1
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Thompson TP, Gilmore BF. Exploring halophilic environments as a source of new antibiotics. Crit Rev Microbiol 2024; 50:341-370. [PMID: 37079280 DOI: 10.1080/1040841x.2023.2197491] [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: 09/16/2022] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
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2
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Fang Y, Wu D, Gao N, Lv M, Zhou M, Ma C, Sun Y, Cui B. Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae. G3 (BETHESDA, MD.) 2024; 14:jkae005. [PMID: 38366555 PMCID: PMC10989896 DOI: 10.1093/g3journal/jkae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.
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Affiliation(s)
- Yuxuan Fang
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Dongmei Wu
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Neng Gao
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Mengxue Lv
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Miao Zhou
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chuangui Ma
- Beijing Jingcheng Biotechnology Co., Ltd, Beijing 100083, China
| | - Yifei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Baokai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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3
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Banu S, Alva S, Prabhu PJ, Krishnan S, Mani MK. Detection of non-ribosomal and polyketide biosynthetic genes in bacteria from green mud crab Scylla serrata gut microbiome and their antagonistic activities. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 5:100104. [PMID: 38162954 PMCID: PMC10755817 DOI: 10.1016/j.fsirep.2023.100104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 01/03/2024] Open
Abstract
Multi-modular enzyme complexes known as non-ribosomal peptide synthetases (NRPSs) and polyketide synthetases (PKSs) have been widely reported in bacteria that produce secondary bioactive metabolites such as non-ribosomal peptides (NRPs) and polyketides (PKs), respectively. These NRPS/PKS pathways contribute to synthesizing several antibiotics, such as vancomycin, rifamycin, and bleomycin, which are vital in human medicine. The present study aimed to isolate gut-associated bacteria from mud crab Scylla serrata, and detect NRPS and PKS gene clusters associated with it. This study included 36 bacterial isolates from five mud crab gut samples. Biosynthetic gene clusters (NRPS and PKS), were detected by PCR using degenerative primers specific to these genes. Three isolates (FKP2-4, FKP4-1, and FKP2-16) were positive for NRPS and two for PKS (FKP2-4 and FKP4-1) genes. The isolates were subjected to 16S rRNA gene amplification and sequenced. In silico analysis of the sequences using the Basic Local Alignment Search Tool (BLAST) identified the isolates FKP2-4, FKP4-1, and FKP2-16 as Acinetobacter variabilis, Vagococcus fluvialis, and Staphylococcus arlettae, respectively, after comparing with the existing sequences available in the National Center for Biotechnology Information (NCBI) database. Compared to the control, it was observed that these isolates exhibited intriguing antagonistic activities against Escherichia coli and Staphylococcus aureus. However, these isolates failed to show significant activity against Candida albicans. Exopolysaccharide production by the isolated organisms was tested using Zobell marine agar (ZMA) with 5% sucrose, but none of the colonies were mucoid or slimy.
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Affiliation(s)
- Shabreen Banu
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Paneer Campus, Deralakatte, Mangalore, Karnataka 575018, India
| | - Shivakiran Alva
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Paneer Campus, Deralakatte, Mangalore, Karnataka 575018, India
| | - Prathiksha J. Prabhu
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Paneer Campus, Deralakatte, Mangalore, Karnataka 575018, India
| | - Sreedharan Krishnan
- ICAR-Central Institute of Fisheries Education, Lahli, Via Anwal, Rohtak, Haryana 124411, India
| | - Madhu K. Mani
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Paneer Campus, Deralakatte, Mangalore, Karnataka 575018, India
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4
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Akmukhanova NR, Leong YK, Seiilbek SN, Konysbay A, Zayadan BK, Sadvakasova AK, Sarsekeyeva FK, Bauenova MO, Bolatkhan K, Alharby HF, Chang JS, Allakhverdiev SI. Eco-friendly biopesticides derived from CO 2-Fixing cyanobacteria. ENVIRONMENTAL RESEARCH 2023; 239:117419. [PMID: 37852466 DOI: 10.1016/j.envres.2023.117419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/10/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
There is currently an escalating global demand for the utilization of plant and natural extracts as pesticides due to their minimal health risks. Cyanobacteria are highly valuable organisms with significant potential in agriculture and are of great interest for the development of agrochemical agents as biopesticides. The flexibility and adaptability of Cyanobacteria to various environmental conditions are facilitated by the presence of specialized enzymes involved in the production of biologically active diverse secondary metabolites, including alkaloids, lipopolysaccharides, non-protein amino acids, non-ribosomal peptides, polyketides, terpenoids, and others. This review focuses on the metabolites synthesized from cyanobacteria that have demonstrated effectiveness as antibacterial, antiviral, antifungal agents, insecticides, herbicides, and more. The potential role of cyanobacteria as an alternative to chemical pesticides for environmental conservation is discussed.
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Affiliation(s)
- Nurziya R Akmukhanova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Yoong Kit Leong
- Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan
| | - Sandugash N Seiilbek
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Aigerim Konysbay
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Bolatkhan K Zayadan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Assemgul K Sadvakasova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Fariza K Sarsekeyeva
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Meruyert O Bauenova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Kenzhegul Bolatkhan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty, 050038, Kazakhstan
| | - Hesham F Alharby
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan, 701, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, 32003, Taiwan.
| | - Suleyman I Allakhverdiev
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia; Faculty of Engineering and Natural Sciences, Bahcesehir University, Istanbul, Turkey.
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5
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Lema NK, Gemeda MT, Woldesemayat AA. Recent Advances in Metagenomic Approaches, Applications, and Challenge. Curr Microbiol 2023; 80:347. [PMID: 37733134 DOI: 10.1007/s00284-023-03451-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/20/2023] [Indexed: 09/22/2023]
Abstract
Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to conventional techniques providing advanced approach to identify novel and uncultivable microorganisms based on their genetic information derived from a particular environment. Shotgun metagenomics involves investigating the DNA of the entire community without the requirement of PCR amplification. It provides access to study all genes present in the sample. On the other hand, amplicon sequencing targets taxonomically important marker genes, the analysis of which is restricted to previously known DNA sequences. While sequence-based metagenomics is used to analyze DNA sequences directly from the environment without the requirement of library construction and with limited identification of novel genes and products that can be complemented by functional genomics, function-based metagenomics requires fragmentation and cloning of extracted metagenome DNA in a suitable host with subsequent functional screening and sequencing clone for detection of a novel gene. Although advances were made in metagenomics, different challenges arise. This review provides insight into advances in the metagenomic approaches combined with next-generation sequencing, their recent applications highlighting the emerging ones, such as in astrobiology, forensic sciences, and SARS-CoV-2 infection diagnosis, and the challenges associated. This review further discusses the different types of metagenomics and outlines advancements in bioinformatics tools and their significance in the analysis of metagenomic datasets.
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Affiliation(s)
- Niguse K Lema
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Department of Biotechnology, Arba Minch University, Arba Minch, Ethiopia
| | - Mesfin T Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Adugna A Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
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Lin S, Guo Y, Huang Z, Tang K, Wang X. Comparative Genomic Analysis of Cold-Water Coral-Derived Sulfitobacter faviae: Insights into Their Habitat Adaptation and Metabolism. Mar Drugs 2023; 21:md21050309. [PMID: 37233503 DOI: 10.3390/md21050309] [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: 04/25/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
Sulfitobacter is one of the major sulfite-oxidizing alphaproteobacterial groups and is often associated with marine algae and corals. Their association with the eukaryotic host cell may have important ecological contexts due to their complex lifestyle and metabolism. However, the role of Sulfitobacter in cold-water corals remains largely unexplored. In this study, we explored the metabolism and mobile genetic elements (MGEs) in two closely related Sulfitobacter faviae strains isolated from cold-water black corals at a depth of ~1000 m by comparative genomic analysis. The two strains shared high sequence similarity in chromosomes, including two megaplasmids and two prophages, while both contained several distinct MGEs, including prophages and megaplasmids. Additionally, several toxin-antitoxin systems and other types of antiphage elements were also identified in both strains, potentially helping Sulfitobacter faviae overcome the threat of diverse lytic phages. Furthermore, the two strains shared similar secondary metabolite biosynthetic gene clusters and genes involved in dimethylsulfoniopropionate (DMSP) degradation pathways. Our results provide insight into the adaptive strategy of Sulfitobacter strains to thrive in ecological niches such as cold-water corals at the genomic level.
