1
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Wang X, Wu J, Wang J, Liu D, Bian Q, Zhong J. Total Synthesis of the Sex Pheromone of Clania variegata Snellen and Its Stereoisomers. Int J Mol Sci 2024; 25:4893. [PMID: 38732112 PMCID: PMC11084484 DOI: 10.3390/ijms25094893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
The paulownia bagworm, Clania variegata Snell, is an economically important pest of agriculture and forests. The sex pheromone of this pest and its stereoisomers were synthesized, and two of the stereoisomers were prepared for the first time. Our strategy was efficient and mainly included the ring-opening reaction of (S)-2-methyloxirane, the coupling of chiral sulfonate, the oxidative cleavage of olefin, and Yamaguchi esterification. Moreover, the overall yields of our synthesis were 23-29%, with eight steps in the longest route.
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Affiliation(s)
| | | | | | | | | | - Jiangchun Zhong
- Department of Applied Chemistry, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, China; (X.W.); (J.W.); (J.W.); (D.L.); (Q.B.)
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2
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Liu M, Li S. Nitrile biosynthesis in nature: how and why? Nat Prod Rep 2024; 41:649-671. [PMID: 38193577 DOI: 10.1039/d3np00028a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.
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Affiliation(s)
- Mingyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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3
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Yamaguchi T, Asano Y. Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review. J Biotechnol 2024; 384:20-28. [PMID: 38395363 DOI: 10.1016/j.jbiotec.2024.02.007] [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: 12/24/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.
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Affiliation(s)
- Takuya Yamaguchi
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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4
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Raio A. Diverse roles played by "Pseudomonas fluorescens complex" volatile compounds in their interaction with phytopathogenic microrganims, pests and plants. World J Microbiol Biotechnol 2024; 40:80. [PMID: 38281212 PMCID: PMC10822798 DOI: 10.1007/s11274-023-03873-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
Pseudomonas fluorescens complex consists of environmental and some human opportunistic pathogenic bacteria. It includes mainly beneficial and few phytopathogenic species that are common inhabitants of soil and plant rhizosphere. Many members of the group are in fact known as effective biocontrol agents of plant pathogens and as plant growth promoters and for these attitudes they are of great interest for biotechnological applications. The antagonistic activity of fluorescent Pseudomonas is mainly related to the production of several antibiotic compounds, lytic enzymes, lipopeptides and siderophores. Several volatile organic compounds are also synthesized by fluorescent Pseudomonas including different kinds of molecules that are involved in antagonistic interactions with other organisms and in the induction of systemic responses in plants. This review will mainly focus on the volatile compounds emitted by some members of P. fluorescens complex so far identified, with the aim to highlight the role played by these molecules in the interaction of the bacteria with phytopathogenic micro and macro-organisms and plants.
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Affiliation(s)
- Aida Raio
- National Research Council, Institute for Sustainable Plant Protection (CNR-IPSP), Via Madonna del Piano, 10., 50019, Sesto Fiorentino, FI, Italy.
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5
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Yin F, Qin Z. Long-Chain Molecules with Agro-Bioactivities and Their Applications. Molecules 2023; 28:5880. [PMID: 37570848 PMCID: PMC10421526 DOI: 10.3390/molecules28155880] [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: 07/10/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Long-chain molecules play a vital role in agricultural production and find extensive use as fungicides, insecticides, acaricides, herbicides, and plant growth regulators. This review article specifically addresses the agricultural biological activities and applications of long-chain molecules. The utilization of long-chain molecules in the development of pesticides is an appealing avenue for designing novel pesticide compounds. By offering valuable insights, this article serves as a useful reference for the design of new long-chain molecules for pesticide applications.
