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Diniz GDFD, Figueiredo JEF, Canuto KM, Cota LV, Souza ASDQ, Simeone MLF, Tinoco SMDS, Ribeiro PRV, Ferreira LVS, Marins MS, de Oliveira-Paiva CA, Dos Santos VL. Chemical and genetic characterization of lipopeptides from Bacillus velezensis and Paenibacillus ottowii with activity against Fusarium verticillioides. Front Microbiol 2024; 15:1443327. [PMID: 39252841 PMCID: PMC11381237 DOI: 10.3389/fmicb.2024.1443327] [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: 06/03/2024] [Accepted: 08/02/2024] [Indexed: 09/11/2024] Open
Abstract
Introduction The fungus Fusarium verticillioides significantly threatens maize crops in tropical soils. In light of this, biological control has emerged as a promising strategy to reduce fungicide costs and environmental risks. In this study, we aimed to test the antifungal activity of cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04) against F. verticillioides, thereby contributing to the development of effective biocontrol measures. Methods The research employed a comprehensive approach. The antifungal activity of the bacterial strains was tested using cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04). The UPLC-MS evaluated the CFS to identify the main bioactive molecules involved in the inhibitory effect on F. verticillioides. Scanning electron microscopy (SEM) was used to assess the impact of CFS on spores and hyphae, and genome sequencing was conducted to identify the genes involved in biological control. These robust methodologies ensure the reliability and validate our findings. Results The CFS of the four strains demonstrated significant inhibition of fungal growth. The UPLC-MS analysis revealed the presence of lipopeptides with antifungal activity, including surfactin and fengycins A and B expressed by the three strains of Bacillus velezensis and iturin A expressed by strains LIS05 and IM14. For Paenibacillus ottowii, fusaricidins, ABCDE, and five previously unreported lipopeptides were detected. Scanning electron microscopy (SEM) showed that treatments with CFS led to significant distortion and breakage of the F. verticillioides hyphae, in addition to the formation of cavities in the membrane. Genome mining confirmed the presence of genes coding for the lipopeptides identified by UPLC-MS, including the gene for iturin in CTO2. Genomic sequencing revealed that CT02, IM14, and LIS05 belong to different strains of Bacillus velezensis, and LIS04 belongs to Paenibacillus ottowii, a species recently described. Discussion The four bacterial strains, including three novel strains identified as Bacillus velezensis and one as the recently described species Paenibacillus ottowii, demonstrate significant potential as biocontrol agents for managing fungal disease. This finding underscores the novelty and potential impact of our research.
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Affiliation(s)
| | | | - Kirley Marques Canuto
- Multiuser Laboratory of Chemistry of Natural Products (LMQPN), Embrapa Tropical Agroindustry, Fortaleza, CE, Brazil
| | - Luciano Viana Cota
- Phytopathology Laboratory, Embrapa Maize and Sorghum, Sete Lagoas, MG, Brazil
| | - Ana Sheila de Queiroz Souza
- Multiuser Laboratory of Chemistry of Natural Products (LMQPN), Embrapa Tropical Agroindustry, Fortaleza, CE, Brazil
| | | | - Sylvia Morais de Sousa Tinoco
- Molecular Biology Laboratory, Embrapa Maize and Sorghum, Sete Lagoas, MG, Brazil
- Federal University of São João del-Rei, São João del Rei, MG, Brazil
| | | | | | - Mikaely Sousa Marins
- Department of Agricultural Microbiology, Federal University of Lavras, Lavras, MG, Brazil
| | | | - Vera Lúcia Dos Santos
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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Chen X, Li B. Analysis of Co-localized Biosynthetic Gene Clusters Identifies a Membrane-Permeabilizing Natural Product. JOURNAL OF NATURAL PRODUCTS 2024; 87:1694-1703. [PMID: 38949271 DOI: 10.1021/acs.jnatprod.3c01231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Combination therapy is an effective strategy to combat antibiotic resistance. Multiple synergistic antimicrobial combinations are produced by enzymes encoded in biosynthetic gene clusters (BGCs) that co-localize on the bacterial genome. This phenomenon led to the hypothesis that mining co-localized BGCs will reveal new synergistic combinations of natural products. Here, we bioinformatically identified 38 pairs of co-localized BGCs, which we predict to produce natural products that are related to known compounds, including polycyclic tetramate macrolactams (PoTeMs). We further showed that ikarugamycin, a PoTeM, increases the membrane permeability of Acinetobacter baumannii and Staphylococcus aureus, which suggests that ikarugamycin might be an adjuvant that facilitates the entry of other natural products. Our work outlines a promising avenue to discover synergistic combinations of natural products by mining bacterial genomes.
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Affiliation(s)
- Xiaoyan Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Haidar R, Compant S, Robert C, Antonielli L, Yacoub A, Grélard A, Loquet A, Brader G, Guyoneaud R, Attard E, Rey P. Two Paenibacillus spp. strains promote grapevine wood degradation by the fungus Fomitiporia mediterranea: from degradation experiments to genome analyses. Sci Rep 2024; 14:15779. [PMID: 38982270 PMCID: PMC11233627 DOI: 10.1038/s41598-024-66620-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Ascomycetes, basidiomycetes and deuteromycetes can degrade wood, but less attention has been paid to basidiomycetes involved in Esca, a major Grapevine Trunk Disease. Using a wood sawdust microcosm system, we compared the wood degradation of three grapevine cultivars inoculated with Fomitiporia mediterranea M. Fisch, a basidiomycete responsible for white-rot development and involved in Esca disease. The grapevine cultivar Ugni blanc was more susceptible to wood degradation caused by F. mediterranea than the cultivars Cabernet Sauvignon and Merlot. Solid-state Nuclear Magnetic Resonance (NMR) spectroscopy showed that F. mediterranea preferentially degrades lignin and hemicellulose over cellulose (preferential, successive or sequential white-rot). In addition, co-inoculation of sawdust with two cellulolytic and xylanolytic bacterial strains of Paenibacillus (Nakamura) Ash (Paenibacillus sp. (S231-2) and P. amylolyticus (S293)), enhanced F. mediterranea ability to degrade Ugni blanc. The NMR data further showed that the increase in Ugni blanc sawdust degradation products was greater when bacteria and fungi were inoculated together. We also demonstrated that these two bacterial strains could degrade the wood components of Ugni blanc sawdust. Genome analysis of these bacterial strains revealed numerous genes predicted to be involved in cellulose, hemicellulose, and lignin degradation, as well as several other genes related to bacteria-fungi interactions and endophytism inside the plant. The occurrence of this type of bacteria-fungus interaction could explain, at least in part, why necrosis develops extensively in certain grapevine varieties such as Ugni blanc.
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Affiliation(s)
- Rana Haidar
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France.