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Affiliation(s)
- Shituan Lin
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zixian Huang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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7
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Dicks LMT, Vermeulen W. Do Bacteria Provide an Alternative to Cancer Treatment and What Role Does Lactic Acid Bacteria Play? Microorganisms 2022; 10:microorganisms10091733. [PMID: 36144335 PMCID: PMC9501580 DOI: 10.3390/microorganisms10091733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is one of the leading causes of mortality and morbidity worldwide. According to 2022 statistics from the World Health Organization (WHO), close to 10 million deaths have been reported in 2020 and it is estimated that the number of cancer cases world-wide could increase to 21.6 million by 2030. Breast, lung, thyroid, pancreatic, liver, prostate, bladder, kidney, pelvis, colon, and rectum cancers are the most prevalent. Each year, approximately 400,000 children develop cancer. Treatment between countries vary, but usually includes either surgery, radiotherapy, or chemotherapy. Modern treatments such as hormone-, immuno- and antibody-based therapies are becoming increasingly popular. Several recent reports have been published on toxins, antibiotics, bacteriocins, non-ribosomal peptides, polyketides, phenylpropanoids, phenylflavonoids, purine nucleosides, short chain fatty acids (SCFAs) and enzymes with anticancer properties. Most of these molecules target cancer cells in a selective manner, either directly or indirectly through specific pathways. This review discusses the role of bacteria, including lactic acid bacteria, and their metabolites in the treatment of cancer.
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Global regulatory factor VeA upregulates the production of antitumor substances in endophytic Fusarium solani. Antonie Van Leeuwenhoek 2022; 115:1085-1100. [PMID: 35789442 DOI: 10.1007/s10482-022-01753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/18/2022] [Indexed: 10/17/2022]
Abstract
A number of studies have demonstrated that endophytic fungi have the potential to produce antitumor active substances with novel structures and significant activities. In our previous studies, we isolated a Fusarium strain from the stem of the medicinal plant Nothapodytes pittosporoides (Oliv.). In this study, we identified this strain as Fusarium solani and found that its crude extract has significant antitumor activity against human alveolar adenocarcinoma cells (A549). We overexpressed the global regulatory factor VeA in F. solani (VeAOE), resulting in a significant increase in antitumor activity. The MTT assay results showed that the inhibition rate of the VeAOE mutant extract on A549 cancer cells was significantly higher than that of the WT extract, as the IC50 decreased from 369.22 to 285.89 μg/mL, and the apoptosis ratio was significantly increased by approximately 4.86-fold. In VeAOE, accumulation of alkaloids, terpenoids, carboxylic acid derivatives, phenols and flavonoid metabolites with potential antitumor activity was significantly increased compared with WT based on metabolomic analysis. Additionally, transcriptome analysis found that the expression patterns of 48 genes related to antitumor activity were significantly changed in VeAOE, mainly involving glycosyl hydrolases, the Zn(2)-Cys(6) class, cytochrome P450 monooxygenase, 3-isopropylmalate dehydratase, and polyketide synthases. These results suggested that VeA mediated the antitumor activity of the metabolites in F. solani HB1-J1 by regulating multiple metabolic pathways.
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9
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A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure. Molecules 2021; 26:molecules26237332. [PMID: 34885912 PMCID: PMC8658942 DOI: 10.3390/molecules26237332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.
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Haro-Moreno JM, López-Pérez M, Rodriguez-Valera F. Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics. Front Microbiol 2021; 12:708782. [PMID: 34512586 PMCID: PMC8430335 DOI: 10.3389/fmicb.2021.708782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
Third-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, second-generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in the assembly of microbes with high microdiversity and retrieval of the flexible (adaptive) fraction of prokaryotic genomes. Here, we have used a third-generation technique to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared PacBio Sequel II with the classical approach using Illumina Nextseq short reads followed by assembly to study the metagenome. Long reads allow for efficient direct retrieval of complete genes avoiding the bias of the assembly step. Besides, the application of long reads on metagenomic assembly allows for the reconstruction of much more complete metagenome-assembled genomes (MAGs), particularly from microbes with high microdiversity such as Pelagibacterales. The flexible genome of reconstructed MAGs was much more complete containing many adaptive genes (some with biotechnological potential). PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. For most applications of metagenomics, from community structure analysis to ecosystem functioning, long reads should be applied whenever possible. Specifically, for in silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be analyzed from raw reads before a computationally demanding (and potentially artifactual) assembly step.
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Affiliation(s)
- Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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11
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Yang J, Zhu Q, Xu F, Yang M, Du H, Bian X, Lu Z, Lu Y, Lu F. Genome Mining, Heterologous Expression, Antibacterial and Antioxidant Activities of Lipoamides and Amicoumacins from Compost-Associated Bacillus subtilis fmb60. Molecules 2021; 26:molecules26071892. [PMID: 33810551 PMCID: PMC8036425 DOI: 10.3390/molecules26071892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities, was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1–3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated.
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Affiliation(s)
- Jie Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Lianyungang 222000, China
| | - Qingzheng Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Feng Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Ming Yang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Hechao Du
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Xiaoying Bian
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Yingjian Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210003, China
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
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12
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Stevenson LJ, Owen JG, Ackerley DF. Metagenome Driven Discovery of Nonribosomal Peptides. ACS Chem Biol 2019; 14:2115-2126. [PMID: 31508935 DOI: 10.1021/acschembio.9b00618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Declining rates of novel natural product discovery and exponential rates of rediscovery heralded the end of the 1940s to 1960s "golden era" of antibiotic discovery. Fifty years later, the implementation of molecular screening methodologies revealed that standard culture-based screening approaches had failed to capture the vast majority of environmental bacteria and that even for the cultivable isolates only a small fraction of the biosynthetic potential had been tapped. A diversity of metagenomic screening and synthetic biology approaches have been developed to address these issues. The nonribosomal peptides have received particular focus, owing to their high levels of bioactivity and the predictability of the biosynthetic logic of the genetically encoded assembly lines that produce them. By uniting advances in next-generation sequencing and bioinformatic analysis with a diversity of traditional disciplines, several pioneering teams have proven that this previously inaccessible resource is no longer out of reach.
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Affiliation(s)
- Luke J. Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Jeremy G. Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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13
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Robertsen HL, Musiol-Kroll EM. Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs. Antibiotics (Basel) 2019; 8:E157. [PMID: 31547063 PMCID: PMC6963833 DOI: 10.3390/antibiotics8040157] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 01/15/2023] Open
Abstract
Actinomycetes are remarkable producers of compounds essential for human and veterinary medicine as well as for agriculture. The genomes of those microorganisms possess several sets of genes (biosynthetic gene cluster (BGC)) encoding pathways for the production of the valuable secondary metabolites. A significant proportion of the identified BGCs in actinomycetes encode pathways for the biosynthesis of polyketide compounds, nonribosomal peptides, or hybrid products resulting from the combination of both polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The potency of these molecules, in terms of bioactivity, was recognized in the 1940s, and started the "Golden Age" of antimicrobial drug discovery. Since then, several valuable polyketide drugs, such as erythromycin A, tylosin, monensin A, rifamycin, tetracyclines, amphotericin B, and many others were isolated from actinomycetes. This review covers the most relevant actinomycetes-derived polyketide drugs with antimicrobial activity, including anti-fungal agents. We provide an overview of the source of the compounds, structure of the molecules, the biosynthetic principle, bioactivity and mechanisms of action, and the current stage of development. This review emphasizes the importance of actinomycetes-derived antimicrobial polyketides and should serve as a "lexicon", not only to scientists from the Natural Products field, but also to clinicians and others interested in this topic.