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Affiliation(s)
| | - Zhaohai Qin
- College of Science, China Agricultural University, Beijing 100193, China;
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6
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Naik H, Maiti S, Amaresan N. Microbial volatile compounds (MVCs): an eco-friendly tool to manage abiotic stress in plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:91746-91760. [PMID: 37531051 DOI: 10.1007/s11356-023-29010-w] [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: 03/16/2023] [Accepted: 07/23/2023] [Indexed: 08/03/2023]
Abstract
Microbial volatile compounds (MVCs) are produced during the metabolism of microorganisms, are widely distributed in nature, and have significant applications in various fields. To date, several MVCs have been identified. Microbial groups such as bacteria and fungi release many organic and inorganic volatile compounds. They are typically small odorous compounds with low molecular masses, low boiling points, and lipophilic moieties with high vapor pressures. The physicochemical properties of MVCs help them to diffuse more readily in nature and allow dispersal to a more profound distance than other microbial non-volatile metabolites. In natural environments, plants communicate with several microorganisms and respond differently to MVCs. Here, we review the following points: (1) MVCs produced by various microbes including bacteria, fungi, viruses, yeasts, and algae; (2) How MVCs are effective, simple, efficient, and can modulate plant growth and developmental processes; and (3) how MVCs improve photosynthesis and increase plant resistance to various abiotic stressors.
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Affiliation(s)
- Hetvi Naik
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, Gujarat, 394 350, India
| | - Saborni Maiti
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Natarajan Amaresan
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, Gujarat, 394 350, India.
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7
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Koteska D, Marter P, Huang S, Pradella S, Petersen J, Schulz S. Volatiles of the Apicomplexan Alga Chromera velia and Associated Bacteria. Chembiochem 2023; 24:e202200530. [PMID: 36416092 PMCID: PMC10107727 DOI: 10.1002/cbic.202200530] [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: 09/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
Volatiles released by the apicomplexan alga Chromera velia CCAP1602/1 and their associated bacteria have been investigated. A metagenome analysis allowed the identification of the most abundant heterotrophic bacteria of the phycosphere, but the isolation of additional strains showed that metagenomics underestimated the complexity of the algal microbiome, However, a culture-independent approach revealed the presence of a planctomycete that likely represents a novel bacterial family. We analysed algal and bacterial volatiles by open-system-stripping analysis (OSSA) on Tenax TA desorption tubes, followed by thermodesorption, cryofocusing and GC-MS-analysis. The analyses of the alga and the abundant bacterial strains Sphingopyxis litoris A01A-101, Algihabitans albus A01A-324, "Coraliitalea coralii" A01A-333 and Litoreibacter sp. A01A-347 revealed sulfur- and nitrogen-containing compounds, ketones, alcohols, aldehydes, aromatic compounds, amides and one lactone, as well as the typical algal products, apocarotenoids. The compounds were identified by gas chromatographic retention indices, comparison of mass spectra and syntheses of reference compounds. A major algal metabolite was 3,4,4-trimethylcyclopent-2-en-1-one, an apocarotenoid indicating the presence of carotenoids related to capsanthin, not reported from algae so far. A low overlap in volatiles bouquets between C. velia and the bacteria was found, and the xenic algal culture almost exclusively released algal components.
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Affiliation(s)
- Diana Koteska
- Institut für Organische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Pia Marter
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Sixing Huang
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Silke Pradella
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Stefan Schulz
- Institut für Organische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
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8
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Carvalho LDC, Henry R, McCullagh JSO, Pollard AM. Unlocking the organic residues preserved in the corrosion from the Pewsey Hoard vessels. Sci Rep 2022; 12:21284. [PMID: 36494389 PMCID: PMC9734644 DOI: 10.1038/s41598-022-24400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
The characterization of archaeological metal corrosion has traditionally been limited to the identification of inorganic compounds usually by X-ray diffraction (XRD), thought to result from the interaction between the metal object and the deposition environment. The discovery of a hoard of Late Roman copper-alloy vessels in Wiltshire, UK presented an unique opportunity to adopt a multi-analytical approach to characterize corrosion combining XRD with Fourier-transform infrared (FTIR) and gas chromatography with quadrupole time-of-flight mass spectrometry using a thermal separation probe (GC-QTOF-MS with TSP). This approach revealed organic compounds potentially historical preserved within crystalline inorganic matrices. It has been known for some time that ceramics can harbour organic residues, which provide crucial evidence about the use of these vessels in the past. Our results confirms that similar residues appear to survive in metal corrosion thus extending the potential for identification of biomaterials used in the past.
