:293. [PMID: 36482304 PMCID: PMC9730576 DOI: 10.1186/s12866-022-02680-1] [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: 12/15/2021] [Accepted: 10/26/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The fungus, Batrachochytrium dendrobatidis, is the causative agent of chytridiomycosis and a leading cause of global decline in amphibian populations. The first stages of chytridiomycosis include: inflammation, hyperkeratosis, lethargy, loss of righting reflex, and disruption of internal electrolyte levels leading to eventual death of the host. Previous work indicates that B. dendrobatidis can produce immunomodulatory compounds and other secreted molecules that regulate the growth of the fungus. In this study, filtrates of the fungus grown in media and water were subjected to ultra-performance liquid chromatography-mass spectrometry and analyzed using Compound Discoverer 3.0. RESULTS Identification of cyclo(phenylalanyl-prolyl), chitobiose, and S-adenosylmethionine were verified by their retention times and fragmentation patterns from B. dendrobatidis supernatants. Previous studies have analyzed the effects of B. dendrobatidis on amphibian models, in vitro, or in cell culture. We studied the effects of live B. dendrobatidis cells, spent culture filtrates containing secreted metabolites, and cyclo(pheylalanyl-prolyl) on wax moth larvae (Galleria mellonella). Concentrated filtrates caused melanization within 24 h, while live B. dendrobatidis caused melanization within 48 h. CONCLUSIONS Here we show B. dendrobatidis produces secreted metabolites previously unreported. The impacts of these chemicals were tested on an alternate non-amphibian model system that has been used for other fungi to study pathogenicity traits in this fungus.
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Affiliation(s)
- Amanda M. Starr
- grid.462127.4Bryant & Stratton College, 8141 Hull Street Road, Richmond, VA 23235 USA ,grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
| | | | - Michael San Francisco
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
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15
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Liu H, An M, Si H, Shan Y, Xu C, Hu G, Xie Y, Liu D, Li S, Qiu R, Zhang C, Wu Y. Identification of Cyclic Dipeptides and a New Compound (6-(5-Hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one) Produced by Streptomyces fungicidicus against Alternaria solani. Molecules 2022; 27:molecules27175649. [PMID: 36080412 PMCID: PMC9458140 DOI: 10.3390/molecules27175649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
As an important microbial resource, Actinomycetes, especially Streptomyces, have important application values in medicine and biotechnology. Streptomyces fungicidicus SYH3 was isolated from soil samples in tomato-growing areas and showed good inhibitory effects on Alternaria solani in tomato. To obtain pure active compounds, SYH3 fermentation broth was subjected to XAD-16 macroporous resin and silica gel column chromatography. Combined with the repeated preparation and separation of preparative high-performance liquid chromatography (HPLC), a total of four monomer compounds were obtained after activity tracking. Compound 4 was identified as a new six-membered lactone ring compound named 6-(5-hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one by 1D and 2D nuclear magnetic resonance (NMR) data and mass spectrometry (MS). The other three active compounds belong to the cyclodipeptide, and their half maximal inhibitory concentration (IC50) values against A. solani were 43.4, 42.9, and 30.6 μg/mL, respectively. Compound 4 significantly inhibited the spore germination and induced swollen and deformed local hyphae of A. solani with an IC50 value of 24.9 μg/mL. Compound 4 also had broad-spectrum antifungal activity and had a good antifungal effect on the tested plant-pathogenic fungi. The modes of action of new compound (4) still require further investigation, representing a novel and effective anti-fungal agent for future application.
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Affiliation(s)
- He Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Hongyang Si
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuhang Shan
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Chuantao Xu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Luzhou Branch of Sichuan Province Tobacco Company, Luzhou 646000, China
| | - Gang Hu
- Sichuan Province Tobacco Company, Chengdu 610017, China
| | - Yunbo Xie
- Sichuan Province Tobacco Company, Chengdu 610017, China
| | - Dongyang Liu
- Liangshanzhou Branch of Sichuan Province Tobacco Company, Xichang 615000, China
| | - Shujun Li
- Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pests in Huanghuai Growing Area, Tobacco Research Institute, Henan Academy of Agricultural Sciences, Xuchang 461000, China
| | - Rui Qiu
- Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pests in Huanghuai Growing Area, Tobacco Research Institute, Henan Academy of Agricultural Sciences, Xuchang 461000, China
| | - Chong Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (C.Z.); (Y.W.)
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (C.Z.); (Y.W.)
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16
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Cui B, Chen X, Guo Q, Song S, Wang M, Liu J, Deng Y. The Cell-Cell Communication Signal Indole Controls the Physiology and Interspecies Communication of Acinetobacter baumannii. Microbiol Spectr 2022; 10:e0102722. [PMID: 35862954 PMCID: PMC9431217 DOI: 10.1128/spectrum.01027-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022] Open
Abstract
Many bacteria utilize quorum sensing (QS) to control group behavior in a cell density-dependent manner. Previous studies have demonstrated that Acinetobacter baumannii employs an N-acyl-L-homoserine lactone (AHL)-based QS system to control biological functions and virulence. Here, we report that indole controls biological functions, virulence and AHL signal production in A. baumannii. The biosynthesis of indole is performed by A1S_3160 (AbiS, Acinetobacter baumannii indole synthase), which is a novel indole synthase annotated as an alpha/beta hydrolase in A. baumannii. Heterologous expression of AbiS in an Escherichia coli indole-deficient mutant also rescued the production of indole by using a distinct biosynthetic pathway from the tryptophanase TnaA, which produces indole directly from tryptophan in E. coli. Moreover, we revealed that indole from A. baumannii reduced the competitive fitness of Pseudomonas aeruginosa by inhibiting its QS systems and type III secretion system (T3SS). As A. baumannii and P. aeruginosa usually coexist in human lungs, our results suggest the crucial roles of indole in both the bacterial physiology and interspecies communication. IMPORTANCE Acinetobacter baumannii is an important human opportunistic pathogen that usually causes high morbidity and mortality. It employs the N-acyl-L-homoserine lactone (AHL)-type quorum sensing (QS) system, AbaI/AbaR, to regulate biological functions and virulence. In this study, we found that A. baumannii utilizes another QS signal, indole, to modulate biological functions and virulence. It was further revealed that indole positively controls the production of AHL signals by regulating abaI expression at the transcriptional levels. Furthermore, indole represses the QS systems and type III secretion system (T3SS) of P. aeruginosa and enhances the competitive ability of A. baumannii. Together, our work describes a QS signaling network where a pathogen uses to control the bacterial physiology and pathogenesis, and the competitive ability in microbial community.
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Affiliation(s)
- Binbin Cui
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xiayu Chen
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Quan Guo
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shihao Song
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jingyun Liu
- Department of Stomatology, Zhengzhou Shuqing Medical College, Zhenzhou, China
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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17
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Sahreen S, Mukhtar H, Imre K, Morar A, Herman V, Sharif S. Exploring the Function of Quorum Sensing Regulated Biofilms in Biological Wastewater Treatment: A Review. Int J Mol Sci 2022; 23:ijms23179751. [PMID: 36077148 PMCID: PMC9456111 DOI: 10.3390/ijms23179751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Quorum sensing (QS), a type of bacterial cell–cell communication, produces autoinducers which help in biofilm formation in response to cell population density. In this review, biofilm formation, the role of QS in biofilm formation and development with reference to biological wastewater treatment are discussed. Autoinducers, for example, acyl-homoserine lactones (AHLs), auto-inducing oligo-peptides (AIPs) and autoinducer 2, present in both Gram-negative and Gram-positive bacteria, with their mechanism, are also explained. Over the years, wastewater treatment (WWT) by QS-regulated biofilms and their optimization for WWT have gained much attention. This article gives a comprehensive review of QS regulation methods, QS enrichment methods and QS inhibition methods in biological waste treatment systems. Typical QS enrichment methods comprise adding QS molecules, adding QS accelerants and cultivating QS bacteria, while typical QS inhibition methods consist of additions of quorum quenching (QQ) bacteria, QS-degrading enzymes, QS-degrading oxidants, and QS inhibitors. Potential applications of QS regulated biofilms for WWT have also been summarized. At last, the knowledge gaps present in current researches are analyzed, and future study requirements are proposed.