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Affiliation(s)
- Helene L Robertsen
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Ewa M Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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14
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Kim Tiam S, Gugger M, Demay J, Le Manach S, Duval C, Bernard C, Marie B. Insights into the Diversity of Secondary Metabolites of Planktothrix Using a Biphasic Approach Combining Global Genomics and Metabolomics. Toxins (Basel) 2019; 11:E498. [PMID: 31461939 PMCID: PMC6784222 DOI: 10.3390/toxins11090498] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with diverse chemical structures and potent biological activities and toxicities. The chemical identification of these compounds remains a major bottleneck. Strategies that can prioritize the most prolific strains and novel compounds are of great interest. Here, we combine chemical analysis and genomics to investigate the chemodiversity of secondary metabolites based on their pattern of distribution within some cyanobacteria. Planktothrix being a cyanobacterial genus known to form blooms worldwide and to produce a broad spectrum of toxins and other bioactive compounds, we applied this combined approach on four closely related strains of Planktothrix. The chemical diversity of the metabolites produced by the four strains was evaluated using an untargeted metabolomics strategy with high-resolution LC-MS. Metabolite profiles were correlated with the potential of metabolite production identified by genomics for the different strains. Although, the Planktothrix strains present a global similarity in terms of a biosynthetic cluster gene for microcystin, aeruginosin, and prenylagaramide for example, we found remarkable strain-specific chemodiversity. Only few of the chemical features were common to the four studied strains. Additionally, the MS/MS data were analyzed using Global Natural Products Social Molecular Networking (GNPS) to identify molecular families of the same biosynthetic origin. In conclusion, we depict an efficient, integrative strategy for elucidating the chemical diversity of a given genus and link the data obtained from analytical chemistry to biosynthetic genes of cyanobacteria.
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Affiliation(s)
- Sandra Kim Tiam
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, 28 rue du Dr Roux, 75724 Paris Cedex 05, France
| | - Justine Demay
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Séverine Le Manach
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Charlotte Duval
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France.
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15
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Khater S, Gupta M, Agrawal P, Sain N, Prava J, Gupta P, Grover M, Kumar N, Mohanty D. SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. Nucleic Acids Res 2019; 45:W72-W79. [PMID: 28460065 PMCID: PMC5570206 DOI: 10.1093/nar/gkx344] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/25/2017] [Indexed: 01/05/2023] Open
Abstract
Genome guided discovery of novel natural products has been a promising approach for identification of new bioactive compounds. SBSPKS web-server has been a valuable resource for analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters. We have developed an updated version - SBSPKSv2 which is based on comprehensive analysis of sequence, structure and secondary metabolite chemical structure data from 311 experimentally characterized PKS/NRPS gene clusters with known biosynthetic products. A completely new feature of SBSPKSv2 is the inclusion of features for search in chemical space. It allows the user to compare the chemical structure of a given secondary metabolite to the chemical structures of biosynthetic intermediates and final products. For identification of catalytic domains, SBSPKS now uses profile based searches, which are computationally faster and have high sensitivity. HMM profiles have also been added for a number of new domains and motif information has been used for distinguishing condensation (C), epimerization (E) and cyclization (Cy) domains of NRPS. In summary, the new and updated SBSPKSv2 is a versatile tool for genome mining and analysis of polyketide and non-ribosomal peptide biosynthetic pathways in chemical space. The server is available at: http://www.nii.ac.in/sbspks2.html.
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Affiliation(s)
- Shradha Khater
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Money Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priyesh Agrawal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Neetu Sain
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jyoti Prava
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priya Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mansi Grover
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Narendra Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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16
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Wang J, Hu X, Sun G, Li L, Jiang B, Li S, Bai L, Liu H, Yu L, Wu L. Genome-Guided Discovery of Pretilactam from Actinosynnema pretiosum ATCC 31565. Molecules 2019; 24:molecules24122281. [PMID: 31248172 PMCID: PMC6631532 DOI: 10.3390/molecules24122281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/12/2019] [Accepted: 06/18/2019] [Indexed: 11/16/2022] Open
Abstract
Actinosynnema is a small but well-known genus of actinomycetes for production of ansamitocin, the payload component of antibody-drug conjugates against cancers. However, the secondary metabolite production profile of Actinosynnema pretiosum ATCC 31565, the most famous producer of ansamitocin, has never been fully explored. Our antiSMASH analysis of the genomic DNA of Actinosynnema pretiosum ATCC 31565 revealed a NRPS-PKS gene cluster for polyene macrolactam. The gene cluster is very similar to gene clusters for mirilactam and salinilactam, two 26-membered polyene macrolactams from Actinosynnema mirum and Salinispora tropica, respectively. Guided by this bioinformatics prediction, we characterized a novel 26-membered polyene macrolactam from Actinosynnema pretiosum ATCC 31565 and designated it pretilactam. The structure of pretilactam was elucidated by a comprehensive analysis of HRMS, 1D and 2D-NMR, with absolute configuration of chiral carbons predicted bioinformatically. Pretilactam features a dihydroxy tetrahydropyran moiety, and has a hexaene unit and a diene unit as its polyene system. A preliminary antibacterial assay indicated that pretilactam is inactive against Bacillus subtilis and Candida albicans.
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Affiliation(s)
- Jing Wang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Xiaowen Hu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Guizhi Sun
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Linli Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Bingya Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Shufen Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Liping Bai
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Hongyu Liu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Liyan Yu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Linzhuan Wu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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17
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Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes. Curr Microbiol 2019; 77:645-656. [PMID: 31069462 DOI: 10.1007/s00284-019-01698-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023]
Abstract
Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.
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18
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Zhao H, Liu YP, Zhang LQ. In silico and Genetic Analyses of Cyclic Lipopeptide Synthetic Gene Clusters in Pseudomonas sp. 11K1. Front Microbiol 2019; 10:544. [PMID: 30941113 PMCID: PMC6433849 DOI: 10.3389/fmicb.2019.00544] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/01/2019] [Indexed: 02/02/2023] Open
Abstract
Pseudomonas sp. 11K1, originally isolated from rhizosphere, possesses inhibitory activity against plant pathogenic fungi and bacteria. Herein, the genome of strain 11K1 was sequenced and subjected to in silico, mutational, and functional analyses. The 11K1 genome is 6,704,877 bp in length, and genome mining identified three potential cyclic lipopeptide (CLP) biosynthetic clusters, subsequently named brasmycin, braspeptin, and brasamide. Insertional and deletion mutants displayed impaired brasmycin and braspeptin production, and lost antifungal activity, but retained antibacterial activity against Xanthomonas oryzae. The structures of these two active CLPs were predicted based on adenylation (A) domains. Brasmycin is composed of nine amino acids and belongs to the syringomycin class, while braspeptin is a 22 amino acid cyclic peptide belonging to the tolaasin group. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry analysis revealed that brasmycin and braspeptin have different molecular weights compared with known syringomycin and tolaasin members, respectively. Mutation of brasmycin and braspeptin gene clusters affected both biofilm formation and colony morphology. Collectively, these results indicate that Pseudomonas sp. 11K1 produces two novel CLPs that may help bacteria compete for nutrients and niches in the environment.