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France.
| | - Stéphane Compant
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Coralie Robert
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Livio Antonielli
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Amira Yacoub
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
| | - Axelle Grélard
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Antoine Loquet
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Günter Brader
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Rémy Guyoneaud
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Eléonore Attard
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
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Nuñez Santiago I, Machushynets NV, Mladic M, van Bergeijk DA, Elsayed SS, Hankemeier T, van Wezel GP. nanoRAPIDS as an analytical pipeline for the discovery of novel bioactive metabolites in complex culture extracts at the nanoscale. Commun Chem 2024; 7:71. [PMID: 38561415 PMCID: PMC10984978 DOI: 10.1038/s42004-024-01153-y] [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: 02/07/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Microbial natural products form the basis of most of the antibiotics used in the clinic. The vast majority has not yet been discovered, among others because the hidden chemical space is obscured by previously identified (and typically abundant) antibiotics in culture extracts. Efficient dereplication is therefore key to the discovery of our future medicines. Here we present an analytical platform for the efficient identification and prioritization of low abundance bioactive compounds at nanoliter scale, called nanoRAPIDS. NanoRAPIDS encompasses analytical scale separation and nanofractionation of natural extracts, followed by the bioassay of interest, automated mass spectrometry identification, and Global Natural Products Social molecular networking (GNPS) for dereplication. As little as 10 μL crude extract is fractionated into 384 fractions. First, bioactive congeners of iturins and surfactins were identified in Bacillus, based on their bioactivity. Subsequently, bioactive molecules were identified in an extensive network of angucyclines elicited by catechol in cultures of Streptomyces sp. This allowed the discovery of a highly unusual N-acetylcysteine conjugate of saquayamycin, despite low production levels in an otherwise abundant molecular family. These data underline the utility and broad application of the technology for the prioritization of minor bioactive compounds in complex extracts.
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Affiliation(s)
- Isabel Nuñez Santiago
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Marija Mladic
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- DSM-Firmenich, Delft, The Netherlands
| | - Doris A van Bergeijk
- Department of Microbiology, KU Leuven, Immunology and Transplantation (Laboratory of Molecular Bacteriology), Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
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Li E, Liu K, Yang S, Li L, Ran K, Sun X, Qu J, Zhao L, Xin Y, Zhu F, Ma J, Song F, Li Z. Analysis of the complete genome sequence of Paenibacillus sp. lzh-N1 reveals its antagonistic ability. BMC Genomics 2024; 25:276. [PMID: 38481158 PMCID: PMC10938842 DOI: 10.1186/s12864-024-10206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Plant diseases caused by pathogenic fungi are devastating. However, commonly used fungicides are harmful to the environment, and some are becoming ineffective due to fungal resistance. Therefore, eco-friendly biological methods to control pathogenic fungi are urgently needed. RESULTS In this study, a strain, Paenibacillus sp. lzh-N1, that could inhibit the growth of the pathogenic fungus Mycosphaerella sentina (Fr) Schrorter was isolated from the rhizosphere soil of pear trees, and the complete genome sequence of the strain was obtained, annotated, and analyzed to reveal the genetic foundation of its antagonistic ability. The entire genome of this strain contained a circular chromosome of 5,641,488 bp with a GC content of 45.50%. The results of species identification show that the strain belongs to the same species as P. polymyxa Sb3-1 and P. polymyxa CJX518. Sixteen secondary metabolic biosynthetic gene clusters were predicted by antiSMASH, including those of the antifungal peptides fusaricidin B and paenilarvins. In addition, biofilm formation-related genes containing two potential gene clusters for cyclic lactone autoinducer, a gene encoding S-ribosylhomocysteine lyase (LuxS), and three genes encoding exopolysaccharide biosynthesis protein were identified. CONCLUSIONS Antifungal peptides and glucanase biosynthesized by Paenibacillus sp. lzh-N1 may be responsible for its antagonistic effect. Moreover, quorum sensing systems may influence the biocontrol activity of this strain directly or indirectly.
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Affiliation(s)
- Ee Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Kaiquan Liu
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Shuhan Yang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Ling Li
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Kun Ran
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Xiaoli Sun
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Jie Qu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Li Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Yuxiu Xin
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Zhu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Jingfang Ma
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Song
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
| | - Zhenghua Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
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Conradie TA, Lawson K, Allsopp M, Jacobs K. Exploring the impact of fungicide exposure and nutritional stress on the microbiota and immune response of the Cape honey bee (Apis mellifera capensis). Microbiol Res 2024; 280:127587. [PMID: 38142516 DOI: 10.1016/j.micres.2023.127587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/26/2023]
Abstract
Honey bees (Apis mellifera) harbour a stable core microbial community within their gut, that is suggested to play a role in metabolic functioning, immune regulation, and host homeostasis. This microbiota presents a unique opportunity to observe the effects of stressors on honey bee health. We examined the effects of two common honey bee stressors: indirect fungicide contamination and nutrient limitation. These effects were observed through changes in their hind- and midgut microbiota using Automated Ribosomal Intergenic Spacer Analysis (ARISA), alongside high-throughput amplicon sequencing. Expression of the honey bees' immune response was examined through the expression of three immune-related genes, namely, immune deficiency (imd), proPhenolOxidase (proPO), and spaetzle (spz). Additionally, longevity of the honey bees was monitored through observation of the expression levels of Vitellogenin (Vg). Both treatment groups were compared to a negative control, and a diseased positive control. There was no effect on the hindgut microbiota due to the stressors, while significant changes in the midgut was observed. This was also observed in the expression of the immune-related genes within the treatment groups. The Imd pathway was substantially downregulated, with upregulation in the prophenoloxidase pathway. However, no significant effect was observed in the expression of spz, and only the pollen treatment group showed reduced longevity through a downregulation of Vg. Overall, the effect of these two common stressors indicate a compromise in honey bee immunity, and potential vulnerabilities within the immune defence mechanisms.
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Affiliation(s)
- Tersia A Conradie
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Kayla Lawson
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Mike Allsopp
- Agricultural Research Council - Plant, Health & Protection, Stellenbosch 7600, South Africa
| | - Karin Jacobs
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa.
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Toopaang W, Bunnak W, Srisuksam C, Wattananukit W, Tanticharoen M, Yang YL, Amnuaykanjanasin A. Microbial polyketides and their roles in insect virulence: from genomics to biological functions. Nat Prod Rep 2022; 39:2008-2029. [PMID: 35822627 DOI: 10.1039/d1np00058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: May 1966 up to January 2022Entomopathogenic microorganisms have potential for biological control of insect pests. Their main secondary metabolites include polyketides, nonribosomal peptides, and polyketide-nonribosomal peptide (PK-NRP) hybrids. Among these secondary metabolites, polyketides have mainly been studied for structural identification, pathway engineering, and for their contributions to medicine. However, little is known about the function of polyketides in insect virulence. This review focuses on the role of bacterial and fungal polyketides, as well as PK-NRP hybrids in insect infection and killing. We also discuss gene distribution and evolutional relationships among different microbial species. Further, the role of microbial polyketides and the hybrids in modulating insect-microbial symbiosis is also explored. Understanding the mechanisms of polyketides in insect pathogenesis, how compounds moderate the host-fungus interaction, and the distribution of PKS genes across different fungi and bacteria will facilitate the discovery and development of novel polyketide-derived bio-insecticides.