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Affiliation(s)
- Sania Sahreen
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
- Correspondence: (H.M.); (K.I.); Tel.: +92-3334245581 (H.M.); +40-256277186 (K.I.)
| | - Kálmán Imre
- Department of Animal Production and Veterinary Public Health, Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania”, 300645 Timisoara, Romania
- Correspondence: (H.M.); (K.I.); Tel.: +92-3334245581 (H.M.); +40-256277186 (K.I.)
| | - Adriana Morar
- Department of Animal Production and Veterinary Public Health, Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania”, 300645 Timisoara, Romania
| | - Viorel Herman
- Department of Infectious Diseases and Preventive Medicine, Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania”, 300645 Timisoara, Romania
| | - Sundas Sharif
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
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18
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Kapadia C, Kachhdia R, Singh S, Gandhi K, Poczai P, Alfarraj S, Ansari MJ, Gafur A, Sayyed RZ. Pseudomonas aeruginosa inhibits quorum-sensing mechanisms of soft rot pathogen Lelliottia amnigena RCE to regulate its virulence factors and biofilm formation. Front Microbiol 2022; 13:977669. [PMID: 36090086 PMCID: PMC9450810 DOI: 10.3389/fmicb.2022.977669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/25/2022] [Indexed: 01/21/2023] Open
Abstract
The quorum-sensing (QS) cascade is responsible for the colonization and phenotypic behavior of the pathogenic organism and the regulation of diverse signal molecules. The disruption of the quorum-sensing system is an effective strategy to overcome the possibility of antibiotic resistance development in the pathogen. The quorum quenching does not kill the microbes. Instead, it hinders the expression of pathogenic traits. In the present experiment, Pseudomonas aeruginosa RKC1 was used to extract the metabolites responsible for quorum-sensing inhibition in soft rot pathogen Lelliottia amnigena RCE. During the initial screening, P. aeruginosa RKC1 was found to be most promising and inhibits violacein of Chromobacterium violaceum MTCC2656 pyocyanin, swarming-swimming motility of P. aeruginosa MTCC2297. The characterization of metabolites produced by the microbes which are responsible for quorum-sensing inhibition through GC-MS is very scarce in scientific literature. The ethyl acetate extract of P. aeruginosa RKC1 inhibits biofilm formation of L. amnigena RCE while inhibiting growth at higher concentrations. The GC-MS analysis suggested that Cyclic dipeptides (CDPs) such as Cyclo (L-prolyl-L-valine), Cyclo (Pro-Leu), and Cyclo(D-phenylalanyl-L-prolyl) were predominantly found in the ethyl acetate extract of the P. aeruginosa RKC1 (93.72%). This diketopiperazine (DKPs) exhibited quorum-sensing inhibition against the pathogen in liquid media during the active growth phase and regulated diverse metabolites of the pathogen. Moreover, the metabolites data from the clear zone around wells showed a higher concentration of DKSs (9.66%) compared to other metabolites. So far, very few reports indicate the role of DKPs or CDPs in inhibiting the quorum-sensing system in plant pathogenic bacteria. This is one such report that exploits metabolites of P. aeruginosa RKC1. The present investigation provided evidence to use quorum-sensing inhibitor metabolites, to suppress microbes' pathogenesis and thus develop an innovative strategy to overcome antibiotic resistance.
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Affiliation(s)
- Chintan Kapadia
- Department of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, India
- *Correspondence: Chintan Kapadia
| | - Rinkal Kachhdia
- Department of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, India
| | - Susheel Singh
- Food Quality Testing Laboratory, N. M. College of Agriculture, Navsari Agricultural University, Navsari, India
| | - Kelvin Gandhi
- Food Quality Testing Laboratory, N. M. College of Agriculture, Navsari Agricultural University, Navsari, India
| | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Peter Poczai
| | - Saleh Alfarraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College, Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Moradabad, India
| | - Abdul Gafur
- Sinarmas Forestry Corporate Research and Development, Perawang, Indonesia
| | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandals, S I Patil Arts, G B Patel Science and STKV Sangh Commerce College, Shahada, India
- R. Z. Sayyed
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19
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Kachhadia R, Kapadia C, Singh S, Gandhi K, Jajda H, Alfarraj S, Ansari MJ, Danish S, Datta R. Quorum Sensing Inhibitory and Quenching Activity of Bacillus cereus RC1 Extracts on Soft Rot-Causing Bacteria Lelliottia amnigena. ACS OMEGA 2022; 7:25291-25308. [PMID: 35910130 PMCID: PMC9330221 DOI: 10.1021/acsomega.2c02202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/28/2022] [Indexed: 05/15/2023]
Abstract
The quorum sensing (QS) system of bacteria helps them to communicate with each other in a density-dependent manner and regulates pathogenicity. The concentrations of autoinducers, peptides, and signaling factors are required for determining the expression of virulence factors in many pathogens. The QS signals of the pathogen are regulated by the signal transduction pathway. The binding of signal molecules to its cognate receptor brings changes in the structure of the receptor, makes it more accessible to the DNA, and thus regulates diverse expression patterns, including virulence factors. Degrading the autoinducer molecules or disturbing the quorum sensing network could be exploited to control the virulence of the pathogen while avoiding multidrug-resistant phenotypes. The rhizosphere is a tremendous source of beneficial microbes that has not yet been explored properly for its anti-quorum sensing potential. Lelliottia amnigena causes soft rot diseases in onion, potato, and other species. The present investigation was carried out with the aim of isolating the anti-quorum sensing metabolites and elucidating their role in controlling the virulence factors of the pathogen by performing a maceration assay. The ethyl acetate extracts of various bacteria are promising for violacein inhibition assay using Chromobacterium violaceum MTCC2656 and pyocyanin inhibition of Pseudomonas aeruginosa MTCC2297. Therefore, the extract was used to deduce its role in attenuation of soft rot in potato, carrot, and cucumber. The maximum reduction of macerated tissue in carrot, potato, and cucumber was given by Bacillus cereus RC1 at 91.22, 97.59, and 88.78%, respectively. The concentration-dependent inhibition of virulence traits was observed during the entire experiment. The quorum quenching potential of the bacterial extract was used to understand the regulatory metabolites. The data of the diffusible zone and gas chromatography-mass spectrometry (GC-MS) analysis showed that diketopiperazines, viz. Cyclo(d-phenylalanyl-l-prolyl), Cyclo Phe-Val, Cyclo(Pro-Ala), Cyclo(l-prolyl-l-valine), Cyclo (Leu-Leu), and Cyclo(-Leu-Pro), are prominent metabolites that could modulate the pathogenicity in L. amnigena RCE. The interaction of bacterial extracts regulates various metabolites of the pathogens during their growth in liquid culture compared to their control counterparts. This study might help in exploiting the metabolites from bacteria to control the pathogens, with concurrent reduction in the pathogenicity of the pathogens without developing antibiotic resistance.
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Affiliation(s)
- Rinkal Kachhadia
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari, Gujarat 396450, India
| | - Chintan Kapadia
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari, Gujarat 396450, India
| | - Susheel Singh
- Food
Quality Testing Laboratory, N. M. College Of Agriculture, Navsari Agricultural University, Navsari, Gujarat 396450, India
| | - Kelvin Gandhi
- Food
Quality Testing Laboratory, N. M. College Of Agriculture, Navsari Agricultural University, Navsari, Gujarat 396450, India
| | - Harsur Jajda
- Gujarat
Agricultural Biotech Institute, Navsari
Agricultural University, Navsari, Gujarat 396450, India
| | - Saleh Alfarraj
- Zoology
Department, College of Science, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Mohammad Javed Ansari
- Department
of Botany, Hindu College Moradabad (Mahatma
Jyotiba Phule Rohilkhand University Bareilly), 244001, India
| | - Subhan Danish
- Hainan
Key
Laboratory for Sustainable Utilization of Tropical Bioresource, College
of Tropical Crops, Hainan University, Haikou 570228, China
| | - Rahul Datta
- Department
of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska 1, Brno 61300, Czech Republic
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20
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Kaushik S, Yadav J, Das S, Singh S, Jyoti A, Srivastava VK, Sharma V, Kumar S, Kumar S. Deciphering the Role of S-adenosyl Homocysteine Nucleosidase in Quorum
Sensing Mediated Biofilm Formation. Curr Protein Pept Sci 2022; 23:211-225. [DOI: 10.2174/1389203723666220519152507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/21/2022] [Accepted: 03/11/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
S-adenosylhomocysteine nucleosidase (MTAN) is a protein that plays a crucial role in several
pathways of bacteria that are essential for its survival and pathogenesis. In addition to the role of
MTAN in methyl-transfer reactions, methionine biosynthesis, and polyamine synthesis, MTAN is also
involved in bacterial quorum sensing (QS). In QS, chemical signaling autoinducer (AI) secreted by
bacteria assists cell to cell communication and is regulated in a cell density-dependent manner. They
play a significant role in the formation of bacterial biofilm. MTAN plays a major role in the synthesis
of these autoinducers. Signaling molecules secreted by bacteria, i.e., AI-1 are recognized as acylated
homoserine lactones (AHL) that function as signaling molecules within bacteria. QS enables bacteria
to establish physical interactions leading to biofilm formation. The formation of biofilm is a primary
reason for the development of multidrug-resistant properties in pathogenic bacteria like Enterococcus
faecalis (E. faecalis). In this regard, inhibition of E. faecalis MTAN (EfMTAN) will block the QS and
alter the bacterial biofilm formation. In addition to this, it will also block methionine biosynthesis and
many other critical metabolic processes. It should also be noted that inhibition of EfMTAN will not
have any effect on human beings as this enzyme is not present in humans. This review provides a comprehensive
overview of the structural-functional relationship of MTAN. We have also highlighted the
current status, enigmas that warrant further studies, and the prospects for identifying potential inhibitors
of EfMTAN for the treatment of E. faecalis infections. In addition to this, we have also reported
structural studies of EfMTAN using homology modeling and highlighted the putative binding sites of
the protein.