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Affiliation(s)
- Hui Zhao
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, China
| | - Yan-Ping Liu
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Li-Qun Zhang
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, China
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19
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Ziko L, Saqr AHA, Ouf A, Gimpel M, Aziz RK, Neubauer P, Siam R. Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool. Microb Cell Fact 2019; 18:56. [PMID: 30885206 PMCID: PMC6423787 DOI: 10.1186/s12934-019-1103-3] [Citation(s) in RCA: 10] [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: 09/18/2018] [Accepted: 03/06/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cancer and infectious diseases are problematic because of continuous emergence of drug resistance. One way to address this enormous global health threat is bioprospecting the unlikeliest environments, such as extreme marine niches, which have tremendous biodiversity that is barely explored. One such environment is the Red Sea brine pool, Atlantis II Deep (ATII). Here, we functionally screened a fosmid library of metagenomic DNA isolated from the ATII lower convective layer (LCL) for antibacterial and anticancer activities. RESULTS Selected clones, 14-7E and 10-2G, displayed antibacterial effects on the marine strain Bacillus sp. Cc6. Moreover, whole cell lysates from 14-7E and 10-2G exhibited decreased cell viability against MCF-7 (39.1% ± 6.6, 42% ± 8.1 at 50% v/v) and U2OS cells (35.7% ± 1.9, 79.9% ± 5.9 at 50% v/v), respectively. By sequencing the insert DNA from 14-7E and 10-2G, we identified two putative orphan biosynthetic gene clusters. Both clusters harbored putative ATP-binding cassette (ABC) transporter permeases and S-adenosylmethionine-related genes. Interestingly, the biosynthetic gene cluster identified on 14-7E is of archaeal origin and harbors a putative transcription factor. Several identified genes may be responsible for the observed antibacterial and anticancer activities. The 14-7E biosynthetic gene cluster may be encoding enzymes producing a specialized metabolite (effect of detected genes involved in C-C bond formation and glycosylation). The bioactivity may also be due to predicted subtilases encoded by this cluster. The 10-2G cluster harbored putative glycosyltransferase and non-ribosomal peptide synthase genes; thus the observed activity of this clone could be caused by a bioactive peptide. CONCLUSIONS The ATII LCL prokaryotic metagenome hosts putative orphan biosynthetic gene clusters that confer antibiotic and anticancer effects. Further biochemical studies should characterize the detected bioactive components, and the potential use of 14-7E metabolite for antibiosis and 10-2G metabolite as a selective anti-breast cancer drug.
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Affiliation(s)
- Laila Ziko
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, Egypt
| | - Al-Hussein A Saqr
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, Cairo, 11835, Egypt
| | - Amged Ouf
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, Egypt
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, Cairo, 11835, Egypt
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK24, 13355, Berlin, Germany
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK24, 13355, Berlin, Germany
| | - Rania Siam
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, Egypt.
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, Cairo, 11835, Egypt.
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20
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Yang RX, Zhang SW, Xue D, Xuan JH, Zhang YB, Peng BB. Culturable Endophytes Diversity Isolated from Paeonia ostii and the Genetic Basis for Their Bioactivity. Pol J Microbiol 2018; 67:441-454. [PMID: 30550230 PMCID: PMC7256872 DOI: 10.21307/pjm-2018-052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2018] [Indexed: 11/11/2022] Open
Abstract
Paeonia ostii is known for its excellent medicinal values as Chinese traditional plant. To date, the diversity of culturable endophytes associated with P. ostii is in its initial phase of exploration. In this study, 56 endophytic bacteria and 51 endophytic fungi were isolated from P. ostii roots in China. Subsequent characterization of 56 bacterial strains by 16S rDNA gene sequence analysis revealed that nine families and 13 different genera were represented. All the fungal strains were classed into six families and 12 genera based on ITS gene sequence. The biosynthetic potential of all the endophytes was further investigated by the detection of putative polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes. The PCR screens were successful in targeting thirteen bacterial PKS, five bacterial NRPS, ten fungal PKS and nine fungal NRPS gene fragments. Bioinformatic analysis of these detected endophyte gene fragments facilitated inference of the potential bioactivity of endophyte bioactive products, suggesting that the isolated endophytes are capable of producing a plethora of secondary metabolites. These results suggest that endophytes isolated from P. ostii had abundant population diversity and biosynthetic potential, which further proved that endophytes are valuable reservoirs of novel bioactive compounds.
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Affiliation(s)
- Rui-Xian Yang
- Department of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology , Luoyang , P.R.China
| | - Shao-Wen Zhang
- Department of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology , Luoyang , P.R.China
| | - Dong Xue
- Department of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology , Luoyang , P.R.China
| | - Jun-Hao Xuan
- Department of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology , Luoyang , P.R.China
| | - Yuan-Bo Zhang
- Department of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology , Luoyang , P.R.China
| | - Biao-Biao Peng
- Department of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology , Luoyang , P.R.China
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21
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Karakasidou K, Nikolouli K, Amoutzias GD, Pournou A, Manassis C, Tsiamis G, Mossialos D. Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study. Microbiologyopen 2018; 7:e00596. [PMID: 29484839 PMCID: PMC6182554 DOI: 10.1002/mbo3.596] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 02/05/2023] Open
Abstract
Paper documents in archives, libraries, and museums often undergo biodeterioration by microorganisms. Fungi and less often bacteria have been described to advance paper staining, so called “foxing” and degradation of paper substrates. In this study, for the first time, the fungal and bacterial diversity in biodeteriorated paper documents of Hellenic General State Archives dating back to the 19th and 20th century has been assessed by culture‐dependent and independent methods. The internally transcribed spacer (ITS) region and 16S rRNA gene were amplified by PCR from fungal and bacterial isolates and amplicons were sequenced. Sequence analysis and phylogeny revealed fungal phylotypes like Penicillium sp., Cladosporium sp., Penicillium citrinum, Alternaria infectoria, Alternaria alternata, Epicoccum nigrum, and Penicillium chrysogenum which are often implicated in paper deterioration. Bacterial phylotypes closely related to known biodeteriogenic bacteria such as Bacillus spp., Micrococcus spp., Kocuria sp. in accordance with previous studies were characterized. Among the fungal phylotypes described in this study are included well‐known allergens such as Penicillium spp., Alternaria spp., and Cladosporium spp. that impose a serious health threat on staff members and scholars. Furthermore, fungal isolates such as Chalastospora gossypii and Trametes ochracea have been identified and implicated in biodeterioration of historical paper manuscripts in this study for the first time. Certain new or less known fungi and bacteria implicated in paper degradation were retrieved, indicating that particular ambient conditions, substrate chemistry, or even location might influence the composition of colonizing microbiota.
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Affiliation(s)
- Kiriaki Karakasidou
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Katerina Nikolouli
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Grigoris D Amoutzias
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Anastasia Pournou
- Department of Conservation of Antiquities and Works of Art, Technological Educational Institute of Athens, Athens, Greece
| | - Christos Manassis
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece
| | - Dimitris Mossialos
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
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Bioactivity Assessment of Indian Origin-Mangrove Actinobacteria against Candida albicans. Mar Drugs 2018; 16:md16020060. [PMID: 29439535 PMCID: PMC5852488 DOI: 10.3390/md16020060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans. GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics.