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Affiliation(s)
- Wachiraporn Toopaang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand. .,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Warapon Bunnak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Chettida Srisuksam
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Wilawan Wattananukit
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Morakot Tanticharoen
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan. .,Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
| | - Alongkorn Amnuaykanjanasin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
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Semenzato G, Alonso-Vásquez T, Del Duca S, Vassallo A, Riccardi C, Zaccaroni M, Mucci N, Padula A, Emiliani G, Palumbo Piccionello A, Puglia AM, Fani R. Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds. Microorganisms 2022; 10:microorganisms10050919. [PMID: 35630363 PMCID: PMC9145963 DOI: 10.3390/microorganisms10050919] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 12/26/2022] Open
Abstract
Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship. Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant Origanum vulgare L. and able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients. The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin A. Endophytes’ adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes. The diesel fuel degrading potential was also tested. Strains grew in minimum media supplemented with diesel fuel, but no n-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds.
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Affiliation(s)
- Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Tania Alonso-Vásquez
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Alberto Vassallo
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Nadia Mucci
- Institute for Environmental Protection and Research, Via Ca’ Fornacetta 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.)
| | - Anna Padula
- Institute for Environmental Protection and Research, Via Ca’ Fornacetta 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.)
| | - Giovanni Emiliani
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Via Madonna del Piano 10, Sesto Fiorentino, 50019 Florence, Italy;
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128 Palermo, Italy; (A.P.P.); (A.M.P.)
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128 Palermo, Italy; (A.P.P.); (A.M.P.)
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
- Correspondence: ; Tel.: +39-0554574742
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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10
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Li JY, Gao TT, Wang Q. Comparative and Functional Analyses of Two Sequenced Paenibacillus polymyxa Genomes Provides Insights Into Their Potential Genes Related to Plant Growth-Promoting Features and Biocontrol Mechanisms. Front Genet 2020; 11:564939. [PMID: 33391337 PMCID: PMC7773762 DOI: 10.3389/fgene.2020.564939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
Many bacteria belonging to Paenibacillus polymyxa are plant growth-promoting rhizobacteria (PGPR) with the potential to promote plant growth and suppress phytopathogens and have been used as biological control agents (BCAs). However, the growth promotion and biocontrol mechanisms of P. polymyxa have not been thoroughly elucidated thus far. In this investigation, the genome sequences of two P. polymyxa strains, ZF129 and ZF197, with broad anti-pathogen activities and potential for growth promotion were comparatively studied. Comparative and functional analyses of the two sequenced P. polymyxa genomes showed that the ZF129 genome consists of one 5,703,931 bp circular chromosome and two 79,020 bp and 37,602 bp plasmids, designated pAP1 and pAP2, respectively. The complete genome sequence of ZF197 consists of one 5,507,169 bp circular chromosome and one 32,065 bp plasmid, designated pAP197. Phylogenetic analysis revealed that ZF129 is highly similar to two P. polymyxa strains, HY96-2 and SQR-21, while ZF197 is highly similar to P. polymyxa strain J. The genes responsible for secondary metabolite synthesis, plant growth-promoting traits, and systemic resistance inducer production were compared between strains ZF129 and ZF197 as well as other P. polymyxa strains. The results indicated that the variation of the corresponding genes or gene clusters between strains ZF129 and ZF197 may lead to different antagonistic activities of their volatiles or cell-free supernatants against Fusarium oxysporum. This work indicates that plant growth promotion by P. polymyxa is largely mediated by phytohormone production, increased nutrient availability and biocontrol mechanisms. This study provides an in-depth understanding of the genome architecture of P. polymyxa, revealing great potential for the application of this bacterium in the fields of agriculture and horticulture as a PGPR.
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Affiliation(s)
- Jin-Yi Li
- MOA Key Lab of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Tan-Tan Gao
- Key Laboratory for Northern Urban Agriculture, Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
| | - Qi Wang
- MOA Key Lab of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
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11
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Beims H, Janke M, von der Ohe W, Steinert M. Rapid identification and genotyping of the honeybee pathogen Paenibacillus larvae by combining culturing and multiplex quantitative PCR. Open Vet J 2020; 10:53-58. [PMID: 32426257 PMCID: PMC7193882 DOI: 10.4314/ovj.v10i1.9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 02/14/2020] [Indexed: 12/04/2022] Open
Abstract
Background: American Foulbrood (AFB) is a devastating disease of honey bee (Apis mellifera) larvae caused by the spore-forming, Gram-positive bacterium Paenibacillus larvae. In most countries, the law requires mandatory reporting of AFB to the veterinary authority. Aim and Methods: To speed up detection and genotyping of P. larvae spores, we compared different culturing protocols on Columbia sheep blood agar and developed a new multiplex quantitative polymerase chain reaction to distinguish between the two relevant P. larvae genotypes enterobacterial repetitive intergenic consensus (ERIC) I and ERIC II. Results and Conclusion: As confirmed by P. larvae reference strains and field isolates, the new identification and genotyping protocol halves the time of current workflows, lessens labor-intension, allows a higher throughput of samples for monitoring, and permits a faster intervention to prevent the spread of AFB.