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Affiliation(s)
- Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
- Structural Biology Lab, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Suraj Singh
- Centre for Bioseparation Technology, VIT University, Vellore-632014, Tamil Nadu, India
| | - Anupam Jyoti
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Chandigarh, India
| | | | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanjit Kumar
- Centre for Bioseparation Technology, VIT University, Vellore-632014, Tamil Nadu, India
| | - Sujeet Kumar
- Centre for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India
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21
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Levipan HA, Reyes-Garcia L, Avendaño-Herrera R. Commentary: Piscirickettsia salmonis Produces a N-Acetyl-L-Homoserine Lactone as a Bacterial Quorum Sensing System-Related Molecule. Front Cell Infect Microbiol 2022; 12:858387. [PMID: 35310837 PMCID: PMC8930913 DOI: 10.3389/fcimb.2022.858387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Héctor A. Levipan
- Laboratorio de Ecopatología y Nanobiomateriales, Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
- *Correspondence: Héctor A. Levipan, ; ; Ruben Avendaño-Herrera, ;
| | - Luis Reyes-Garcia
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
- *Correspondence: Héctor A. Levipan, ; ; Ruben Avendaño-Herrera, ;
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22
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Wang Y, Zheng Q, Li L, Pan L, Zhu H. Anti-Quorum-Sensing Activity of Tryptophan-Containing Cyclic Dipeptides. Mar Drugs 2022; 20:md20020085. [PMID: 35200615 PMCID: PMC8924889 DOI: 10.3390/md20020085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Quorum sensing (QS) can regulate the pathogenicity of bacteria and the production of some virulence factors. It is a promising target for screening to find anti-virulence agents in the coming post-antibiotics era. Cyclo (L-Trp-L-Ser), one variety of cyclic dipeptides (CDPs), isolated from a marine bacterium Rheinheimera aquimaris, exhibited anti-QS activity against Chromobacterium violaceum CV026 and Pseudomonas aeruginosa PAO1. Unlike the CDPs composed of phenylalanine or tyrosine, the anti-QS activity has been widely studied; however, cyclo (L-Trp-L-Ser) and derivatives, containing one tryptophan unit and one non-aromatic amino acid, have not been systematically explored. Herein, the cyclo (L-Trp-L-Ser) and seven derivatives were synthesized and evaluated. All tryptophane-contained CDPs were able to decrease the production of violacein in C.violaceum CV026 and predicted as binding within the same pocket of receptor protein CviR, but in lower binding energy compared with the natural ligand C6HSL. As for P. aeruginosa PAO1, owning more complicated QS systems, these CDPs also exhibited inhibitory effects on pyocyanin production, swimming motility, biofilm formation, and adhesion. These investigations suggested a promising way to keep the tryptophan untouched and make modifications on the non-aromatic unit to increase the anti-QS activity and decrease the cytotoxicity, thus developing a novel CDP-based anti-virulence agent.
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23
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Vivero-Gomez RJ, Mesa GB, Higuita-Castro J, Robledo SM, Moreno-Herrera CX, Cadavid-Restrepo G. Detection of Quorum Sensing Signal Molecules, Particularly N-Acyl Homoserine Lactones, 2-Alky-4-Quinolones, and Diketopiperazines, in Gram-Negative Bacteria Isolated From Insect Vector of Leishmaniasis. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.760228] [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
Gram-negative bacteria are known to use a quorum sensing system to facilitate and stimulate cell to cell communication, mediated via regulation of specific genes. This system is further involved in the modulation of cell density and metabolic and physiological processes that putatively either affect the survival of insect vectors or the establishment of pathogens transmitted by them. The process of quorum sensing generally involves N-acyl homoserine lactones and 2-alkyl-4-quinolones signaling molecules. The present study aimed to detect and identify quorum sensing signaling molecules of AHLs and AHQs type that are secreted by intestinal bacteria, and link their production to their extracellular milieu and intracellular content. Isolates for assessment were obtained from the intestinal tract of Pintomyia evansi (Leishmania insect vector). AHLs and AHQs molecules were detected using chromatography (TLC) assays, with the aid of specific and sensitive biosensors. For identity confirmation, ultra-high-performance liquid chromatography coupled with mass spectrometry was used. TLC assays detected quorum sensing molecules (QSM) in the supernatant of the bacterial isolates and intracellular content. Interestingly, Pseudomonas otitidis, Enterobacter aerogenes, Enterobacter cloacae, and Pantoea ananatis isolates showed a migration pattern similar to the synthetic molecule 3-oxo-C6-HSL (OHHL), which was used as a control. Enterobacter cancerogenus secreted C6-HSL, a related molecules to N-hexanoyl homoserine lactone (HHL), while Acinetobacter gyllenbergii exhibited a migration pattern similar to 2-heptyl-4-quinolone (HHQ) molecules. In comparison to this, 3-oxo-C12-HSL (OdDHL) type molecules were produced by Lysobacter soli, Pseudomonas putida, A. gyllenbergii, Acinetobacter calcoaceticus, and Pseudomonas aeruginosa, while Enterobacter cloacae produced molecules similar to 2-heptyl-3-hydroxy-4-quinolone (PQS). For Pseudomonas putida, Enterobacter aerogenes, P. ananatis, and Pseudomonas otitidis extracts, peak chromatograms with distinct retention times and areas, consistent with the molecules described in case of TLC, were obtained using HPLC. Importantly, P. ananatis produced a greater variety of high QSM concentration, and thus served as a reference for confirmation and identification by UHPLC-MRM-MS/MS. The molecules that were identified included N-hexanoyl-L-homoserine lactone [HHL, C10H18NO3, (M + H)], N-(3-oxohexanoyl)-L-homoserine lactone [OHHL, C10H16NO4, (M + H)], N-(3-oxododecanoyl)-L-homoserine lactone [OdDHL, C16H28NO4, (M + H)], and 2-heptyl-3-hydroxy-4(1H)-quinolone [PQS, C16H22NO2, (M + H)]. Besides this, the detection of diketopiperazines, namely L-Pro-L-Tyr and ΔAla-L-Val cyclopeptides was reported for P. ananatis. These molecules might be potentially associated with the regulation of QSM system, and might represent another small molecule-mediated bacterial sensing system. This study presents the first report regarding the detection and identification of QSM and diketopiperazines in the gut sand fly bacteria. The possible effect of QSM on the establishment of Leishmania must be explored to determine its role in the modulation of intestinal microbiome and the life cycle of Pi. evansi.
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Abstract
Dissolved exometabolites mediate algal interactions in aquatic ecosystems, but microalgal exometabolomes remain understudied. We conducted an untargeted metabolomic analysis of nonpolar exometabolites exuded from four phylogenetically and ecologically diverse eukaryotic microalgal strains grown in the laboratory, freshwater Chlamydomonas reinhardtii, brackish Desmodesmus sp., marine Phaeodactylum tricornutum, and marine Microchloropsis salina, to identify released metabolites based on relative enrichment in the exometabolomes compared to cell pellet metabolomes. Exudates from the different taxa were distinct, but we did not observe clear phylogenetic patterns. We used feature-based molecular networking to explore the identities of these metabolites, revealing several distinct di- and tripeptides secreted by each of the algae, lumichrome, a compound that is known to be involved in plant growth and bacterial quorum sensing, and novel prostaglandin-like compounds. We further investigated the impacts of exogenous additions of eight compounds selected based on exometabolome enrichment on algal growth. Of these compounds, five (lumichrome, 5′-S-methyl-5′-thioadenosine, 17-phenyl trinor prostaglandin A2, dodecanedioic acid, and aleuritic acid) impacted growth in at least one of the algal cultures. Two of these compounds (dodecanedioic acid and aleuritic acid) produced contrasting results, increasing growth in some algae and decreasing growth in others. Together, our results reveal new groups of microalgal exometabolites, some of which could alter algal growth when provided exogenously, suggesting potential roles in allelopathy and algal interactions. IMPORTANCE Microalgae are responsible for nearly half of primary production on earth and play an important role in global biogeochemical cycling as well as in a range of industrial applications. Algal exometabolites are important mediators of algal-algal and algal-bacterial interactions that ultimately affect algal growth and physiology. In this study, we characterize exometabolomes across marine and freshwater algae to gain insights into the diverse metabolites they release into their environments (“exudates”). We observe that while phylogeny can play a role in exometabolome content, environmental conditions or habitat origin (freshwater versus marine) are also important. We also find that several of these compounds can influence algal growth (as measured by chlorophyll production) when provided exogenously, highlighting the importance of characterization of these novel compounds and their role in microalgal ecophysiology.