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Affiliation(s)
- Luciana da Costa Carvalho
- grid.4991.50000 0004 1936 8948School of Archaeology, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Richard Henry
- grid.9435.b0000 0004 0457 9566Department of Archaeology, University of Reading, Reading, UK
| | - James S. O. McCullagh
- grid.4991.50000 0004 1936 8948Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - A. Mark Pollard
- grid.4991.50000 0004 1936 8948School of Archaeology, University of Oxford, Oxford, UK
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9
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Yan S, Zeng M, Wang H, Zhang H. Micromonospora: A Prolific Source of Bioactive Secondary Metabolites with Therapeutic Potential. J Med Chem 2022; 65:8735-8771. [PMID: 35766919 DOI: 10.1021/acs.jmedchem.2c00626] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Micromonospora, one of the most important actinomycetes genera, is well-known as the treasure trove of bioactive secondary metabolites (SMs). Herein, together with an in-depth genomic analysis of the reported Micromonospora strains, all SMs from this genus are comprehensively summarized, containing structural features, bioactive properties, and mode of actions as well as their biosynthetic and chemical synthesis pathways. The perspective enables a detailed view of Micromonospora-derived SMs, which will enrich the chemical diversity of natural products and inspire new drug discovery in the pharmaceutical industry.
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Affiliation(s)
- Suqi Yan
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Mingyuan Zeng
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
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10
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Scotti C, Barlow JW. Natural Products Containing the Nitrile Functional Group and Their Biological Activities. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221099973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The importance of nitriles as a key class of chemicals with applications across the sciences is widely appreciated. The natural world is an underappreciated source of chemically diverse nitriles. With this in mind, this review describes novel nitrile-containing molecules isolated from natural sources from 1998 to 2021, as well as a discussion of the biological activity of these compounds. This study gathers 192 molecules from varied origins across the plant, animal, and microbial worlds. Their biological activity is extremely diverse, with many potential medicinal applications.
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Affiliation(s)
- Camille Scotti
- Ecole Nationale Supérieure de Chimie de Mulhouse, Université de Haute Alsace, Mulhouse, France
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - James W. Barlow
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
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11
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Chironomus ramosus Larval Microbiome Composition Provides Evidence for the Presence of Detoxifying Enzymes. Microorganisms 2021; 9:microorganisms9081571. [PMID: 34442650 PMCID: PMC8398091 DOI: 10.3390/microorganisms9081571] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Chironomids (Diptera; Chironomidae) are aquatic insects that are abundant in freshwater. We aimed to study the endogenous microbiota composition of Chironomus ramosus larvae that were sampled from the Mutha River and a laboratory culture in India. Furthermore, we performed a metagenomic analysis of the larval microbiome, sampled from the Mutha River. Significant differences were found between the bacterial community composition of C. ramosus larvae that were sampled from the Mutha River and the laboratory culture. A total of 54.7% of the amplicon sequence variants (ASVs) that were identified in the larvae from the Mutha River were unique, compared to only 12.9% of unique ASVs that were identified from the laboratory-reared larvae. The four most abundant phyla across all samples were: Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes, while the nine most abundant genera were: Aeromonas, Alkanindiges, Breznakia, Cetobacterium, Chryseobacterium, Desulfovibrio, Dysgonomonas, Thiothrix, and Vibrio. Moreover, in the metagenomic analysis, we detected bacterial genes and bacterial pathways that demonstrated the ability to degrade different toxic compounds, detoxify metal, and confer resistance to antibiotics and UV radiation, amongst other functions. The results illuminate the fact that there are detoxifying enzymes in the C. ramosus larval microbiome that possibly play a role in protecting the insect in polluted environments.