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Affiliation(s)
- Hannes Beims
- Lower Saxony State Office for Consumer Protection and Food Safety, Institute of Apiculture, Celle 29221, Germany.,Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Martina Janke
- Lower Saxony State Office for Consumer Protection and Food Safety, Institute of Apiculture, Celle 29221, Germany
| | - Werner von der Ohe
- Lower Saxony State Office for Consumer Protection and Food Safety, Institute of Apiculture, Celle 29221, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig 38106, Germany
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12
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Turner M, Tremblay O, Heney K, Lugo M, Ebeling J, Genersch E, Merrill A. Characterization of C3larvinA, a novel RhoA-targeting ADP-ribosyltransferase toxin produced by the honey bee pathogen, Paenibacillus larvae. Biosci Rep 2020; 40:BSR20193405. [PMID: 31844879 PMCID: PMC6954368 DOI: 10.1042/bsr20193405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/15/2019] [Accepted: 12/13/2019] [Indexed: 01/13/2023] Open
Abstract
C3larvinA is a putative virulence factor produced by Paenibacillus larvae enterobacterial-repetitive-intergenic-consensus (ERIC) III/IV (strain 11-8051). Biochemical, functional and structural analyses of C3larvinA revealed that it belongs to the C3-like mono-ADP-ribosylating toxin subgroup. Mammalian RhoA was the target substrate for its transferase activity suggesting that it may be the biological target of C3larvinA. The kinetic parameters of the NAD+ substrate for the transferase (KM = 75 ± 10 µM) and glycohydrolase (GH) (KM = 107 ± 20 µM) reactions were typical for a C3-like bacterial toxin, including the Plx2A virulence factor from Paenibacillus larvae ERIC I. Upon cytoplasmic expression in yeast, C3larvinA caused a growth-defective phenotype indicating that it is an active C3-like toxin and is cytotoxic to eukaryotic cells. The catalytic variant of the Q187-X-E189 motif in C3larvinA showed no cytotoxicity toward yeast confirming that the cytotoxicity of this factor depends on its enzymatic activity. A homology consensus model of C3larvinA with NAD+ substrate was built on the structure of Plx2A, provided additional confirmation that C3larvinA is a member of the C3-like mono-ADP-ribosylating toxin subgroup. A homology model of C3larvinA with NADH and RhoA was built on the structure of the C3cer-NADH-RhoA complex which provided further evidence that C3larvinA is a C3-like toxin that shares an identical catalytic mechanism with C3cer from Bacillus cereus. C3larvinA induced actin cytoskeleton reorganization in murine macrophages, whereas in insect cells, vacuolization and bi-nucleated cells were observed. These cellular effects are consistent with C3larvinA disrupting RhoA function by covalent modification that is shared among C3-like bacterial toxins.
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Affiliation(s)
- Madison Turner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Olivier Tremblay
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Kayla A. Heney
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Miguel R. Lugo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Julia Ebeling
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf 16540, Germany
| | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf 16540, Germany
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen, Berlin 14163, Germany
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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13
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Beims H, Bunk B, Erler S, Mohr KI, Spröer C, Pradella S, Günther G, Rohde M, von der Ohe W, Steinert M. Discovery of Paenibacillus larvae ERIC V: Phenotypic and genomic comparison to genotypes ERIC I-IV reveal different inventories of virulence factors which correlate with epidemiological prevalences of American Foulbrood. Int J Med Microbiol 2020; 310:151394. [PMID: 31959580 DOI: 10.1016/j.ijmm.2020.151394] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/16/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022] Open
Abstract
Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious brood disease of honey bees (Apis mellifera). AFB requires mandatory reporting to the veterinary authority in many countries and until now four genotypes, P. larvae ERIC I-IV, have been identified. We isolated a new genotype, ERIC V, from a Spanish honey sample. After a detailed phenotypic comparison with the reference strains of the ERIC I-IV genotypes, including spore morphology, non-ribosomal peptide (NRP) profiling, and in vivo infections of A. mellifera larvae, we established a genomic DNA Macrorestriction Fragment Pattern Analysis (MRFPA) scheme for future epidemiologic discrimination. Whole genome comparison of the reference strains and the new ERIC V genotype (DSM 106052) revealed that the respective virulence gene inventories of the five genotypes corresponded with the time needed to kill 100 % of the infected bee larvae (LT100) in in vivo infection assays. The rarely isolated P. larvae genotypes ERIC II I-V with a fast-killing phenotype (LT100 3 days) harbor genes with high homology to virulence factors of other insect pathogens. These virulence genes are absent in the epidemiologically prevalent genotypes ERIC I (LT100 12 days) and ERIC II (LT100 7 days), which exhibit slower killing phenotypes. Since killing-retardation is known to reduce the success of hygienic cleaning by nurse bees, the identified absence of virulence factors might explain the epidemiological prevalences of ERIC genotypes. The discovery of the P. larvae ERIC V isolate suggests that more unknown ERIC genotypes exist in bee colonies. Since inactivation or loss of a few genes can transform a fast-killing phenotype into a more dangerous slow-killing phenotype, these rarely isolated genotypes may represent a hidden reservoir for future AFB outbreaks.
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Affiliation(s)
- Hannes Beims
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany; Lower Saxony State Office for Consumer Protection and Food Safety, Institute of Apiculture, Celle, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silvio Erler
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biologie-Zoologie, Halle, Germany
| | - Kathrin I Mohr
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Department Microbial Drugs, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silke Pradella
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gabi Günther
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Department Microbial Drugs, Braunschweig, Germany
| | - Werner von der Ohe
- Lower Saxony State Office for Consumer Protection and Food Safety, Institute of Apiculture, Celle, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany.
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14
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Antimicrobial secondary metabolites from agriculturally important bacteria as next-generation pesticides. Appl Microbiol Biotechnol 2019; 104:1013-1034. [PMID: 31858191 DOI: 10.1007/s00253-019-10300-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
The whole organisms can be packaged as biopesticides, but secondary metabolites secreted by microorganisms can also have a wide range of biological activities that either protect the plant against pests and pathogens or act as plant growth promotors which can be beneficial for the agricultural crops. In this review, we have compiled information about the most important secondary metabolites of three important bacterial genera currently used in agriculture pest and disease management.
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15
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Erban T, Zitek J, Bodrinova M, Talacko P, Bartos M, Hrabak J. Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors. Virulence 2019; 10:363-375. [PMID: 30957692 PMCID: PMC6527061 DOI: 10.1080/21505594.2019.1603133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 11/12/2022] Open
Abstract
American foulbrood is a quarantine disease of the honeybee Apis mellifera L. in many countries and contributes greatly to colony losses. We performed a label-free proteomics study of exoprotein fractions produced in vitro by Paenibacillus larvae reference strains of the ERIC I-IV genotypes. A quantitative comparison was performed of previous studied protein-based virulence factors and many newly identified putative virulence factors. Among the multiple proteases identified, key virulence factors included the microbial collagenase ColA and immune inhibitor A (InhA, an analog of the Bacillus thuringiensis protein InhA). Both of these virulence factors were detected in ERICs II-IV but were absent from ERIC I. Furthermore, the different S-layer proteins and polysaccharide deacetylases prevailed in ERICs II-IV. Thus, the expression patterns of these virulence factors corresponded with the different speeds at which honeybee larvae are known to be killed by ERICs II-IV compared to ERIC I. In addition, putative novel toxin-like proteins were identified, including vegetative insecticidal protein Vip1, a mosquitocidal toxin, and epsilon-toxin type B, which exhibit similarity to homologs present in Bacillus thuringiensis or Lysinibacillus sphaericus. Furthermore, a putative bacteriocin similar to Lactococcin 972 was identified in all assayed genotypes. It appears that P. larvae shares virulence factors similar to those of the Bacillus cereus group. Overall, the results provide novel information regarding P. larvae virulence potential, and a comprehensive exoprotein comparison of all four ERICs was performed for the first time. The identification of novel virulence factors can explain differences in the virulence of isolates.