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Bidirectional Cell-Cell Communication via Indole and Cyclo(Pro-Tyr) Modulates Interspecies Biofilm Formation. Appl Environ Microbiol 2021; 87:e0127721. [PMID: 34469193 DOI: 10.1128/aem.01277-21] [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: 11/20/2022] Open
Abstract
The extracellular signaling molecule indole plays a pivotal role in biofilm formation by the enteric gammaproteobacterium Escherichia coli; this process is particularly correlated with the extracellular indole concentration. Using the indole-biodegrading betaproteobacterium Burkholderia unamae, we examined the mechanism by which these two bacteria modulate biofilm formation in an indole-dependent manner. We quantified the spatial organization of cocultured microbial communities at the micrometer scale through computational image analysis, ultimately identifying how bidirectional cell-to-cell communication modulated the physical relationships between them. Further analysis allowed us to determine the mechanism by which the B. unamae-derived signaling diketopiperazine cyclo(Pro-Tyr) considerably upregulated indole biosynthesis and enhanced E. coli biofilm formation. We also determined that the presence of unmetabolized indole enhanced the production of cyclo(Pro-Tyr). Thus, bidirectional cell-to-cell communication that occurred via interspecies signaling molecules modulated the formation of a mixed-species biofilm between indole-producing and indole-consuming species. IMPORTANCE Indole is a relatively stable N-heterocyclic aromatic compound that is widely found in nature. To date, the correlations between indole-related bidirectional cell-to-cell communications and interspecies communal organization remain poorly understood. In this study, we used an experimental model, which consisted of indole-producing and indole-degrading bacteria, to evaluate how bidirectional cell-to-cell communication modulated interspecies biofilm formation via intrinsic and environmental cues. We identified a unique spatial patterning of indole-producing and indole-degrading bacteria within mixed-species biofilms. This spatial patterning was an active process mediated by bidirectional physicochemical interactions. Our findings represent an important step in gaining a more thorough understanding of the process of polymicrobial biofilm formation and advance the possibility of using indole-degrading bacteria to address biofilm-related health and industry issues.
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Ha J, Gao Y, Zhang R, Li K, Zhang Y, Niu X, Chen X, Luo K, Chen Y. Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava ( Manihot esculenta Crantz) Genotypes. Front Microbiol 2021; 12:729022. [PMID: 34659156 PMCID: PMC8515189 DOI: 10.3389/fmicb.2021.729022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.
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Affiliation(s)
- Jingwen Ha
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yu Gao
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Rui Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Ke Li
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yijie Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiaolei Niu
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kai Luo
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yinhua Chen
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
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Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Biomolecules 2021; 11:1515. [PMID: 34680148 PMCID: PMC8533947 DOI: 10.3390/biom11101515] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Istvan Toth
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Sherif Elnagdy
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Maha AlKhazindar
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
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28
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Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
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Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
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29
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Domzalski A, Perez SD, Yoo B, Velasquez A, Vigo V, Pasolli HA, Oldham AL, Henderson DP, Kawamura A. Uncovering potential interspecies signaling factors in plant-derived mixed microbial culture. Bioorg Med Chem 2021; 42:116254. [PMID: 34119697 PMCID: PMC8273658 DOI: 10.1016/j.bmc.2021.116254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/05/2021] [Accepted: 05/28/2021] [Indexed: 01/04/2023]
Abstract
Microbes use signaling factors for intraspecies and interspecies communications. While many intraspecies signaling factors have been found and characterized, discovery of factors for interspecies communication is lagging behind. To facilitate the discovery of such factors, we explored the potential of a mixed microbial culture (MMC) derived from wheatgrass, in which heterogeneity of this microbial community might elicit signaling factors for interspecies communication. The stability of Wheatgrass MMC in terms of community structure and metabolic output was first characterized by 16S ribosomal RNA amplicon sequencing and liquid chromatography/mass spectrometry (LC/MS), respectively. In addition, detailed MS analyses led to the identification of 12-hydroxystearic acid (12-HSA) as one of the major metabolites produced by Wheatgrass MMC. Stereochemical analysis revealed that Wheatgrass MMC produces mostly the (R)-isomer, although a small amount of the (S)-isomer was also observed. Furthermore, 12-HSA was found to modulate planktonic growth and biofilm formation of various marine bacterial strains. The current study suggests that naturally derived MMCs could serve as a simple and reproducible platform to discover potential signaling factors for interspecies communication. In addition, the study indicates that hydroxylated long-chain fatty acids, such as 12-HSA, may constitute a new class of interspecies signaling factors.
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Affiliation(s)
- Alison Domzalski
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, 365 5(th) Ave, New York, NY 10016, USA; Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Susan D Perez
- Department of Biology, University of Texas of the Permian Basin, 4901 E. University Blvd, Odessa, TX, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Alexandria Velasquez
- Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Valeria Vigo
- Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Athenia L Oldham
- Department of Biology, University of Texas of the Permian Basin, 4901 E. University Blvd, Odessa, TX, USA
| | - Douglas P Henderson
- Department of Biology, University of Texas of the Permian Basin, 4901 E. University Blvd, Odessa, TX, USA
| | - Akira Kawamura
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, 365 5(th) Ave, New York, NY 10016, USA; Chemistry Ph.D. Program, The Graduate Center of CUNY, 365 5(th) Ave, New York, NY 10016, USA; Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
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Ho XY, Katermeran NP, Deignan LK, Phyo MY, Ong JFM, Goh JX, Ng JY, Tun K, Tan LT. Assessing the Diversity and Biomedical Potential of Microbes Associated With the Neptune's Cup Sponge, Cliona patera. Front Microbiol 2021; 12:631445. [PMID: 34267732 PMCID: PMC8277423 DOI: 10.3389/fmicb.2021.631445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sponges are known to host a complex microbial consortium that is essential to the health and resilience of these benthic invertebrates. These sponge-associated microbes are also an important source of therapeutic agents. The Neptune's Cup sponge, Cliona patera, once believed to be extinct, was rediscovered off the southern coast of Singapore in 2011. The chance discovery of this sponge presented an opportunity to characterize the prokaryotic community of C. patera. Sponge tissue samples were collected from the inner cup, outer cup and stem of C. patera for 16S rRNA amplicon sequencing. C. patera hosted 5,222 distinct OTUs, spanning 26 bacterial phyla, and 74 bacterial classes. The bacterial phylum Proteobacteria, particularly classes Gammaproteobacteria and Alphaproteobacteria, dominated the sponge microbiome. Interestingly, the prokaryotic community structure differed significantly between the cup and stem of C. patera, suggesting that within C. patera there are distinct microenvironments. Moreover, the cup of C. patera had lower diversity and evenness as compared to the stem. Quorum sensing inhibitory (QSI) activities of selected sponge-associated marine bacteria were evaluated and their organic extracts profiled using the MS-based molecular networking platform. Of the 110 distinct marine bacterial strains isolated from sponge samples using culture-dependent methods, about 30% showed quorum sensing inhibitory activity. Preliminary identification of selected QSI active bacterial strains revealed that they belong mostly to classes Alphaproteobacteria and Bacilli. Annotation of the MS/MS molecular networkings of these QSI active organic extracts revealed diverse classes of natural products, including aromatic polyketides, siderophores, pyrrolidine derivatives, indole alkaloids, diketopiperazines, and pyrone derivatives. Moreover, potential novel compounds were detected in several strains as revealed by unique molecular families present in the molecular networks. Further research is required to determine the temporal stability of the microbiome of the host sponge, as well as mining of associated bacteria for novel QS inhibitors.