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Kim IH, Aryal SK, Aghai DT, Casanova-Torres ÁM, Hillman K, Kozuch MP, Mans EJ, Mauer TJ, Ogier JC, Ensign JC, Gaudriault S, Goodman WG, Goodrich-Blair H, Dillman AR. The insect pathogenic bacterium Xenorhabdus innexi has attenuated virulence in multiple insect model hosts yet encodes a potent mosquitocidal toxin. BMC Genomics 2017; 18:927. [PMID: 29191166 PMCID: PMC5709968 DOI: 10.1186/s12864-017-4311-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/16/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Xenorhabdus innexi is a bacterial symbiont of Steinernema scapterisci nematodes, which is a cricket-specialist parasite and together the nematode and bacteria infect and kill crickets. Curiously, X. innexi expresses a potent extracellular mosquitocidal toxin activity in culture supernatants. We sequenced a draft genome of X. innexi and compared it to the genomes of related pathogens to elucidate the nature of specialization. RESULTS Using green fluorescent protein-expressing X. innexi we confirm previous reports using culture-dependent techniques that X. innexi colonizes its nematode host at low levels (~3-8 cells per nematode), relative to other Xenorhabdus-Steinernema associations. We found that compared to the well-characterized entomopathogenic nematode symbiont X. nematophila, X. innexi fails to suppress the insect phenoloxidase immune pathway and is attenuated for virulence and reproduction in the Lepidoptera Galleria mellonella and Manduca sexta, as well as the dipteran Drosophila melanogaster. To assess if, compared to other Xenorhabdus spp., X. innexi has a reduced capacity to synthesize virulence determinants, we obtained and analyzed a draft genome sequence. We found no evidence for several hallmarks of Xenorhabdus spp. toxicity, including Tc and Mcf toxins. Similar to other Xenorhabdus genomes, we found numerous loci predicted to encode non-ribosomal peptide/polyketide synthetases. Anti-SMASH predictions of these loci revealed one, related to the fcl locus that encodes fabclavines and zmn locus that encodes zeamines, as a likely candidate to encode the X. innexi mosquitocidal toxin biosynthetic machinery, which we designated Xlt. In support of this hypothesis, two mutants each with an insertion in an Xlt biosynthesis gene cluster lacked the mosquitocidal compound based on HPLC/MS analysis and neither produced toxin to the levels of the wild type parent. CONCLUSIONS The X. innexi genome will be a valuable resource in identifying loci encoding new metabolites of interest, but also in future comparative studies of nematode-bacterial symbiosis and niche partitioning among bacterial pathogens.
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Affiliation(s)
- Il-Hwan Kim
- Department of Entomology, University of Wisconsin-Madison, Madison, WI USA
- Present address: Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD USA
| | | | - Dariush T. Aghai
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
| | | | - Kai Hillman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
| | - Michael P. Kozuch
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
| | - Erin J. Mans
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN USA
| | - Terra J. Mauer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN USA
| | | | - Jerald C. Ensign
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
| | | | - Walter G. Goodman
- Department of Entomology, University of Wisconsin-Madison, Madison, WI USA
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN USA
| | - Adler R. Dillman
- Department of Nematology, University of California, Riverside, CA USA
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Agrawal S, Acharya D, Adholeya A, Barrow CJ, Deshmukh SK. Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential. Front Pharmacol 2017; 8:828. [PMID: 29209209 PMCID: PMC5702503 DOI: 10.3389/fphar.2017.00828] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/31/2017] [Indexed: 11/13/2022] Open
Abstract
Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs). Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi. In recent years large numbers of nonribosomal have been discovered from marine microbes using multi-disciplinary approaches. The present review covers the NRPs discovered from marine microbes and their pharmacological potential along with role of genomics, proteomics and bioinformatics in discovery and development of nonribosomal peptides drugs.
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Affiliation(s)
- Shivankar Agrawal
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India.,Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Debabrata Acharya
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
| | - Alok Adholeya
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Sunil K Deshmukh
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
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A strategy for the identification of patterns in the biosynthesis of nonribosomal peptides by Betaproteobacteria species. Sci Rep 2017; 7:10400. [PMID: 28871139 PMCID: PMC5583390 DOI: 10.1038/s41598-017-11314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/22/2017] [Indexed: 11/17/2022] Open
Abstract
Nonribosomal peptides have an important pharmacological role due to their extensive biological properties. The singularities in the biosynthesis of these natural products allowed the development of genome-mining strategies which associate them to their original biosynthetic gene clusters. Generally, these compounds present complex architectures that make their identification difficult. Based on these evidences, genomes from species of the class Betaproteobacteria were studied with the purpose of finding biosynthetic similarities among them. These organisms were applied as templates due to their large number of biosynthetic gene clusters and the natural products isolated from them. The strategy for Rapid Identification of Nonribosomal Peptides Portions (RINPEP) proposed in this work was built by reorganizing the data obtained from antiSMASH and NCBI with a product-centered way. The verification steps of RINPEP comprehended the fragments of existent compounds and predictions obtained in silico with the purpose of finding common subunits expressed by different genomic sequences. The results of this strategy revealed patterns in a global overview of the biosynthesis of nonribosomal peptides by Betaproteobacteria.
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Parada RB, Marguet ER, Vallejo M. Aislamiento y caracterización parcial de actinomicetos de suelos con actividad antimicrobiana contra bacterias multidrogo-resistentes. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2017. [DOI: 10.15446/rev.colomb.biote.v19n2.64098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Con el objetivo de evaluar la actividad antimicrobiana frente a bacterias multi-drogo resistentes, se estudiaron 234 cepas de actinobacterias aisladas de suelo de Argentina y Perú. Se seleccionaron 13 cepas sobre la base de su actividad antagonista contra Staphylococcus aureus meticilina-resistente (SAMR) y Enterococcus resistente a vancomicina (EVR-van A y van B). La presencia de los genes NRPS, PKS-I y PKS-II fueron investigados por técnicas de PCR. Entre las 13 actinobacterias seleccionadas, la cepa AC69C mostró la mayor actividad en las pruebas de difusión en medio sólido y se evaluó posteriormente la producción de metabolitos antagonistas en medios líquidos. Los mejores resultados se lograron en caldo de fermentación con carbohidratos, al usarse en combinación almidón y glucosa. Se obtuvieron actividades antimicrobianas de 640 unidades arbitrarias (UA), 320 UA, 320 UA y 80 UA contra EVR-van A, EVR-van B, Listeria monocytogenes ATCC7644 y SAMR, respectivamente. La amplificación por PCR del gen ARNr 16S y el análisis filogenético subsecuente de la cepa AC69C exhibieron una homología del 100 % con Streptomyces antibioticus NRRL B-1701. No fue posible establecer una correlación entre los genes amplificados y la actividad antimicrobiana de las 13 cepas seleccionadas. Los resultados de este trabajo demuestran la amplia distribución de las actinobacterias en suelo y la importancia del aislamiento de cepas para la búsqueda de nuevos metabolitos activos contra bacterias multi-drogo resistentes de origen clínico.
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28
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Mishra VK, Passari AK, Leo VV, Singh BP. Molecular Diversity and Detection of Endophytic Fungi Based on Their Antimicrobial Biosynthetic Genes. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ferrara M, Perrone G, Gambacorta L, Epifani F, Solfrizzo M, Gallo A. Identification of a Halogenase Involved in the Biosynthesis of Ochratoxin A in Aspergillus carbonarius. Appl Environ Microbiol 2016; 82:5631-41. [PMID: 27422838 PMCID: PMC5007760 DOI: 10.1128/aem.01209-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/27/2016] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED Aspergillus carbonarius is the main responsible fungus of ochratoxin A (OTA) contamination of grapes and derived products. To date, the biosynthetic mechanism of this mycotoxin has been partially elucidated. Availability of genome sequence of A. carbonarius has allowed the identification of a putative gene cluster involved in OTA biosynthesis. This region hosts the previously characterized AcOTAnrps and AcOTApks genes encoding two key enzymes of the biosynthetic pathway. At about 4,400 nucleotides downstream of these loci, a gene encoding a putative flavin dependent-halogenase came out from the annotation data. Its proximity to OTA biosynthetic genes and its sequence analysis have suggested a role in the biosynthesis of OTA, directed to the introduction of the chlorine atom in the C-5 position of the final molecular structure of this mycotoxin. The deduced protein sequence of the halogenase gene, we designated AcOTAhal, shows a high similarity to a halogenase that is located in the OTA cluster of A. niger The deletion of the halogenase gene completely eliminated the production of ochratoxin A in A. carbonarius and determined a significant increase of ochratoxin B, as confirmed by mass spectrometry analysis. Moreover, its expression profile was similar to the two biosynthetic genes previously identified, AcOTApks and AcOTAnrps, indicating a strong correlation of the AcOTAhal gene with the kinetics of OTA accumulation in A. carbonarius. Therefore, experimental evidence confirmed that the chlorination step which converts OTB in OTA represents the final stage of the biosynthetic pathway, supporting our earlier hypothesis on the order of enzymatic steps of OTA biosynthesis in A. carbonarius IMPORTANCE Ochratoxin A is a potent mycotoxin classified as a possible carcinogen for humans, and Aspergillus carbonarius is the main agent responsible for OTA accumulation in grapes. We demonstrate here that a flavin-halogenase is implicated in the biosynthesis of OTA in A. carbonarius The encoding gene, AcOTAhal, is contiguous to biosynthetic genes that we have already described (nrps and pks), resulting as part of the biosynthetic cluster. The encoded protein is responsible of the introduction of chlorine atom in the final molecular structure and acts at the last step in the pathway. This study can be considered a continuation of an earlier study wherein we started to clarify the molecular basis of OTA biosynthesis in A. carbonarius, which has not been completely elucidated until now. This research represents an important step forward to a better understanding of the production mechanism, which will contribute to the development of improved control strategies to reduce the risk of OTA contamination in food products.