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Affiliation(s)
- Tomas Erban
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
| | - Justyna Zitek
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Prague 2, Czechia
| | - Miroslava Bodrinova
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
| | - Pavel Talacko
- Proteomics Core Facility, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Milan Bartos
- BioVendor – Laboratorni medicina a.s., Brno, Czechia
| | - Jaroslav Hrabak
- Laboratory of Antibiotic Resistance and Applications of Mass Spectrometry in Microbiology, Biomedical Center and Institute of Microbiology, Faculty of Medicine in Plzen, Charles University, Plzen, Czechia
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16
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Dunlap CA, Bowman MJ, Rooney AP. Iturinic Lipopeptide Diversity in the Bacillus subtilis Species Group - Important Antifungals for Plant Disease Biocontrol Applications. Front Microbiol 2019; 10:1794. [PMID: 31440222 PMCID: PMC6693446 DOI: 10.3389/fmicb.2019.01794] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/22/2019] [Indexed: 11/30/2022] Open
Abstract
Iturins and closely related lipopeptides constitute a family of antifungal compounds known as iturinic lipopeptides that are produced by species in the Bacillus subtilis group. The compounds that comprise the family are: iturin, bacillomycin D, bacillomycin F, bacillomycin L, mycosubtilin, and mojavensin. These lipopeptides are prominent in many Bacillus strains that have been commercialized as biological control agents against fungal plant pathogens and as plant growth promoters. The compounds are cyclic heptapeptides with a variable length alkyl sidechain, which confers surface activity properties resulting in an affinity for fungal membranes. Above a certain concentration, enough molecules enter the fungal cell membrane to create a pore in the cell wall, which leads to loss of cell contents and cell death. This study identified 330 iturinic lipopeptide clusters in publicly available genomes from the B. subtilis species group. The clusters were subsequently assigned into distinguishable types on the basis of their unique amino acid sequences and then verified by HPLC MS/MS analysis. The results show some lipopeptides are only produced by one species, whereas certain others can produce up to three. In addition, four species previously not known to produce iturinic lipopeptides were identified. The distribution of these compounds among the B. subtilis group species suggests that they play an important role in their speciation and evolution.
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Affiliation(s)
- Christopher A Dunlap
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL, United States
| | - Michael J Bowman
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL, United States
| | - Alejandro P Rooney
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL, United States
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17
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Alternative Biosynthetic Starter Units Enhance the Structural Diversity of Cyanobacterial Lipopeptides. Appl Environ Microbiol 2019; 85:AEM.02675-18. [PMID: 30504214 DOI: 10.1128/aem.02675-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022] Open
Abstract
Puwainaphycins (PUWs) and minutissamides (MINs) are structurally analogous cyclic lipopeptides possessing cytotoxic activity. Both types of compound exhibit high structural variability, particularly in the fatty acid (FA) moiety. Although a biosynthetic gene cluster responsible for synthesis of several PUW variants has been proposed in a cyanobacterial strain, the genetic background for MINs remains unexplored. Herein, we report PUW/MIN biosynthetic gene clusters and structural variants from six cyanobacterial strains. Comparison of biosynthetic gene clusters indicates a common origin of the PUW/MIN hybrid nonribosomal peptide synthetase and polyketide synthase. Surprisingly, the biosynthetic gene clusters encode two alternative biosynthetic starter modules, and analysis of structural variants suggests that initiation by each of the starter modules results in lipopeptides of differing lengths and FA substitutions. Among additional modifications of the FA chain, chlorination of minutissamide D was explained by the presence of a putative halogenase gene in the PUW/MIN gene cluster of Anabaena minutissima strain UTEX B 1613. We detected PUW variants bearing an acetyl substitution in Symplocastrum muelleri strain NIVA-CYA 644, consistent with an O-acetyltransferase gene in its biosynthetic gene cluster. The major lipopeptide variants did not exhibit any significant antibacterial activity, and only the PUW F variant was moderately active against yeast, consistent with previously published data suggesting that PUWs/MINs interact preferentially with eukaryotic plasma membranes.IMPORTANCE Herein, we deciphered the most important biosynthetic traits of a prominent group of bioactive lipopeptides. We reveal evidence for initiation of biosynthesis by two alternative starter units hardwired directly in the same gene cluster, eventually resulting in the production of a remarkable range of lipopeptide variants. We identified several unusual tailoring genes potentially involved in modifying the fatty acid chain. Careful characterization of these biosynthetic gene clusters and their diverse products could provide important insight into lipopeptide biosynthesis in prokaryotes. Some of the variants identified exhibit cytotoxic and antifungal properties, and some are associated with a toxigenic biofilm-forming strain. The findings may prove valuable to researchers in the fields of natural product discovery and toxicology.
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18
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Olishevska S, Nickzad A, Déziel E. Bacillus and Paenibacillus secreted polyketides and peptides involved in controlling human and plant pathogens. Appl Microbiol Biotechnol 2019; 103:1189-1215. [DOI: 10.1007/s00253-018-9541-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/25/2022]
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19
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Luo Y, Cheng Y, Yi J, Zhang Z, Luo Q, Zhang D, Li Y. Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism. Front Microbiol 2018; 9:1520. [PMID: 30050512 PMCID: PMC6052121 DOI: 10.3389/fmicb.2018.01520] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other P. polymyxa strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the P. polymyxa strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in P. polymyxa were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.
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Affiliation(s)
| | | | | | | | | | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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20
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Fünfhaus A, Göbel J, Ebeling J, Knispel H, Garcia-Gonzalez E, Genersch E. Swarming motility and biofilm formation of Paenibacillus larvae, the etiological agent of American Foulbrood of honey bees (Apis mellifera). Sci Rep 2018; 8:8840. [PMID: 29892084 PMCID: PMC5995878 DOI: 10.1038/s41598-018-27193-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
American Foulbrood is a worldwide distributed, fatal disease of the brood of the Western honey bee (Apis mellifera). The causative agent of this fatal brood disease is the Gram-positive, spore-forming bacterium Paenibacillus larvae, which can be classified into four different genotypes (ERIC I-IV), with ERIC I and II being the ones isolated from contemporary AFB outbreaks. P. larvae is a peritrichously flagellated bacterium and, hence, we hypothesized that P. larvae is capable of coordinated and cooperative multicellular behaviors like swarming motility and biofilm formation. In order to analyze these behaviors of P. larvae, we firstly established appropriate functional assays. Using these assays we demonstrated that P. larvae ERIC II, but not P. larvae ERIC I, was capable of swarming. Swarming motility was hampered in a P. larvae ERIC II-mutant lacking production of paenilarvin, an iturin-like lipopeptide exclusively expressed by this genotype. Both genotypes were able to form free floating biofilm aggregates loosely attached to the walls of the culture wells. Visualizing the biofilms by Congo red and thioflavin S staining suggested structural differences between the biofilms formed. Biofilm formation was shown to be independent from paenilarvin production because the paenilarvin deficient mutant was comparably able to form a biofilm.