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Affiliation(s)
- Xin Yi Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nursheena Parveen Katermeran
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Lindsey Kane Deignan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ma Yadanar Phyo
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Ji Fa Marshall Ong
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Jun Xian Goh
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Juat Ying Ng
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Karenne Tun
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
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Dat TTH, Cuc NTK, Cuong PV, Smidt H, Sipkema D. Diversity and Antimicrobial Activity of Vietnamese Sponge-Associated Bacteria. Mar Drugs 2021; 19:md19070353. [PMID: 34206202 PMCID: PMC8307940 DOI: 10.3390/md19070353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
This study aimed to assess the diversity and antimicrobial activity of cultivable bacteria associated with Vietnamese sponges. In total, 460 bacterial isolates were obtained from 18 marine sponges. Of these, 58.3% belonged to Proteobacteria, 16.5% to Actinobacteria, 18.0% to Firmicutes, and 7.2% to Bacteroidetes. At the genus level, isolated strains belonged to 55 genera, of which several genera, such as Bacillus, Pseudovibrio, Ruegeria, Vibrio, and Streptomyces, were the most predominant. Culture media influenced the cultivable bacterial composition, whereas, from different sponge species, similar cultivable bacteria were recovered. Interestingly, there was little overlap of bacterial composition associated with sponges when the taxa isolated were compared to cultivation-independent data. Subsequent antimicrobial assays showed that 90 isolated strains exhibited antimicrobial activity against at least one of seven indicator microorganisms. From the culture broth of the isolated strain with the strongest activity (Bacillus sp. M1_CRV_171), four secondary metabolites were isolated and identified, including cyclo(L-Pro-L-Tyr) (1), macrolactin A (2), macrolactin H (3), and 15,17-epoxy-16-hydroxy macrolactin A (4). Of these, compounds 2-4 exhibited antimicrobial activity against a broad spectrum of reference microorganisms.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
| | - Nguyen Thi Kim Cuc
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Pham Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
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Brescia F, Vlassi A, Bejarano A, Seidl B, Marchetti-Deschmann M, Schuhmacher R, Puopolo G. Characterisation of the Antibiotic Profile of Lysobacter capsici AZ78, an Effective Biological Control Agent of Plant Pathogenic Microorganisms. Microorganisms 2021; 9:microorganisms9061320. [PMID: 34204563 PMCID: PMC8235233 DOI: 10.3390/microorganisms9061320] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Determining the mode of action of microbial biocontrol agents plays a key role in their development and registration as commercial biopesticides. The biocontrol rhizobacterium Lysobacter capsici AZ78 (AZ78) is able to inhibit a vast array of plant pathogenic oomycetes and Gram-positive bacteria due to the release of antimicrobial secondary metabolites. A combination of MALDI-qTOF-MSI and UHPLC-HRMS/M was applied to finely dissect the AZ78 metabolome and identify the main secondary metabolites involved in the inhibition of plant pathogenic microorganisms. Under nutritionally limited conditions, MALDI-qTOF-MSI revealed that AZ78 is able to release a relevant number of antimicrobial secondary metabolites belonging to the families of 2,5-diketopiperazines, cyclic lipodepsipeptides, macrolactones and macrolides. In vitro tests confirmed the presence of secondary metabolites toxic against Pythium ultimum and Rhodococcus fascians in AZ78 cell-free extracts. Subsequently, UHPLC-HRMS/MS was used to confirm the results achieved with MALDI-qTOF-MSI and investigate for further putative antimicrobial secondary metabolites known to be produced by Lysobacter spp. This technique confirmed the presence of several 2,5-diketopiperazines in AZ78 cell-free extracts and provided the first evidence of the production of the cyclic depsipeptide WAP-8294A2 in a member of L. capsici species. Moreover, UHPLC-HRMS/MS confirmed the presence of dihydromaltophilin/Heat Stable Antifungal Factor (HSAF) in AZ78 cell-free extracts. Due to the production of HSAF by AZ78, cell-free supernatants were effective in controlling Plasmopara viticola on grapevine leaf disks after exposure to high temperatures. Overall, our work determined the main secondary metabolites involved in the biocontrol activity of AZ78 against plant pathogenic oomycetes and Gram-positive bacteria. These results might be useful for the future development of this bacterial strain as the active ingredient of a microbial biopesticide that might contribute to a reduction in the chemical input in agriculture.
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Affiliation(s)
- Francesca Brescia
- Research and Innovation Centre, Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (F.B.); (A.B.)
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Torino, Italy
| | - Anthi Vlassi
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), 3430 Tulln, Austria; (A.V.); (B.S.); (R.S.)
| | - Ana Bejarano
- Research and Innovation Centre, Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (F.B.); (A.B.)
- Center of Agriculture, Food, Environment, University of Trento, 38098 San Michele all’Adige, Italy
| | - Bernard Seidl
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), 3430 Tulln, Austria; (A.V.); (B.S.); (R.S.)
| | - Martina Marchetti-Deschmann
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), 1060 Vienna, Austria;
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), 3430 Tulln, Austria; (A.V.); (B.S.); (R.S.)
| | - Gerardo Puopolo
- Research and Innovation Centre, Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (F.B.); (A.B.)
- Center of Agriculture, Food, Environment, University of Trento, 38098 San Michele all’Adige, Italy
- Correspondence:
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Sittmann J, Bae M, Mevers E, Li M, Quinn A, Sriram G, Clardy J, Liu Z. Bacterial diketopiperazines stimulate diatom growth and lipid accumulation. PLANT PHYSIOLOGY 2021; 186:1159-1170. [PMID: 33620482 PMCID: PMC8195512 DOI: 10.1093/plphys/kiab080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/03/2021] [Indexed: 06/10/2023]
Abstract
Diatoms are photosynthetic microalgae that fix a significant fraction of the world's carbon. Because of their photosynthetic efficiency and high-lipid content, diatoms are priority candidates for biofuel production. Here, we report that sporulating Bacillus thuringiensis and other members of the Bacillus cereus group, when in co-culture with the marine diatom Phaeodactylum tricornutum, significantly increase diatom cell count. Bioassay-guided purification of the mother cell lysate of B. thuringiensis led to the identification of two diketopiperazines (DKPs) that stimulate both P. tricornutum growth and increase its lipid content. These findings may be exploited to enhance P. tricornutum growth and microalgae-based biofuel production. As increasing numbers of DKPs are isolated from marine microbes, the work gives potential clues to bacterial-produced growth factors for marine microalgae.
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Affiliation(s)
- John Sittmann
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Andrew Quinn
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Tung TT, Quoc TN. Discovery of novel β-turn mimetic-based peptides as novel quorum sensing inhibitors of gram-negative bacteria. Bioorg Med Chem Lett 2021; 46:128170. [PMID: 34091042 DOI: 10.1016/j.bmcl.2021.128170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/29/2021] [Indexed: 12/28/2022]
Abstract
To date, a very limited number of peptides reported as quorum sensing inhibitors. Herein, we report the synthesis and evaluation of a series of β-turn mimetic-based peptides as potent quorum sensing inhibitors and antibiofilm formation. In this series, peptides P1, P4, and P5 showed very promising anti-quorum sensing activity on lasB-gfp reporter strain of Pseudomonas aeruginosa without affecting bacterial growth. Under our condition, these compounds also showed good anti-violacein production of Chromobacterium violaceum. In terms of antibiofilm formation, except P5, two β-turn mimetic-based peptides P1 and P4 showed maximum inhibition of 80% total biomass of Pseudomonas aeruginosa. This report provides the first β-turn mimetic-based scaffold for future drug development.
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Affiliation(s)
- Truong Thanh Tung
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Viet Nam; PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Viet Nam.
| | - Thang Nguyen Quoc
- Nuclear Medicine Unit, Vinmec International Hospital, Hanoi 10000, Viet Nam
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Friends or Foes-Microbial Interactions in Nature. BIOLOGY 2021; 10:biology10060496. [PMID: 34199553 PMCID: PMC8229319 DOI: 10.3390/biology10060496] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability. Abstract Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.
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Wang Y, Wang Y, Wang Y, Chen X, Liu C, Zhang M, Liu K, Zhao Y, Li Z. Untargeted Global Metabolomic Analysis Reveals the Mechanism of Tripropylamine-Enhanced Lycopene Accumulation in Blakeslea trispora. Front Bioeng Biotechnol 2021; 9:673225. [PMID: 34150732 PMCID: PMC8207141 DOI: 10.3389/fbioe.2021.673225] [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: 02/27/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
We previously determined that the cyclase inhibitor tripropylamine (TPA) significantly enhances lycopene accumulation in Blakeslea trispora. To elucidate the mechanism of TPA-enhanced lycopene accumulation, the untargeted metabolome of B. trispora treated with TPA was analyzed by UHPLC-Q-TOF/MS. Forty-two differential metabolites were identified, of which 15 significantly differential metabolites meeting the following parameters were screened: variable importance for the projection > 1, P < 0.05, and fold change > 1.5. The down-regulated metabolites were mainly cyclic dipeptides, bacteriostatic compounds, and lipids, while the up-regulated metabolites were mainly unsaturated fatty acid. Furthermore, the bacteriostatic ability was poor, the extracellular and intracellular pH levels were high, and hyphae with vesicles were swollen locally in B. trispora after treatment with TPA. Our data suggest that the TPA enhances lycopene accumulation not only by inhibiting the cyclization of β-carotene but also by down-regulating cyclic dipeptides for quorum sensing; up-regulating unsaturated fatty acids, 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine, and 4-hydroxybenzoate and down-regulating choline, resulting in locally swelling mycelium with vacuoles; and down-regulating bacteriostatic metabolites for metabolic flux redistribution.