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12
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Xiao J, Guo F, Li Y, Li F, Li Q, Tang ZL. Iodine Promoted Conversion of Esters to Nitriles and Ketones under Metal-Free Conditions. J Org Chem 2021; 86:2028-2035. [PMID: 33397102 DOI: 10.1021/acs.joc.0c02794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a novel strategy to prepare valuable nitriles and ketones through the conversion of esters under metal-free conditions. By using the I2/PCl3 system, various substrates including aliphatic and aromatic esters could react with acetonitrile and arenes to afford the desired products in good to excellent yields. This method is compatible with a number of functional groups and provides a simple and practical approach for the synthesis of nitrile compounds and aryl ketones.
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Affiliation(s)
- Jing Xiao
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Fengzhe Guo
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yinfeng Li
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Fangshao Li
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Qiang Li
- Institution of Functional Organic Molecules and Materials, School of Chemistry and Chemical Engineering, Liaocheng University, No. 1, Hunan Street, Liaocheng, Shandong 252059, China
| | - Zi-Long Tang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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13
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Netzker T, Shepherdson EMF, Zambri MP, Elliot MA. Bacterial Volatile Compounds: Functions in Communication, Cooperation, and Competition. Annu Rev Microbiol 2020; 74:409-430. [PMID: 32667838 DOI: 10.1146/annurev-micro-011320-015542] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria produce a multitude of volatile compounds. While the biological functions of these deceptively simple molecules are unknown in many cases, for compounds that have been characterized, it is clear that they serve impressively diverse purposes. Here, we highlight recent studies that are uncovering the volatile repertoire of bacteria, and the functional relevance and impact of these molecules. We present work showing the ability of volatile compounds to modulate nutrient availability in the environment; alter the growth, development, and motility of bacteria and fungi; influence protist and arthropod behavior; and impact plant and animal health. We further discuss the benefits associated with using volatile compounds for communication and competition, alongside the challenges of studying these molecules and their functional roles. Finally, we address the opportunities these compounds present from commercial, clinical, and agricultural perspectives.
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Affiliation(s)
- Tina Netzker
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada; , , ,
| | - Evan M F Shepherdson
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada; , , ,
| | - Matthew P Zambri
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada; , , ,
| | - Marie A Elliot
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada; , , ,
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14
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Sala S, Fromont J, Gomez O, Vuong D, Lacey E, Flematti GR. Albanitriles A-G: Antiprotozoal Polyacetylene Nitriles from a Mycale Marine Sponge. JOURNAL OF NATURAL PRODUCTS 2019; 82:3450-3455. [PMID: 31833368 DOI: 10.1021/acs.jnatprod.9b00840] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Seven new nitrile-bearing polyacetylenes, named albanitriles A-G, were isolated from a marine sponge of the Mycale genus (Order: Poecilosclerida, Family: Mycalidae) collected near Albany, Western Australia. Structural elucidation was achieved using a combination of high-resolution mass spectrometry and ultraviolet/visible, infrared, and nuclear magnetic resonance spectroscopy. The compounds were found to possess moderate activity against Giardia duodenalis when compared to a metronidazole positive control.
