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Ma Z. Genome mining and chemical characterization of a new cyclic lipopeptide associated with MDN-0066 from Pseudomonas moraviensis HN2 cultured in a valine-rich medium. J Antibiot (Tokyo) 2023; 76:244-248. [PMID: 36702935 DOI: 10.1038/s41429-023-00597-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/27/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023]
Abstract
A new cyclic lipopeptide (CLP) MDN-0066-β (1) and MDN-0066 (2) were isolated and characterized from the bacterial cultures of P. moraviensis HN2 in this study. The CLPs were purified by solid-phase extraction (SPE) and reversed-phase high performance liquid chromatography (RP-HPLC). Moreover, chemical structures of two CLPs were characterized by genome mining and analysis, nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HR-MS), Marfey's method and (C-H)α NMR fingerprint matching approach. MDN-0066 (2) has an amino acid sequence of L-Leu1, D-Glu2, D-allo-Thr3, D-Leu4, D-Leu5, D-Ser6, L-Leu7, L-Ile8 linked to a saturated C10 β-hydroxyl fatty acid moiety (R-configuration for 3-OH). The new CLP MDN-0066-β (1) differs MDN-0066 (2) in the 8th position of L-valine in its peptide moiety, this variation in structure could be attributed to the supplement of L-valine in the cultural medium during liquid fermentation. Further antimicrobial tests showed that the two CLPs display moderate antagonistic activity against Staphylococcus aureus and Escherichia coli.
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Affiliation(s)
- Zongwang Ma
- College of Life Science, Northwest Normal University, 967 East Anning Road, 730070, Lanzhou, China.
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Zhou J, Xie Y, Liao Y, Li X, Li Y, Li S, Ma X, Lei S, Lin F, Jiang W, He YQ. Characterization of a Bacillus velezensis strain isolated from Bolbostemmatis Rhizoma displaying strong antagonistic activities against a variety of rice pathogens. Front Microbiol 2022; 13:983781. [PMID: 36246295 PMCID: PMC9555170 DOI: 10.3389/fmicb.2022.983781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/30/2022] [Indexed: 11/25/2022] Open
Abstract
Biological control is an effective measure in the green control of rice diseases. To search for biocontrol agents with broad-spectrum and high efficiency against rice diseases, in this study, a strain of antagonistic bacterium BR-01 with strong inhibitory effect against various rice diseases was isolated from Bolbostemmatis Rhizoma by plate confrontation method. The strain was identified as Bacillus velezensis by morphological observation, physiological and biochemical identification, and molecular characterization by 16S rDNA and gyrB gene sequencing analysis. The confrontation test (dual culture) and Oxford cup assays demonstrated that B. velezensis BR-01 had strong antagonistic effects on Magnaporthe oryzae, Ustilaginoidea virens, Fusarium fujikuroi, Xanthomonas oryzae pv. Oryzicola, and Xanthomonas oryzae pv. oryzae, the major rice pathogens. The genes encoding antimicrobial peptides (ituA, ituD, bmyB, bmyC, srfAA, fenB, fenD, bacA, and bacD) were found in B. velezensis BR-01 by PCR amplification with specific primers. B. velezensis BR-01 could produce protease, cellulase, β-1,3-glucanase, chitinase, indoleacetic acid, siderophore, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and might produce three lipopeptide antibiotics, surfactin, iturin, and fengycin based on Liquid chromatography–mass spectrometry (LC-MS) results. Furthermore, the plant assays showed that B. velezensis BR-01 had significant control effects on rice bacterial blight and bacterial leaf streak by pot experiments in greenhouse. In conclusion, B. velezensis BR-01 is a broad-spectrum antagonistic bacterium and has the potential as the ideal biocontrol agent in controlling multiple rice diseases with high efficiency.