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Affiliation(s)
- Yanlong Wang
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Yulong Wang
- College of Teacher Education, Qilu Normal University, Jinan, China
| | - Yicun Wang
- Shandong Institute for Product Quality Inspection, Jinan, China
| | - Xin Chen
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Cunping Liu
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Meng Zhang
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Keying Liu
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Yuechao Zhao
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Zexu Li
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
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Yu H, Wang J, Li X, Quan C. Effect of the environmental factors on diketopiperazine cyclo(Pro-Phe) production and antifungal activity of Bacillus amyloliquefaciens Q-426. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00722-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Nathalia O, Waturangi DE. Extract from phyllosphere bacteria with antibiofilm and quorum quenching activity to control several fish pathogenic bacteria. BMC Res Notes 2021; 14:202. [PMID: 34034823 PMCID: PMC8146661 DOI: 10.1186/s13104-021-05612-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/13/2021] [Indexed: 11/14/2022] Open
Abstract
Objective The objective of this research were to screen quorum quenching activity compound from phyllosphere bacteria as well as antibiofilm activity against several fish pathogen bacteria such as Aeromonas hydrophila, Streptococcus agalactiae, and Vibrio harveyi. Results We found eight phyllosphere bacteria isolates with potential quorum quenching activity to inhibit Chromobacterium violaceum as indicator bacteria. Crude extracts (20 mg/mL) showed various antibiofilm activity against fish pathogenic bacteria used in this study. Isolate JB 17B showed the highest activity to inhibit biofilm formation of A. hydrophila and V. harveyi, meanwhile isolate JB 3B showed the highest activity to inhibit biofilm of S. agalactiae. From destruction assay, isolate JB 8F showed the highest activity to disrupt biofilm of A. hydrophila isolate JB 20B showed the highest activity to disrupt biofilm of V. harveyi, isolate JB 17B also showed the highest activity to disrupt biofilm of S. agalactiae.
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Affiliation(s)
- Olivia Nathalia
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman 51, Jakarta, 12930, Indonesia
| | - Diana Elizabeth Waturangi
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman 51, Jakarta, 12930, Indonesia.
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Chamberlain CA, Hatch M, Garrett TJ. Extracellular Vesicle Analysis by Paper Spray Ionization Mass Spectrometry. Metabolites 2021; 11:metabo11050308. [PMID: 34065030 PMCID: PMC8151837 DOI: 10.3390/metabo11050308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/23/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022] Open
Abstract
Paper spray ionization mass spectrometry (PSI-MS) is a direct MS analysis technique with several reported bacterial metabolomics applications. As with most MS-based bacterial studies, all currently reported PSI-MS bacterial analyses have focused on the chemical signatures of the cellular unit. One dimension of the bacterial metabolome that is often lost in such analyses is the exometabolome (extracellular metabolome), including secreted metabolites, lipids, and peptides. A key component of the bacterial exometabolome that is gaining increased attention in the microbiology and biomedical communities is extracellular vesicles (EVs). These excreted structures, produced by cells in all domains of life, contain a variety of biomolecules responsible for a wide array of cellular functions, thus representing a core component of the bacterial secreted metabolome. Although previously examined using other MS approaches, no reports currently exist for a PSI-MS analysis of bacterial EVs, nor EVs from any other organism (exosomes, ectosomes, etc.). PSI-MS holds unique analytical strengths over other commonly used MS platforms and could thus provide an advantageous approach to EV metabolomics. To address this, we report a novel application representing, to our knowledge, the first PSI-MS analysis of EVs from any organism (using the human gut resident Oxalobacter formigenes as the experimental model, a bacterium whose EVs were never previously investigated). In this report, we show how we isolated and purified EVs from bacterial culture supernatant by EV-specific affinity chromatography, confirmed and characterized these vesicles by nanoparticle tracking analysis, analyzed the EV isolate by PSI-MS, and identified a panel of EV-derived metabolites, lipids, and peptides. This work serves as a pioneering study in the field of MS-based EV analysis and provides a new, rapid, sensitive, and economical approach to EV metabolomics.
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Shi T, Zheng L, Li XQ, Dai JJ, Zhang YT, Yu YY, Hu WP, Shi DY. Nitrogenous Compounds from the Antarctic Fungus Pseudogymnoascus sp. HSX2#-11. Molecules 2021; 26:molecules26092636. [PMID: 33946466 PMCID: PMC8124204 DOI: 10.3390/molecules26092636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
The species Pseudogymnoascus is known as a psychrophilic pathogenic fungus which is ubiquitously distributed in Antarctica. While the studies of its secondary metabolites are infrequent. Systematic research of the metabolites of the Antarctic fungus Pseudogymnoascus sp. HSX2#-11 led to the isolation of one new pyridine derivative, 4-(2-methoxycarbonyl-ethyl)-pyridine-2-carboxylic acid methyl ester (1), together with one pyrimidine, thymine (2), and eight diketopiperazines, cyclo-(dehydroAla-l-Val) (3), cyclo-(dehydroAla-l-Ile) (4), cyclo-(dehydroAla-l-Leu) (5), cyclo-(dehydroAla-l-Phe) (6), cyclo-(l-Val-l-Phe) (7), cyclo-(l-Leu-l-Phe) (8), cyclo-(l-Trp-l-Ile) (9) and cyclo-(l-Trp-l-Phe) (10). The structures of these compounds were established by extensive spectroscopic investigation, as well as by detailed comparison with literature data. This is the first report to discover pyridine, pyrimidine and diketopiperazines from the genus of Pseudogymnoascus.
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Affiliation(s)
- Ting Shi
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (T.S.); (X.-Q.L.); (J.-J.D.); or (Y.-T.Z.); (Y.-Y.Y.); (W.-P.H.)
| | - Li Zheng
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China;
- Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xiang-Qian Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (T.S.); (X.-Q.L.); (J.-J.D.); or (Y.-T.Z.); (Y.-Y.Y.); (W.-P.H.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jia-Jia Dai
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (T.S.); (X.-Q.L.); (J.-J.D.); or (Y.-T.Z.); (Y.-Y.Y.); (W.-P.H.)
| | - Yi-Ting Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (T.S.); (X.-Q.L.); (J.-J.D.); or (Y.-T.Z.); (Y.-Y.Y.); (W.-P.H.)
| | - Yan-Yan Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (T.S.); (X.-Q.L.); (J.-J.D.); or (Y.-T.Z.); (Y.-Y.Y.); (W.-P.H.)
| | - Wen-Peng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (T.S.); (X.-Q.L.); (J.-J.D.); or (Y.-T.Z.); (Y.-Y.Y.); (W.-P.H.)
| | - Da-Yong Shi
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (T.S.); (X.-Q.L.); (J.-J.D.); or (Y.-T.Z.); (Y.-Y.Y.); (W.-P.H.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Correspondence: ; Tel.: +86-532-5863-1523
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Zhao L, Duan F, Gong M, Tian X, Guo Y, Jia L, Deng S. (+)-Terpinen-4-ol Inhibits Bacillus cereus Biofilm Formation by Upregulating the Interspecies Quorum Sensing Signals Diketopiperazines and Diffusing Signaling Factors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3496-3510. [PMID: 33724028 DOI: 10.1021/acs.jafc.0c07826] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacillus cereus is a Gram-positive endospore-forming foodborne pathogen that causes lethal food poisoning and significant economic losses, usually through biofilm- and endospore-induced recurrent cross- and postprocessing contamination. Due to the lack of critical inhibitory targets and control strategies, B. cereus biofilm contamination is a problem that urgently needs a solution. In this study, the antibacterial and antibiofilm activities of several natural potential bacterial quorum sensing (QS) interferers, a group of spice-originated monoterpenoids, were screened, and terpinen-4-ol effectively inhibited B. cereus growth and biofilm and spore germination with minimum growth inhibition and 50% biofilm inhibitory concentrations of 8 and 2 μmol/mL, respectively. FESEM/CLSM and phenotypic research illustrated that in addition to a decrease in the number of attached B. cereus cells, (+)-terpinen-4-ol also obviously reduced extracellular matrix synthesis, especially exopolysaccharides, and inhibited the swarming motility and protease activity of B. cereus. (+)-Terpinen-4-ol did not exert a significant effect on AI-2 signals in B. cereus. Accordingly, the B. cereus-produced interspecies QS signals diffusing signal factors (DSFs, C8-C15) and diketopiperazines (DKPs) were detected and identified here, which suppressed B. cereus biofilm formation in a concentration-dependent manner. (+)-Terpinen-4-ol significantly increased the levels of specific DSF and DKP signals in B. cereus and down-regulated the gene expression of some rpfB homologues in transcription level. Moreover, both DKPs and DSFs inhibited swarming motility and protease activity in B. cereus, while just the DSF signals 2-dodecenoic acid and 11-methyl-2-dodecenoic acid inhibited exopolysaccharide synthesis like (+)-terpinen-4-ol. In summary, B. cereus strains were found to produce nine DSF- and six DKP-type QS signaling molecules, which repressed B. cereus biofilm formation. (+)-Terpinen-4-ol was confirmed to be a promising antibacterial and antibiofilm agent against B. cereus upregulating DSFs and DKPs levels, and it could target the critical genes rpfB for DSFs turnover.