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Affiliation(s)
- Massimo Ferrara
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Giancarlo Perrone
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Lucia Gambacorta
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Filomena Epifani
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Michele Solfrizzo
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Antonia Gallo
- Institute of Sciences of Food Production, National Research Council, Lecce, Italy
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Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes. Mar Drugs 2016; 14:md14040080. [PMID: 27092515 PMCID: PMC4849084 DOI: 10.3390/md14040080] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/01/2016] [Accepted: 04/08/2016] [Indexed: 11/17/2022] Open
Abstract
Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. In many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (NRPs) and polyketides (PKs) are synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSes) and type-I polyketide synthases (PKSes-I), respectively. Novel findings regarding the mechanisms underlying NRPS and PKS evolution demonstrate how microorganisms could leverage their metabolic potential. Moreover, these findings could facilitate synthetic biology approaches leading to novel bioactive compounds. Ongoing advances in bioinformatics and next-generation sequencing (NGS) technologies are driving the discovery of NRPs and PKs derived from marine microbiomes mainly through two strategies: genome-mining and metagenomics. Microbial genomes are now sequenced at an unprecedented rate and this vast quantity of biological information can be analyzed through genome mining in order to identify gene clusters encoding NRPSes and PKSes of interest. On the other hand, metagenomics is a fast-growing research field which directly studies microbial genomes and their products present in marine environments using culture-independent approaches. The aim of this review is to examine recent developments regarding discovery strategies of bioactive compounds synthesized by NRPS and type-I PKS derived from marine microbiomes and to highlight the vast diversity of NRPSes and PKSes present in marine environments by giving examples of recently discovered bioactive compounds.
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31
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Miura T, Nishizawa A, Nishizawa T, Asayama M, Shirai M. Actinophage R4 integrase-based site-specific chromosomal integration of non-replicative closed circular DNA. J Basic Microbiol 2016; 56:635-44. [PMID: 26870903 DOI: 10.1002/jobm.201500658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/27/2016] [Indexed: 11/07/2022]
Abstract
The actinophage R4 integrase (Sre)-based molecular genetic engineering system was developed for the chromosomal integration of multiple genes in Escherichia coli. A cloned DNA fragment containing two attP sites, green fluorescent protein (gfp) as a first transgene, and an antibiotic resistance gene as a selection marker was self-ligated to generate non-replicative closed circular DNA (nrccDNA) for integration. nrccDNA was introduced into attB-inserted E. coli cells harboring the plasmid expressing Sre by electroporation. The expressed Sre catalyzed site-specific integration between one of the two attP sites on nrccDNA and the attB site on the E. coli chromosome. The integration frequency was affected by the chromosomal location of the target site. A second nrccDNA containing two attB sites, lacZα encoding the alpha fragment of β-galactosidase as a transgene, and another antibiotic resistance gene was integrated into the residual attP site on the gfp-integrated E. coli chromosome via one of the two attB sites according to reiterating site-specific recombination. The integrants clearly exhibited β-galactosidase activity and green fluorescence, suggesting the simultaneous expression of multiple recombinant proteins in E. coli. The results of the present study showed that a step-by-step integration procedure using nrccDNA achieved the chromosomal integration of multiple genes.
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Affiliation(s)
- Takamasa Miura
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Akito Nishizawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Tomoyasu Nishizawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Munehiko Asayama
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Makoto Shirai
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
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Chávez R, Fierro F, García-Rico RO, Vaca I. Filamentous fungi from extreme environments as a promising source of novel bioactive secondary metabolites. Front Microbiol 2015; 6:903. [PMID: 26441853 PMCID: PMC4563253 DOI: 10.3389/fmicb.2015.00903] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/17/2015] [Indexed: 12/12/2022] Open
Abstract
Natural product search is undergoing resurgence upon the discovery of a huge previously unknown potential for secondary metabolite (SM) production hidden in microbial genomes. This is also the case for filamentous fungi, since their genomes contain a high number of "orphan" SM gene clusters. Recent estimates indicate that only 5% of existing fungal species have been described, thus the potential for the discovery of novel metabolites in fungi is huge. In this context, fungi thriving in harsh environments are of particular interest since they are outstanding producers of unusual chemical structures. At present, there are around 16 genomes from extreme environment-isolated fungi in databases. In a preliminary analysis of three of these genomes we found that several of the predicted SM gene clusters are probably involved in the biosynthesis of compounds not yet described. Genome mining strategies allow the exploitation of the information in genome sequences for the discovery of new natural compounds. The synergy between genome mining strategies and the expected abundance of SMs in fungi from extreme environments is a promising path to discover new natural compounds as a source of medically useful drugs.
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Affiliation(s)
- Renato Chávez
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile Santiago, Chile
| | - Francisco Fierro
- División de Ciencias Biológicas y de la Salud, Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa México D.F., Mexico
| | - Ramón O García-Rico
- Grupo GIMBIO, Facultad de Ciencias Básicas, Departamento de Microbiología, Universidad de Pamplona Pamplona, Colombia
| | - Inmaculada Vaca
- Facultad de Ciencias, Departamento de Química, Universidad de Chile Santiago, Chile
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33
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Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 2015; 14:111-29. [PMID: 25614221 DOI: 10.1038/nrd4510] [Citation(s) in RCA: 1508] [Impact Index Per Article: 167.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
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Affiliation(s)
- Alan L Harvey
- 1] Research and Innovation Support, Dublin City University, Dublin 9, Ireland. [2] Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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Hojo M, Omi A, Hamanaka G, Shindo K, Shimada A, Kondo M, Narita T, Kiyomoto M, Katsuyama Y, Ohnishi Y, Irie N, Takeda H. Unexpected link between polyketide synthase and calcium carbonate biomineralization. ZOOLOGICAL LETTERS 2015; 1:3. [PMID: 26605048 PMCID: PMC4604110 DOI: 10.1186/s40851-014-0001-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/15/2014] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Calcium carbonate biominerals participate in diverse physiological functions. Despite intensive studies, little is known about how mineralization is initiated in organisms. RESULTS We analyzed the medaka spontaneous mutant, ha, defective in otolith (calcareous ear stone) formation. ha lacks a trigger for otolith mineralization, and the causative gene was found to encode polyketide synthase (pks), a multifunctional enzyme mainly found in bacteria, fungi, and plant. Subsequent experiments demonstrate that the products of medaka PKS, most likely polyketides or their derivatives, act as nucleation facilitators in otolith mineralization. The generality of this novel PKS function is supported by the essential role of echinoderm PKS in calcareous skeleton formation together with the presence of PKSs in a much wider range of animals from coral to vertebrates. CONCLUSION The present study first links PKS to biomineralization and provides a genetic cue for biogeochemistry of carbon and calcium cycles.