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Affiliation(s)
- Jianping Zhou
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Yunqiao Xie
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yuhong Liao
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Xinyang Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yiming Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Shuping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Xiuguo Ma
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Shimin Lei
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Fei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Wei Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
- *Correspondence: Wei Jiang,
| | - Yong-Qiang He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
- Yong-Qiang He,
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Ma Z. Analysis of the complete genome sequence of a rhizosphere-derived Pseudomonas sp. HN3-2 leads to the characterization of a cyclic lipopeptide-type antibiotic bananamide C. 3 Biotech 2022; 12:35. [PMID: 35070625 PMCID: PMC8727653 DOI: 10.1007/s13205-021-03100-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/26/2021] [Indexed: 01/03/2023] Open
Abstract
A fluorescence and biosurfactant-producing strain HN3-2 was isolated from a rhizosphere soil sample of wheat plants and the chromosome of the strain HN3-2 was sequenced and was analyzed by multiple bioinformatics tools in this study. The genome size of the strain HN3-2 is 6,441,476 bp, with a GC content of 60.54%. 16Sr RNA-based phylogeny analysis showed that the strain HN3-2 belongs to Pseudomonas koreensis subgroup in Pseudomonas species. Preliminary data from genome mining have showed that the strain Pseudomonas sp. HN3-2 is capable of producing a peptide-type metabolite. Solid-phase extraction, reversed-phase high performance liquid chromatography (RP-HPLC) together with liquid chromatography-mass spectrometry, high-resolution mass spectrometry and tandem mass spectrometry analysis have led to the purification and identification of a cyclic lipopeptide (CLP) bananamide C (1) from the fermentative broth of the strain Pseudomonas sp. HN3-2. Moreover, the biological activity tests showed that banananmide 3 displays moderate antagonistic activity against Staphylococcus aureus and Escherichia coli. Collectively, these results provide the possibility of developing the CLP bananamide C as a drug leads for medical applications.
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Affiliation(s)
- Zongwang Ma
- College of Life Science, Northwest Normal University, 967 East Anning Road, Lanzhou, 730070 China
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Bacillus velezensis: A Treasure House of Bioactive Compounds of Medicinal, Biocontrol and Environmental Importance. FORESTS 2021. [DOI: 10.3390/f12121714] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacillus velezensis gram-positive bacterium, is frequently isolated from diverse niches mainly soil, water, plant roots, and fermented foods. B. velezensis is ubiquitous, non-pathogenic and endospore forming. Being frequently isolated from diverse plant holobionts it is considered host adapted microorganism and recognized of high economic importance given its ability to promote plant growth under diverse biotic and abiotic stress conditions. Additionally, the species suppress many plant diseases, including bacterial, oomycete, and fungal diseases. It is also able after plant host root colonization to induce unique physiological situation of host plant called primed state. Primed host plants are able to respond more rapidly and/or effectively to biotic or abiotic stress. Moreover, B. velezenis have the ability to resist diverse environmental stresses and help host plants to cope with, including metal and xenobiotic stresses. Within species B. velezensis strains have unique abilities allowing them to adopt different life styles. Strain level abilities knowledge is warranted and could be inferred using the ever-expanding new genomes list available in genomes databases. Pangenome analysis and subsequent identification of core, accessory and unique genomes is actually of paramount importance to decipher species full metabolic capacities and fitness across diverse environmental conditions shaping its life style. Despite the crucial importance of the pan genome, its assessment among large number of strains remains sparse and systematic studies still needed. Extensive knowledge of the pan genome is needed to translate genome sequencing efforts into developing more efficient biocontrol agents and bio-fertilizers. In this study, a genome survey of B. velezensis allowed us to (a) highlight B. velezensis species boundaries and show that Bacillus suffers taxonomic imprecision that blurs the debate over species pangenome; (b) identify drivers of their successful acquisition of specific life styles and colonization of new niches; (c) describe strategies they use to promote plant growth and development; (d) reveal the unlocked strain specific orphan secondary metabolite gene clusters (biosynthetic clusters with corresponding metabolites unknown) that product identification is still awaiting to amend our knowledge of their putative role in suppression of pathogens and plant growth promotion, and (e) to describe a dynamic pangenome with a secondary metabolite rich accessory genome.
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Makałowski W, Shabardina V. Bioinformatics of nanopore sequencing. J Hum Genet 2019; 65:61-67. [PMID: 31451715 DOI: 10.1038/s10038-019-0659-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 12/12/2022]
Abstract
Nanopore sequencing is one of the most exciting new technologies that undergo dynamic development. With its development, a growing number of analytical tools are becoming available for researchers. To help them better navigate this ever changing field, we discuss a range of software available to analyze sequences obtained using nanopore technology.
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Affiliation(s)
- Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, 48149, Münster, Germany.
| | - Victoria Shabardina
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, 48149, Münster, Germany
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