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Affiliation(s)
- Anne Fünfhaus
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Josefine Göbel
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Julia Ebeling
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Henriette Knispel
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Eva Garcia-Gonzalez
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany.
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen, Berlin, Germany.
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21
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Ganley JG, Carr G, Ioerger TR, Sacchettini JC, Clardy J, Derbyshire ER. Discovery of Antimicrobial Lipodepsipeptides Produced by aSerratiasp. within Mosquito Microbiomes. Chembiochem 2018; 19:1590-1594. [DOI: 10.1002/cbic.201800124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Jack G. Ganley
- Department of Chemistry; Duke University; 124 Science Drive Durham NC 27708-0346 USA
| | - Gavin Carr
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; 240 Longwood Avenue Boston MA 02115 USA
| | - Thomas R. Ioerger
- Department of Computer Science; Texas A&M University; College Station TX 77843 USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics; Texas A&M University; College Station TX 77843 USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; 240 Longwood Avenue Boston MA 02115 USA
| | - Emily R. Derbyshire
- Department of Chemistry; Duke University; 124 Science Drive Durham NC 27708-0346 USA
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22
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Felicioli A, Turchi B, Fratini F, Giusti M, Nuvoloni R, Dani FR, Sagona S. Proteinase pattern of honeybee prepupae from healthy and American Foulbrood infected bees investigated by zymography. Electrophoresis 2018; 39:2160-2167. [PMID: 29761912 DOI: 10.1002/elps.201800112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 11/05/2022]
Abstract
American foulbrood disease (AFB) is the main devastating disease that affects honeybees' brood, caused by Paenibacillus larvae. The trend of the research on AFB has addressed the mechanisms by which P. larvae bacteria kill honeybee larvae. Since prepupae could react to the infection of AFB by increasing protease synthesis, the aim of this work was to compare protease activity in worker prepupae belonging to healthy colonies and to colonies affected by AFB. This investigation was performed by zymography. In gel, proteolytic activity was observed in prepupae extracts belonging only to the healthy colonies. In the prepupae extracts, 2D zimography followed by protein identification by MS allowed to detect Trypsin-1 and Chymotrypsin-1, which were not observed in diseased specimens. Further investigations are needed to clarify the involvement of these proteinases in the immune response of honeybee larvae and the mechanisms by which P. larvae inhibits protease production in its host.
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Affiliation(s)
| | - Barbara Turchi
- Department of Veterinary Science, Pisa University, Pisa, Italy
| | - Filippo Fratini
- Department of Veterinary Science, Pisa University, Pisa, Italy
| | - Matteo Giusti
- Department of Veterinary Science, Pisa University, Pisa, Italy
| | | | - Francesca Romana Dani
- Department of Biology, University of Firenze, Sesto Fiorentino, Italy.,Mass Spectrometry Centre (CISM) of Florence University, Sesto Fiorentino, Italy
| | - Simona Sagona
- Department of Veterinary Science, Pisa University, Pisa, Italy
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23
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Zhao P, Xue Y, Gao W, Li J, Zu X, Fu D, Bai X, Zuo Y, Hu Z, Zhang F. Bacillaceae-derived peptide antibiotics since 2000. Peptides 2018; 101:10-16. [PMID: 29269072 DOI: 10.1016/j.peptides.2017.12.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 10/18/2022]
Abstract
Members of the Bacillaceae family, including Bacillus spp., Brevibacillus spp., Paenibacillus spp., Aneurinibacillus sp., and Halobacillus sp., are an important source of structurally diverse classes of short peptides of ∼ 30 residues or fewer possessing peculiar and rapid killing activity against various pathogens. Additionally, many have unique structures that enhance resistance to hydrolysis by proteases, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic lead compounds is urgent, and this review summarises 119 Bacillaceae compounds published since 2000, including 12 surfactin-like lipopeptides, 16 iturinic lipopeptides, fengycin C, 33 other cyclic lipopeptides, 26 linear lipopeptides, two thiopeptides, four 2,5-diketopiperazines, 20 typical cyclic peptides, and five standard linear peptides. The current and potential therapeutic applications of these peptides, including structure, antibacterial, antifungal, and antiviral activities, are discussed.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Dongliao Fu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuefei Bai
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yanjun Zuo
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Zhigang Hu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Fengshou Zhang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
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24
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Vater J, Herfort S, Doellinger J, Weydmann M, Borriss R, Lasch P. Genome Mining of the Lipopeptide Biosynthesis of Paenibacillus polymyxa
E681 in Combination with Mass Spectrometry: Discovery of the Lipoheptapeptide Paenilipoheptin. Chembiochem 2018; 19:744-753. [DOI: 10.1002/cbic.201700615] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Joachim Vater
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Stefanie Herfort
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Joerg Doellinger
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Max Weydmann
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Rainer Borriss
- Humboldt Universität Berlin; Fachgebiet Phytomedizin; Lentzeallee 55-57 14195 Berlin Germany
- NordReet UG; Marienstrasse 27a 17489 Greifswald Germany
| | - Peter Lasch
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
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25
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First Insights into the Draft Genome Sequence of the Endophyte Paenibacillus amylolyticus Strain GM1FR, Isolated from Festuca rubra L. GENOME ANNOUNCEMENTS 2018; 6:6/4/e01516-17. [PMID: 29371353 PMCID: PMC5786679 DOI: 10.1128/genomea.01516-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Paenibacillus amylolyticus strain GM1FR is an endophyte isolated from aerial plant tissues of Festuca rubra L. Here, we report the draft genome sequence (7.3 Mb) of GM1FR containing 6,241 protein-coding genes, some of which are potentially involved in plant growth promotion and biocontrol.