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Affiliation(s)
- Lijun Zhao
- Department of Food Engineering, College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Feixia Duan
- Department of Food Engineering, College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Meng Gong
- Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, 88 Keyuan South Road, Hi-Tech Zone, Chengdu 610041, P. R. China
| | - Xue Tian
- Department of Food Engineering, College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Yan Guo
- Sichuan Center for Disease Control and Prevention, Chengdu 610041, P. R. China
| | - Lirong Jia
- Department of Food Engineering, College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Sha Deng
- Department of Food Engineering, College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
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Yu X, Li L, Sun S, Chang A, Dai X, Li H, Wang Y, Zhu H. A Cyclic Dipeptide from Marine Fungus Penicillium chrysogenum DXY-1 Exhibits Anti-quorum Sensing Activity. ACS OMEGA 2021; 6:7693-7700. [PMID: 33778279 PMCID: PMC7992161 DOI: 10.1021/acsomega.1c00020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Bacterial quorum sensing (QS) is anticipated as a new potential target for the development of antimicrobial drugs. An anti-QS substance against Chromobacterium violaceum CV026 and Pseudomonas aeruginosa PA01 has been isolated and purified from the crude extracts of the marine fungus Penicillium chrysogenum DXY-1, and the accurate structure was identified as cyclo(l-Tyr-l-Pro). This cyclic dipeptide at sub-minimum inhibitory concentration can decrease the QS-regulated violacein production of C. violaceum CV026 by 79% and QS-mediated pyocyanin production, proteases, and elastase activity of P. aeruginosa PA01 by 41%, 20%, and 32%, respectively. In addition, it can also destroy the biofilm formation and decrease QS gene expression of P. aeruginosa PA01. Molecular docking was further performed, and the obtained data indicated that this dipeptide blocks the effect of QS autoinducers through competitive binding to the same pocket of the receptor proteins. We expect this anti-QS cyclic dipeptide to be a potential pro-drug treating drug-resistant P. aeruginosa infections, and these findings could relieve the alarming problem of microbial resistance to antimicrobial drugs.
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Affiliation(s)
- Xiaodan Yu
- Engineering
Research Center of Industrial Biocatalysis, Fujian Province University,
Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical
Engineering, Fujian Provincial Key Laboratory of Polymer Materials,
Key Laboratory of OptoElectronic Science and Technology for Medicine
of Ministry of Education, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, People’s Republic
of China
| | - Li Li
- Engineering
Research Center of Industrial Biocatalysis, Fujian Province University,
Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical
Engineering, Fujian Provincial Key Laboratory of Polymer Materials,
Key Laboratory of OptoElectronic Science and Technology for Medicine
of Ministry of Education, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, People’s Republic
of China
| | - Shiwei Sun
- Department
of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, 308 Ningxia Road, Qingdao 266071, People’s Republic of China
| | - Aiping Chang
- Engineering
Research Center of Industrial Biocatalysis, Fujian Province University,
Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical
Engineering, Fujian Provincial Key Laboratory of Polymer Materials,
Key Laboratory of OptoElectronic Science and Technology for Medicine
of Ministry of Education, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, People’s Republic
of China
| | - Xiaoyun Dai
- Centre
for Bioengineering and Biotechnology, China
University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, People’s
Republic of China
| | - Hui Li
- Centre
for Bioengineering and Biotechnology, China
University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, People’s
Republic of China
| | - Yinglu Wang
- Engineering
Research Center of Industrial Biocatalysis, Fujian Province University,
Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical
Engineering, Fujian Provincial Key Laboratory of Polymer Materials,
Key Laboratory of OptoElectronic Science and Technology for Medicine
of Ministry of Education, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, People’s Republic
of China
| | - Hu Zhu
- Engineering
Research Center of Industrial Biocatalysis, Fujian Province University,
Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical
Engineering, Fujian Provincial Key Laboratory of Polymer Materials,
Key Laboratory of OptoElectronic Science and Technology for Medicine
of Ministry of Education, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, People’s Republic
of China
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Abstract
The complexity of animal microbiomes presents challenges to defining signaling molecules within the microbial consortium and between the microbes and the host. By focusing on the binary symbiosis between Vibrio fischeri and Euprymna scolopes, we have combined genetic analysis with direct imaging to define and study small molecules in the intact symbiosis. The lifelong relationship between the Hawaiian bobtail squid Euprymna scolopes and its microbial symbiont Vibrio fischeri represents a simplified model system for studying microbiome establishment and maintenance. The bacteria colonize a dedicated symbiotic light organ in the squid, from which bacterial luminescence camouflages the host in a process termed counterillumination. The squid host hatches without its symbionts, which must be acquired from the ocean amidst a diversity of nonbeneficial bacteria, such that precise molecular communication is required for initiation of the specific relationship. Therefore it is likely there are specialized metabolites used in the light organ microenvironment to modulate these processes. To identify small molecules that may influence the establishment of this symbiosis, we used imaging mass spectrometry to analyze metabolite production in V. fischeri with altered biofilm production, which correlates directly to colonization capability in its host. “Biofilm-up” and “biofilm-down” mutants were compared to a wild-type strain, and ions that were more abundantly produced by the biofilm-up mutant were detected. Using a combination of structural elucidation and synthetic chemistry, one such signal was determined to be a diketopiperazine, cyclo(d-histidyl-l-proline). This diketopiperazine modulated luminescence in V. fischeri and, using imaging mass spectrometry, was directly detected in the light organ of the colonized host. This work highlights the continued need for untargeted discovery efforts in host-microbe interactions and showcases the benefits of the squid-Vibrio system for identification and characterization of small molecules that modulate microbiome behaviors.
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Medapati MR, Bhagirath AY, Singh N, Chelikani P. Pharmacology of T2R Mediated Host-Microbe Interactions. Handb Exp Pharmacol 2021; 275:177-202. [PMID: 33580389 DOI: 10.1007/164_2021_435] [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: 12/12/2022]
Abstract
Bitter taste receptors (T2Rs) belong to the G protein-coupled receptor superfamily. Humans express 25 T2Rs that are known to detect several bitter compounds including bacterial quorum sensing molecules (QSM). Primarily found to be key receptors for bitter sensation T2Rs are known to play an important role in mediating innate immune responses in oral and extraoral tissues. Several studies have led to identification of Gram-negative and Gram-positive bacterial QSMs as agonists for T2Rs in airway epithelial cells and immune cells. However, the pharmacological characterization for many of the QSM-T2R interactions remains poorly defined. In this chapter, we discuss the extraoral roles including localization of T2Rs in extracellular vesicles, molecular pharmacology of QSM-T2R interactions, role of T2Rs in mediating innate immune responses, and some of the challenges in understanding T2R pharmacology.
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Affiliation(s)
- Manoj Reddy Medapati
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Anjali Y Bhagirath
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Nisha Singh
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Prashen Chelikani
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, MB, Canada.