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Affiliation(s)
- Motoki Hojo
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24–1, Hyakunincho, Shinju-ku, Tokyo 169-0073 Japan
| | - Ai Omi
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022 Japan
| | - Gen Hamanaka
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Kazutoshi Shindo
- />Department of Food and Nutrition, Japan Women’s University, 2-8-1, Mejirodai, Bunkyo-ku, Tokyo 112-8681 Japan
| | - Atsuko Shimada
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Mariko Kondo
- />Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225 Japan
| | - Takanori Narita
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Laboratory of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa 252-0880 Japan
| | - Masato Kiyomoto
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Yohei Katsuyama
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Naoki Irie
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hiroyuki Takeda
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
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Luo F, Wang Q, Yin C, Ge Y, Hu F, Huang B, Zhou H, Bao G, Wang B, Lu R, Li Z. Differential metabolic responses of Beauveria bassiana cultured in pupae extracts, root exudates and its interactions with insect and plant. J Invertebr Pathol 2015; 130:154-64. [PMID: 25584432 DOI: 10.1016/j.jip.2015.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 12/01/2022]
Abstract
Beauveria bassiana is a kind of world-wide entomopathogenic fungus and can also colonize plant rhizosphere. Previous researches showed differential expression of genes when entomopathogenic fungi are cultured in insect or plant materials. However, so far there is no report on metabolic alterations of B. bassiana in the environments of insect or plant. The purpose of this paper is to address this problem. Herein, we first provide the metabolomic analysis of B. bassiana cultured in insect pupae extracts (derived from Euproctis pseudoconspersa and Bombyx mori, EPP and BMP), plant root exudates (derived from asparagus and carrot, ARE and CRE), distilled water and minimal media (MM), respectively. Principal components analysis (PCA) shows that mycelia cultured in pupae extracts and root exudates are evidently separated and individually separated from MM, which indicates that fungus accommodates to insect and plant environments by different metabolic regulation mechanisms. Subsequently, orthogonal projection on latent structure-discriminant analysis (OPLS-DA) identifies differential metabolites in fungus under three environments relative to MM. Hierarchical clustering analysis (HCA) is performed to cluster compounds based on biochemical relationships, showing that sphingolipids are increased in BMP but are decreased in EPP. This observation further implies that sphingolipid metabolism may be involved in the adaptation of fungus to different hosts. In the meantime, sphingolipids are significantly decreased in root exudates but they are not decreased in distilled water, suggesting that some components of the root exudates can suppress sphingolipid to down-regulate sphingolipid metabolism. Pathway analysis finds that fatty acid metabolism is maintained at high level but non-ribosomal peptides (NRP) synthesis is unaffected in mycelia cultured in pupae extracts. In contrast, fatty acid metabolism is not changed but NRP synthesis is high in mycelia cultured in root exudates and distilled water. This indicates that fungal fatty acid metabolism is enhanced when contacting insect, but when in the absence of insect hosts NRP synthesis is increased. Ornithine, arginine and GABA are decreased in mycelia cultured in pupae extracts and root exudates but remain unchanged in distilled water, which suggests that they may be associated with fungal cross-talk with insects and plants. Trehalose and mannitol are decreased while adenine is increased in three conditions, signifying carbon shortage in cells. Together, these results unveil that B. bassiana has differential metabolic responses in pupae extracts and root exudates, and metabolic similarity in root exudates and distilled water is possibly due to the lack of insect components.
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Affiliation(s)
- Feifei Luo
- Anhui Agricultural University, Hefei 230036, China; Shanghai Institute of Physiology and Ecology, Shanghai 200032, China
| | - Qian Wang
- Anhui Agricultural University, Hefei 230036, China
| | - Chunlin Yin
- Anhui Agricultural University, Hefei 230036, China
| | - Yinglu Ge
- Anhui Agricultural University, Hefei 230036, China
| | - Fenglin Hu
- Anhui Agricultural University, Hefei 230036, China.
| | - Bo Huang
- Anhui Agricultural University, Hefei 230036, China
| | - Hong Zhou
- Naval Postgraduate School, Monterey, CA 93943, USA
| | - Guanhu Bao
- Anhui Agricultural University, Hefei 230036, China
| | - Bin Wang
- Anhui Agricultural University, Hefei 230036, China
| | - Ruili Lu
- Anhui Agricultural University, Hefei 230036, China.
| | - Zengzhi Li
- Anhui Agricultural University, Hefei 230036, China
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Handtke S, Volland S, Methling K, Albrecht D, Becher D, Nehls J, Bongaerts J, Maurer KH, Lalk M, Liesegang H, Voigt B, Daniel R, Hecker M. Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach. J Biotechnol 2014; 192 Pt A:204-14. [PMID: 25281541 DOI: 10.1016/j.jbiotec.2014.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 12/18/2022]
Abstract
Members of the species Bacillus pumilus get more and more in focus of the biotechnological industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182 cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS, IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed metabolic pathways. In the genome sequence a functional secretion system including the components of the Sec- and Tat-secretion machinery was found. Analysis of the exoproteome revealed secretion of about 70 proteins with predicted secretion signals. In addition, selected production-relevant genome features such as restriction modification systems and NRPS clusters of B. pumilus Jo2 are discussed.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Sonja Volland
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Karen Methling
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Jenny Nehls
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Heinrich-Mußmannstr. 1, 52428 Jülich, Germany.
| | | | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Birgit Voigt
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
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Hernández- Macedo ML, Nunes Barreto E, de Souza Cavalcanti AC, da Silva RS, dos Anjos Brandão ECT, Miranda Fernandes RP, Talamini V, Cardamone Diniz LE, Fernandes MF. Antimicrobial potential of Actinomycetes by NRPS and PKS-I pathways. BMC Proc 2014. [PMCID: PMC4210698 DOI: 10.1186/1753-6561-8-s4-p175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Agha R, Quesada A. Oligopeptides as biomarkers of cyanobacterial subpopulations. Toward an understanding of their biological role. Toxins (Basel) 2014; 6:1929-50. [PMID: 24960202 PMCID: PMC4073138 DOI: 10.3390/toxins6061929] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/09/2014] [Accepted: 06/16/2014] [Indexed: 11/25/2022] Open
Abstract
Cyanobacterial oligopeptides comprise a wide range of bioactive and/or toxic compounds. While current research is strongly focused on exploring new oligopeptide variants and their bioactive properties, the biological role of these compounds remains elusive. Oligopeptides production abilities show a remarkably patchy distribution among conspecific strains. This observation has prompted alternative approaches to unveil their adaptive value, based on the use of cellular oligopeptide compositions as biomarkers of intraspecific subpopulations or chemotypes in freshwater cyanobacteria. Studies addressing the diversity, distribution, and dynamics of chemotypes in natural systems have provided important insights into the structure and ecology of cyanobacterial populations and the adaptive value of oligopeptides. This review presents an overview of the fundamentals of this emerging approach and its most relevant findings, and discusses our current understanding of the role of oligopeptides in the ecology of cyanobacteria.
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Affiliation(s)
- Ramsy Agha
- Departamento de Biología, Universidad Autónoma de Madrid, C/Darwin, 2, Madrid 28049, Spain.
| | - Antonio Quesada
- Departamento de Biología, Universidad Autónoma de Madrid, C/Darwin, 2, Madrid 28049, Spain.