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26
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Forsgren E, Locke B, Sircoulomb F, Schäfer MO. Bacterial Diseases in Honeybees. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0083-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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27
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Descamps T, De Smet L, De Vos P, de Graaf D. Unbiased random mutagenesis contributes to a better understanding of the virulent behaviour ofPaenibacillus larvae. J Appl Microbiol 2017; 124:28-41. [DOI: 10.1111/jam.13611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/09/2017] [Accepted: 09/28/2017] [Indexed: 01/12/2023]
Affiliation(s)
- T. Descamps
- Laboratory of Molecular Entomology and Bee Pathology; Faculty of Sciences; Ghent University; Ghent Belgium
| | - L. De Smet
- Laboratory of Molecular Entomology and Bee Pathology; Faculty of Sciences; Ghent University; Ghent Belgium
| | - P. De Vos
- Laboratory of Microbiology; Faculty of Sciences; Ghent University; Ghent Belgium
| | - D.C. de Graaf
- Laboratory of Molecular Entomology and Bee Pathology; Faculty of Sciences; Ghent University; Ghent Belgium
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28
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Molloy EM, Hertweck C. Antimicrobial discovery inspired by ecological interactions. Curr Opin Microbiol 2017; 39:121-127. [PMID: 29169087 DOI: 10.1016/j.mib.2017.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023]
Abstract
Bacteria represent an unparalleled source of antibiotics used to treat infectious diseases. Yet, genome analyses have revealed that their full biosynthetic potential is much larger than expected. Valuable strategies to unearth hidden antibiotics are genome mining, pathway engineering and triggering, as well as co-cultivation approaches. Nevertheless, there is growing understanding that it is often essential to consider the ecological context and that there is a great potential for antimicrobial discovery from bacteria engaged in well-defined interactions with other organisms. Various ecological scenarios involving antimicrobial agents are outlined in this review: predator-prey and pathogenic interactions, the protection of insect assets such as offspring and cultivars, as well as host protection in symbiotic relationships with plants, invertebrates and animals/humans. The illustrative examples given reinforce the idea that examination of interactions between organisms can yield new antimicrobial compounds, and ultimately further our understanding of the function of these molecules in the environment.
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Affiliation(s)
- Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany.
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29
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Flury P, Vesga P, Péchy-Tarr M, Aellen N, Dennert F, Hofer N, Kupferschmied KP, Kupferschmied P, Metla Z, Ma Z, Siegfried S, de Weert S, Bloemberg G, Höfte M, Keel CJ, Maurhofer M. Antimicrobial and Insecticidal: Cyclic Lipopeptides and Hydrogen Cyanide Produced by Plant-Beneficial Pseudomonas Strains CHA0, CMR12a, and PCL1391 Contribute to Insect Killing. Front Microbiol 2017; 8:100. [PMID: 28217113 PMCID: PMC5289993 DOI: 10.3389/fmicb.2017.00100] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/13/2017] [Indexed: 01/30/2023] Open
Abstract
Particular groups of plant-beneficial fluorescent pseudomonads are not only root colonizers that provide plant disease suppression, but in addition are able to infect and kill insect larvae. The mechanisms by which the bacteria manage to infest this alternative host, to overcome its immune system, and to ultimately kill the insect are still largely unknown. However, the investigation of the few virulence factors discovered so far, points to a highly multifactorial nature of insecticidal activity. Antimicrobial compounds produced by fluorescent pseudomonads are effective weapons against a vast diversity of organisms such as fungi, oomycetes, nematodes, and protozoa. Here, we investigated whether these compounds also contribute to insecticidal activity. We tested mutants of the highly insecticidal strains Pseudomonas protegens CHA0, Pseudomonas chlororaphis PCL1391, and Pseudomonas sp. CMR12a, defective for individual or multiple antimicrobial compounds, for injectable and oral activity against lepidopteran insect larvae. Moreover, we studied expression of biosynthesis genes for these antimicrobial compounds for the first time in insects. Our survey revealed that hydrogen cyanide and different types of cyclic lipopeptides contribute to insecticidal activity. Hydrogen cyanide was essential to full virulence of CHA0 and PCL1391 directly injected into the hemolymph. The cyclic lipopeptide orfamide produced by CHA0 and CMR12a was mainly important in oral infections. Mutants of CMR12a and PCL1391 impaired in the production of the cyclic lipopeptides sessilin and clp1391, respectively, showed reduced virulence in injection and feeding experiments. Although virulence of mutants lacking one or several of the other antimicrobial compounds, i.e., 2,4-diacetylphloroglucinol, phenazines, pyrrolnitrin, or pyoluteorin, was not reduced, these metabolites might still play a role in an insect background since all investigated biosynthetic genes for antimicrobial compounds of strain CHA0 were expressed at some point during insect infection. In summary, our study identified new factors contributing to insecticidal activity and extends the diverse functions of antimicrobial compounds produced by fluorescent pseudomonads from the plant environment to the insect host.
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Affiliation(s)
- Pascale Flury
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Pilar Vesga
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Maria Péchy-Tarr
- Department of Fundamental Microbiology, University of LausanneLausanne, Switzerland
| | - Nora Aellen
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Francesca Dennert
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Nicolas Hofer
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | | | - Peter Kupferschmied
- Department of Fundamental Microbiology, University of LausanneLausanne, Switzerland
| | - Zane Metla
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
- Laboratory of Experimental Entomology, Institute of Biology, University of LatviaRiga, Latvia
| | - Zongwang Ma
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Sandra Siegfried
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
| | - Sandra de Weert
- Microbial Biotechnology and Health, Institute of Biology Leiden, Leiden UniversityLeiden, Netherlands
| | - Guido Bloemberg
- Microbial Biotechnology and Health, Institute of Biology Leiden, Leiden UniversityLeiden, Netherlands
| | - Monica Höfte
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Christoph J. Keel
- Department of Fundamental Microbiology, University of LausanneLausanne, Switzerland
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürich, Switzerland
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30
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Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203. [PMID: 27905924 PMCID: PMC5134293 DOI: 10.1186/s12934-016-0603-7] [Citation(s) in RCA: 445] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/24/2016] [Indexed: 12/11/2022] Open
Abstract
Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.
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Affiliation(s)
- Elliot Nicholas Grady
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
| | - Linda Liu
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Alex Richman
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
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31
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Zhao X, Kuipers OP. Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. BMC Genomics 2016; 17:882. [PMID: 27821051 PMCID: PMC5100339 DOI: 10.1186/s12864-016-3224-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. RESULTS We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. CONCLUSIONS Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.
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Affiliation(s)
- Xin Zhao
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.
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32
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Hertlein G, Seiffert M, Gensel S, Garcia-Gonzalez E, Ebeling J, Skobalj R, Kuthning A, Süssmuth RD, Genersch E. Biological Role of Paenilarvins, Iturin-Like Lipopeptide Secondary Metabolites Produced by the Honey Bee Pathogen Paenibacillus larvae. PLoS One 2016; 11:e0164656. [PMID: 27760211 PMCID: PMC5070912 DOI: 10.1371/journal.pone.0164656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/28/2016] [Indexed: 12/16/2022] Open
Abstract
The Gram-positive bacterium Paenibacillus larvae (P. larvae) is the causative agent of a deadly honey bee brood disease called American Foulbrood (AFB). AFB is a notifiable epizootic in most countries and, hence, P. larvae is of considerable relevance for veterinarians and apiculturists alike. Over the last decade, much progress has been made in the understanding of the (patho)biology of P. larvae. Recently, several non-ribosomally produced peptides (NRP) and peptide/polyketide (NRP/PK) hybrids produced by P. larvae were identified. Among these NRPs were iturin-like lipopeptides, the paenilarvins A-C. Iturins are known to exhibit strong anti-fungal activity; for some iturins, cytotoxic activity towards mammalian erythrocytes and human cancer cell lines are described. We here present our results on the analysis of the natural function of the paenilarvins during pathogenesis of P. larvae infections. We demonstrated production of paenilarvins in infected larvae. However, we could neither demonstrate cytotoxicity of paenilarvins towards cultured insect cells nor towards larvae in feeding assays. Accordingly, exposure bioassays performed with larvae infected by wild-type P. larvae and a knockout mutant of P. larvae lacking production of paenilarvins did not substantiate a role for the paenilarvins as virulence factor. Further experiments are necessary to analyze the relevance of the paenilarvins' anti-fungal activity for P. larvae infections in the presence of fungal competitors in the larval midgut or cadaver.