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
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Thomas SG, Abajorga M, Glover MA, Wengert PC, Parthasarathy A, Savka MA, Wadsworth CB, Shipman PA, Hudson AO. Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669-Potential Zoonotic Pathogens Isolated from Spotted Turtles. Microorganisms 2020; 8:microorganisms8111805. [PMID: 33212916 PMCID: PMC7698337 DOI: 10.3390/microorganisms8111805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the biggest challenges of the 21st century, and biofilm formation enables bacteria to resist antibiotic at much higher concentrations than planktonic cells. Earlier, we showed that the Gram-negative Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669 (closely related to C. freundii NBRC 12681) from infected spotted turtles (Clemmys guttata), formed biofilms and upregulated toxin expression on plastic surfaces, and were predicted to possess multiple antibiotic resistance genes. Here, we show that they each resist several antibiotics in the planktonic phase, but were susceptible to neomycin, and high concentrations of tetracycline and cotrimoxazole. The susceptibility of their biofilms to neomycin and cotrimoxazole was tested using the Calgary device. For A. hydrophila, the minimum inhibitory concentration (MIC) = 500-1000, and the minimum biofilm eradication concentration (MBEC) > 1000 μg/mL, using cotrimoxazole, and MIC = 32.3-62.5, and MBEC > 1000 μg/mL, using neomycin. For C. freundii MIC = 7.8-15.6, and, MBEC > 1000 μg/mL, using cotrimoxazole, and MIC = 7.8, and MBEC > 1000 μg/mL, using neomycin. Both A. hydrophila and C. portucalensis activated an acyl homoserine lactone (AHL) dependent biosensor, suggesting that quorum sensing could mediate biofilm formation. Their multidrug resistance in the planktonic form, and weak biofilm eradication even with neomycin and cotrimoxazole, indicate that A. hydrophila and C. portucalensis are potential zoonotic pathogens, with risks for patients living with implants.
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Zhao K, Xing R, Yan X. Cyclic dipeptides: Biological activities and self‐assembled materials. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24202] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kaili Zhao
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences Beijing China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing China
| | - Ruirui Xing
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences Beijing China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences Beijing China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing China
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Soh YNA, Kunacheva C, Webster RD, Stuckey DC. Composition and biotransformational changes in soluble microbial products (SMPs) along an anaerobic baffled reactor (ABR). CHEMOSPHERE 2020; 254:126775. [PMID: 32320833 DOI: 10.1016/j.chemosphere.2020.126775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
This work examined the production and catabolism/biotransformation dynamics of SMPs down the length of an eight-compartment-anaerobic baffled reactor (ABR) which physically separates the biological processes, in contrast to completely mixed reactors which do not enable these dynamics to measured, and this is totally novel. SMPs were extracted and characterised by gas and liquid chromatography coupled mass spectrometry to determine their composition and production/catabolism. 60%-70% of the feed compounds decreased from the first to fourth compartment; the increase in SMPs after the fourth compartment suggested a mixture of degraded and biotransformed compounds, and microbial products. High concentrations of low MW alkanes and alkenes, and higher MW (up to 2000 Da) lipids and amino acid derivatives accumulate in the last compartment at pseudo-steady state, and past work identifying polysaccharides/peptides as major membrane biofoulants have excluded these lipids. In addition, lipids and changes detected during feed transients have not been noted before in previous work. Finally, feed step-increases also increased some amino acid derivatives used in cell-signalling. Interestingly, some natural products from plant and fungal extracts were also found in the fourth compartment, where methanogenesis was the dominant process.
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Affiliation(s)
- Yan Ni Annie Soh
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Clean Tech One, Singapore, 637141, Singapore; Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 61 Nanyang Drive, Academic Block North, ABN-01b-11, Singapore, 637335, Singapore
| | - Chinagarn Kunacheva
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Clean Tech One, Singapore, 637141, Singapore
| | - Richard D Webster
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - David C Stuckey
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Clean Tech One, Singapore, 637141, Singapore; Department of Chemical Engineering, Imperial College London, SW7 2AZ, UK.
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Khan F, Oloketuyi SF, Kim YM. Diversity of Bacteria and Bacterial Products as Antibiofilm and Antiquorum Sensing Drugs Against Pathogenic Bacteria. Curr Drug Targets 2020; 20:1156-1179. [PMID: 31020938 DOI: 10.2174/1389450120666190423161249] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 04/12/2019] [Indexed: 12/14/2022]
Abstract
The increase in antibiotic resistance of pathogenic bacteria has led to the development of new therapeutic approaches to inhibit biofilm formation as well as interfere quorum sensing (QS) signaling systems. The QS system is a phenomenon in which pathogenic bacteria produce signaling molecules that are involved in cell to cell communication, production of virulence factors, biofilm maturation, and several other functions. In the natural environment, several non-pathogenic bacteria are present as mixed population along with pathogenic bacteria and they control the behavior of microbial community by producing secondary metabolites. Similarly, non-pathogenic bacteria also take advantages of the QS signaling molecule as a sole carbon source for their growth through catabolism with enzymes. Several enzymes are produced by bacteria which disrupt the biofilm architecture by degrading the composition of extracellular polymeric substances (EPS) such as exopolysaccharide, extracellular- DNA and protein. Thus, the interference of QS system by bacterial metabolic products and enzymatic catalysis, modification of the QS signaling molecules as well as enzymatic disruption of biofilm architecture have been considered as the alternative therapeutic approaches. This review article elaborates on the diversity of different bacterial species with respect to their metabolic products as well as enzymes and their molecular modes of action. The bacterial enzymes and metabolic products will open new and promising perspectives for the development of strategies against the pathogenic bacterial infections.
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Affiliation(s)
- Fazlurrahman Khan
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan 48513, South Korea
| | | | - Young-Mog Kim
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan 48513, South Korea.,Department of Food Science and Technology, Pukyong National University, Busan 48513, South Korea
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Induction of mitochondria-mediated apoptosis and suppression of tumor growth in zebrafish xenograft model by cyclic dipeptides identified from Exiguobacterium acetylicum. Sci Rep 2020; 10:13721. [PMID: 32792514 PMCID: PMC7426938 DOI: 10.1038/s41598-020-70516-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 07/30/2020] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer is the most common type of gastrointestinal cancers with poor survival and limited therapeutic options. In this study, four structurally different cyclic dipeptides (or diketopiperazine) were isolated and identified as cyclo (l-Pro-l-Leu), cyclo (l-Pro-l-Val), cyclo (l-Pro-l-Phe) and cyclo (l-Pro-l-Tyr) from the ethyl acetate extract in the cell-free filtrate of Exiguobacterium acetylicum S01. The anticancer potential of identified DKPs on colorectal cancer HT-29 cells in vitro and in vivo zebrafish xenograft model was evaluated. The MTT (3-(4, 5-dimethylthiazol-2yl)-2, 5-diphenyltetrazolium bromide)) assay showed that four DKPs exhibited significant inhibition of HT-29 cells viability in a dose-dependent manner whereas there were no cytotoxic effects on normal mouse fibroblast 3T3 cells. Also, we observed that all DKPs induce early and late apoptotic cell death in HT-29 cells. Moreover, the expression levels of apoptotic (cytochrome-c, caspase-3 and Bid) and anti-apoptotic (Bcl-2) markers were up- and down-regulated in HT-29 cells in response to DKPs treatments. Furthermore, these four DKPs remarkably inhibited the tumor progression in a zebrafish xenograft model within a nonlethal dose range. Overall, our findings suggest that cyclic dipeptides derived from E. acetylicum S01 could be promising chemopreventive/ therapeutic candidates against cancer.
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Sikdar R, Elias M. Quorum quenching enzymes and their effects on virulence, biofilm, and microbiomes: a review of recent advances. Expert Rev Anti Infect Ther 2020; 18:1221-1233. [PMID: 32749905 DOI: 10.1080/14787210.2020.1794815] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Numerous bacterial behaviors are regulated by a cell-density dependent mechanism known as Quorum Sensing (QS). QS relies on communication between bacterial cells using diffusible signaling molecules known as autoinducers. QS regulates physiological processes such as metabolism, virulence, and biofilm formation. Quorum Quenching (QQ) is the inhibition of QS using chemical or enzymatic means to counteract behaviors regulated by QS. AREAS COVERED We examine the main, diverse QS mechanisms present in bacterial species, with a special emphasis on AHL-mediated QS. We also discuss key in vitro and in vivo systems in which interference in QS was investigated. Additionally, we highlight promising developments, such as the substrate preference of the used enzymatic quencher, in the application of interference in QS to counter bacterial virulence. EXPERT OPINION Enabled via the recent isolation of highly stable quorum quenching enzymes and/or molecular engineering efforts, the effects of the interference in QS were recently evaluated outside of the traditional model of single species culture. Signal disruption in complex microbial communities was shown to result in the disruption of complex microbial behaviors, and changes in population structures. These new findings, and future studies, may result in significant changes in the traditional views about QS.
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Affiliation(s)
- Rakesh Sikdar
- Biochemistry, Molecular Biology & Biophysics Department and BioTechnology Institute, University of Minnesota , Saint Paul, Minnesota, USA
| | - Mikael Elias
- Biochemistry, Molecular Biology & Biophysics Department and BioTechnology Institute, University of Minnesota , Saint Paul, Minnesota, USA
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