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Dudnik A, Dudler R. Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses. Pathogens 2014; 3:121-48. [PMID: 25437611 PMCID: PMC4235733 DOI: 10.3390/pathogens3010121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/14/2022] Open
Abstract
The Pseudomonas syringae species complex has recently been named the number one plant pathogen, due to its economic and environmental impacts, as well as for its role in scientific research. The bacterium has been repeatedly reported to cause outbreaks on bean, cucumber, stone fruit, kiwi and olive tree, as well as on other crop and non-crop plants. It also serves as a model organism for research on the Type III secretion system (T3SS) and plant-pathogen interactions. While most of the current work on this pathogen is either carried out on one of three model strains found on dicot plants with completely sequenced genomes or on isolates obtained from recent outbreaks, not much is known about strains isolated from grasses (Poaceae). Here, we use comparative genomics in order to identify putative virulence-associated genes and other Poaceae-specific adaptations in several newly available genome sequences of strains isolated from grass species. All strains possess only a small number of known Type III effectors, therefore pointing to the importance of non-Type III secreted virulence factors. The implications of this finding are discussed.
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Affiliation(s)
- Alexey Dudnik
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
| | - Robert Dudler
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
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Metagenomic approaches for exploiting uncultivated bacteria as a resource for novel biosynthetic enzymology. ACTA ACUST UNITED AC 2013; 20:636-47. [PMID: 23706630 DOI: 10.1016/j.chembiol.2013.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/28/2013] [Accepted: 04/16/2013] [Indexed: 12/24/2022]
Abstract
Most biologically active microbial natural products are known from strains that can be isolated and cultivated in the laboratory. However, the genomics era has revealed that cultured bacteria represent a mere fraction of total estimated bacterial biodiversity. With the development of community genomics, termed metagenomics, the uncultivated majority became accessible for functional analysis. Through metagenomic studies, novel biocatalysts and biosynthetic pathways are being discovered at a pace previously not possible using traditional molecular biology techniques. Additionally, the study of uncultivated bacteria has provided valuable insights into previously overlooked biocatalysts from cultured strains. This perspective highlights recent discoveries from metagenomics of uncultivated bacteria and discusses the impact of those findings on the field of natural products.
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Desriac F, Jégou C, Balnois E, Brillet B, Le Chevalier P, Fleury Y. Antimicrobial peptides from marine proteobacteria. Mar Drugs 2013; 11:3632-60. [PMID: 24084784 PMCID: PMC3826127 DOI: 10.3390/md11103632] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 01/03/2023] Open
Abstract
After years of inadequate use and the emergence of multidrug resistant (MDR) strains, the efficiency of "classical" antibiotics has decreased significantly. New drugs to fight MDR strains are urgently needed. Bacteria hold much promise as a source of unusual bioactive metabolites. However, the potential of marine bacteria, except for Actinomycetes and Cyanobacteria, has been largely underexplored. In the past two decades, the structures of several antimicrobial compounds have been elucidated in marine Proteobacteria. Of these compounds, polyketides (PKs), synthesised by condensation of malonyl-coenzyme A and/or acetyl-coenzyme A, and non-ribosomal peptides (NRPs), obtained through the linkage of (unusual) amino acids, have recently generated particular interest. NRPs are good examples of naturally modified peptides. Here, we review and compile the data on the antimicrobial peptides isolated from marine Proteobacteria, especially NRPs.
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Affiliation(s)
- Florie Desriac
- University of Brest, LUBEM EA 3882, SFR 148, Quimper 29000, France.
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From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules. Antonie van Leeuwenhoek 2013; 104:551-67. [PMID: 23982431 DOI: 10.1007/s10482-013-0007-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/14/2013] [Indexed: 01/19/2023]
Abstract
Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development.
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Cyanobacterial toxin degrading bacteria: who are they? BIOMED RESEARCH INTERNATIONAL 2013; 2013:463894. [PMID: 23841072 PMCID: PMC3690202 DOI: 10.1155/2013/463894] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/21/2013] [Indexed: 11/17/2022]
Abstract
Cyanobacteria are ubiquitous in nature and are both beneficial and detrimental to humans. Benefits include being food supplements and producing bioactive compounds, like antimicrobial and anticancer substances, while their detrimental effects are evident by toxin production, causing major ecological problems at the ecosystem level. To date, there are several ways to degrade or transform these toxins by chemical methods, while the biodegradation of these compounds is understudied. In this paper, we present a meta-analysis of the currently available 16S rRNA and mlrA (microcystinase) genes diversity of isolates known to degrade cyanobacterial toxins. The available data revealed that these bacteria belong primarily to the Proteobacteria, with several strains from the sphingomonads, and one from each of the Methylobacillus and Paucibacter genera. Other strains belonged to the genera Arthrobacter, Bacillus, and Lactobacillus. By combining the ecological knowledge on the distribution, abundance, and ecophysiology of the bacteria that cooccur with toxic cyanobacterial blooms and newly developed molecular approaches, it is possible not only to discover more strains with cyanobacterial toxin degradation abilities, but also to reveal the genes associated with the degradation of these toxins.
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Abstract
INTRODUCTION Natural products have long been instrumental for discovering antibiotics, but many pharmaceutical companies abandoned this field and new antibiotics declined. In contrast, microbial resistance to current antibiotics has approached critical levels. AREAS COVERED This article gives historical perspectives by providing background about present-day economic realities and medical needs for antibiotic research, whose pipeline is mostly focused toward older known agents and newer semi-synthetic derivatives. Future research trends and projected technological developments open many innovative opportunities to discover novel antibacterials and find ways to control pathogenic bacteria without conventional antibiotics that provoke resistance. EXPERT OPINION The successful registration of daptomycin, retapamulin and fidaxomicin indicate the re-emergence of natural products has already begun. Semi-synthetic derivatives from other under-explored classes are progressing. More effort is being put into approaches such as total synthesis, discovery of new structural scaffolds for synthesis, alterations of biosynthetic pathways, combinatorial biosynthesis, new screening targets and new resources from which to isolate natural products. A return to successful screening of actinomycetes depends on solving the rate-limiting dereplication obstacle. Long-term solutions need to come from greater exploration of the massive numbers of uncultured microbes. An ultimate solution to the antibiotic-promoted microbial resistance cycle may lie in finding ways to control bacteria by non-lethal means.
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Rosconi F, Davyt D, Martínez V, Martínez M, Abin-Carriquiry JA, Zane H, Butler A, de Souza EM, Fabiano E. Identification and structural characterization of serobactins, a suite of lipopeptide siderophores produced by the grass endophyteHerbaspirillum seropedicae. Environ Microbiol 2013; 15:916-27. [DOI: 10.1111/1462-2920.12075] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 12/11/2022]
Affiliation(s)
| | - Danilo Davyt
- Cátedra de Química Farmacéutica; Facultad de Química; Montevideo; Uruguay
| | - Verónica Martínez
- Cátedra de Química Farmacéutica; Facultad de Química; Montevideo; Uruguay
| | | | | | - Hannah Zane
- Department of Chemistry and Biochemistry; UCSB; Santa Barbara; USA
| | - Alison Butler
- Department of Chemistry and Biochemistry; UCSB; Santa Barbara; USA
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Antimicrobials, drug discovery, and genome mining. Appl Microbiol Biotechnol 2012; 97:969-78. [PMID: 23233204 DOI: 10.1007/s00253-012-4609-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 11/18/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Over the years, antibiotics have provided an effective treatment for a number of microbial diseases. However recently, there has been an increase in resistant microorganisms that have adapted to our current antibiotics. One of the most dangerous pathogens is methicillin-resistant Staphylococcus aureus (MRSA). With the rise in the cases of MRSA and other resistant pathogens such as vancomycin-resistant Staphylococcus aureus, the need for new antibiotics increases every day. Many challenges face the discovery and development of new antibiotics, making it difficult for these new drugs to reach the market, especially since many of the pharmaceutical companies have stopped searching for antibiotics. With the advent of genome sequencing, new antibiotics are being found by the techniques of genome mining, offering hope for the future.
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