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Affiliation(s)
- Gillian Hertlein
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Marlene Seiffert
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Sebastian Gensel
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Eva Garcia-Gonzalez
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Julia Ebeling
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Ranko Skobalj
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Anja Kuthning
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | | | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen, Berlin, Germany
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33
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The Draft Genome Sequence of Paenibacillus polymyxa Strain CCI-25 Encompasses High Potential for Secondary Metabolite Production. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00366-16. [PMID: 27198015 PMCID: PMC4889004 DOI: 10.1128/genomea.00366-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We report here the draft genome sequence of Paenibacillus polymyxa strain CCI-25, which displays strong antifungal and antibacterial activities in vitro. The genome encompasses nonribosomal peptide synthetases predicted to encode a tridecaptin, polymyxin, fusaricidin, an iturin-like synthetase, a lantibiotic similar to paenicidin A, as well as a type 1 polyketide synthase.
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34
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Vater J, Niu B, Dietel K, Borriss R. Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1548-1558. [PMID: 26100395 DOI: 10.1007/s13361-015-1130-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/18/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
Paenibacillus polymyxa-M1 is a potent producer of bioactive compounds, such as lipopeptides, polyketides, and lantibiotics of biotechnological and medical interest. Genome sequencing revealed nine gene clusters for nonribosomal biosynthesis of such agents. Here we report on the investigation of the fusaricidins, a complex of cyclic lipopeptides containing 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid component by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). More than 20 variants of these compounds were detected and characterized in detail. Mass spectrometric sequence analysis was performed by MALDI-LIFT-TOF/TOF fragment analysis. The obtained product ion spectra show a specific processing in the fatty acid part. GHPD is cleaved between the α- and ß-position yielding two fragments a and b, one bearing the end-standing guanidine group and another one comprising the residual two C-atoms of GHPD with the attached peptide moiety. The complete sequence of all fusaricidins was derived from sets of bn- and yn-ions. The fusaricidin complex can be divided into four lipopeptide families, three of them showing variations of the amino acid in position 3, Val or Ile for the first and Tyr or Phe for families 2 and 3, respectively. A collection of novel fusaricidins was detected differing from those of families 1-3 by an additional residue of 71 Da (family 4). LIFT-TOF/TOF fragment spectra of these species imply that in their peptide moiety, an Ala-residue is attached by an ester bond to the free hydroxyl group of Thr4. More than 10 novel fusaricidins were characterized mass spectrometrically.
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Affiliation(s)
- Joachim Vater
- Institut für Chemie, Technische Universität Berlin, Mueller-Breslau-Straße 10, 10623, Berlin, Germany,
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35
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Poppinga L, Genersch E. Molecular pathogenesis of American Foulbrood: how Paenibacillus larvae kills honey bee larvae. CURRENT OPINION IN INSECT SCIENCE 2015; 10:29-36. [PMID: 29588011 DOI: 10.1016/j.cois.2015.04.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 06/08/2023]
Abstract
American Foulbrood caused by Paenibacillus larvae is one of the unsolved health problems honey bee colonies are suffering from. In the recent past, considerable progress has been achieved in understanding molecular details of P. larvae infections of honey bee larvae. This was facilitated by the development of molecular tools for manipulating P. larvae and by the availability of complete genome sequences of different P. larvae genotypes. We here report on several peptides and proteins that have recently been identified, biochemically analyzed, and proposed to act as virulence factors of P. larvae. For some of them, experimental proof for their role as virulence factor has been provided allowing presenting a preliminary model for the molecular pathogenesis of American Foulbrood.
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Affiliation(s)
- Lena Poppinga
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany
| | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany.
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36
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Müller S, Garcia-Gonzalez E, Genersch E, Süssmuth RD. Involvement of secondary metabolites in the pathogenesis of the American foulbrood of honey bees caused by Paenibacillus larvae. Nat Prod Rep 2015; 32:765-78. [DOI: 10.1039/c4np00158c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Gram-positive spore-forming bacterium Paenibacillus larvae is the causative agent of the fatal disease American Foulbrood of the western honey bee. This article highlights recent findings on secondary metabolites synthesized by P. larvae.
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Affiliation(s)
| | - Eva Garcia-Gonzalez
- Institute for Bee Research
- Department of Molecular Microbiology and Bee Diseases
- Hohen Neuendorf
- Germany
| | - Elke Genersch
- Institute for Bee Research
- Department of Molecular Microbiology and Bee Diseases
- Hohen Neuendorf
- Germany
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Tang Y, Frewert S, Harmrolfs K, Herrmann J, Karmann L, Kazmaier U, Xia L, Zhang Y, Müller R. Heterologous expression of an orphan NRPS gene cluster from Paenibacillus larvae in Escherichia coli revealed production of sevadicin. J Biotechnol 2014; 194:112-4. [PMID: 25529345 DOI: 10.1016/j.jbiotec.2014.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/08/2014] [Accepted: 12/11/2014] [Indexed: 12/11/2022]
Abstract
The Gram-positive bacterium Paenibacillus larvae is the causative agent of the fateful honey bee disease American Foulbrood (AFB). Sequence analysis of P. larvae genomic DNA showed the presence of numerous nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) encoding gene clusters, not correlating with secondary metabolite production. As NRPS and PKS derived metabolites are known to exhibit diverse biological activities, their identification is of particular interest for infection and drug research. Here an 11.6kb orphan NRPS gene cluster was directly cloned from the genomic DNA of P. larvae and expressed in Escherichia coli resulting in the production of sevadicin. Isolation of the metabolite was followed by structural characterization, synthesis and bioactivity studies.
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Affiliation(s)
- Ying Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, PR China; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Simon Frewert
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Kirsten Harmrolfs
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Lisa Karmann
- Institute for Organic Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Uli Kazmaier
- Institute for Organic Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, PR China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Life Science College, Shandong University, 250100 Jinan, PR China.
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany.
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