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Affiliation(s)
- Samuele Sala
- School of Molecular Sciences , The University of Western Australia , Crawley , WA 6009 , Australia
| | - Jane Fromont
- Western Australian Museum , Welshpool , WA 6106 , Australia
| | - Oliver Gomez
- Western Australian Museum , Welshpool , WA 6106 , Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd. , Smithfield , NSW 2164 , Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd. , Smithfield , NSW 2164 , Australia
| | - Gavin R Flematti
- School of Molecular Sciences , The University of Western Australia , Crawley , WA 6009 , Australia
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15
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Vidal P, Martinez M, Hernandez C, Adhikari AR, Mao Y, Materon L, Lozano K. Development of chromatic biosensor for quick bacterial detection based on polyvinyl butyrate-polydiacetylene nonwoven fiber composites. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.109284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Vanoye L, Hammoud A, Gérard H, Barnes A, Philippe R, Fongarland P, de Bellefon C, Favre-Réguillon A. Direct Synthesis of Nitriles from Carboxylic Acids Using Indium-Catalyzed Transnitrilation: Mechanistic and Kinetic Study. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Laurent Vanoye
- Université Lyon, Laboratoire de Génie des Procédés Catalytiques UMR 5285, CNRS-CPE Lyon-UCBL, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Ahmad Hammoud
- Université Lyon, Laboratoire de Génie des Procédés Catalytiques UMR 5285, CNRS-CPE Lyon-UCBL, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Hélène Gérard
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, F-75252 Paris, France
| | - Alexandra Barnes
- Université Lyon, Laboratoire de Génie des Procédés Catalytiques UMR 5285, CNRS-CPE Lyon-UCBL, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Régis Philippe
- Université Lyon, Laboratoire de Génie des Procédés Catalytiques UMR 5285, CNRS-CPE Lyon-UCBL, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Pascal Fongarland
- Université Lyon, Laboratoire de Génie des Procédés Catalytiques UMR 5285, CNRS-CPE Lyon-UCBL, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Claude de Bellefon
- Université Lyon, Laboratoire de Génie des Procédés Catalytiques UMR 5285, CNRS-CPE Lyon-UCBL, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Alain Favre-Réguillon
- Université Lyon, Laboratoire de Génie des Procédés Catalytiques UMR 5285, CNRS-CPE Lyon-UCBL, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
- Conservatoire National des Arts et Métiers, EPN 7, 2 rue Conté, 75003 Paris, France
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17
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Bruns H, Herrmann J, Müller R, Wang H, Wagner Döbler I, Schulz S. Oxygenated N-Acyl Alanine Methyl Esters (NAMEs) from the Marine Bacterium Roseovarius tolerans EL-164. JOURNAL OF NATURAL PRODUCTS 2018; 81:131-139. [PMID: 29261310 DOI: 10.1021/acs.jnatprod.7b00757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The marine bacterium Roseovarius tolerans EL-164 (Rhodobacteraceae) can produce unique N-acylalanine methyl esters (NAMEs) besides strucutrally related N-acylhomoserine lactones (AHLs), bacterial signaling compounds widespread in the Rhodobacteraceae. The structures of two unprecedented NAMEs carrying a rare terminally oxidized acyl chain are reported here. The compounds (Z)-N-16-hydroxyhexadec-9-enoyl-l-alanine methyl ester (Z9-16-OH-C16:1-NAME, 3) and (Z)-N-15-carboxypentadec-9-enoyl-l-alanine methyl ester (16COOH-C16:1-NAME, 4) were isolated, and the structures were determined by NMR and MS experiments. Both compounds were synthesized to prove assignments and to test their biological activity. Finally, non-natural, structurally related Z9-3-OH-C16:1-NAME (18) was synthesized to investigate the mass spectroscopy of structurally related NAMEs. Compound 3 showed moderate antibacterial activity against microorganisms such as Bacillus, Streptococcus, Micrococcus, or Mucor strains. In contrast to AHLs, quorum-sensing or quorum-quenching activity was not observed.
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Affiliation(s)
- Hilke Bruns
- Institute of Organic Chemistry, Technische Universität Braunschweig , Hagenring 30, 38106 Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Hui Wang
- Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Irene Wagner Döbler
- Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig , Hagenring 30, 38106 Braunschweig, Germany
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18
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Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, Frey JE, Robinson MD, Wollscheid B, Ahrens CH. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Res 2017; 27:2083-2095. [PMID: 29141959 PMCID: PMC5741054 DOI: 10.1101/gr.218255.116] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 10/25/2017] [Indexed: 12/18/2022]
Abstract
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensive Bartonella henselae proteomics data set against such an iPtgxDB allowed us to unambiguously identify novel ORFs uniquely predicted by each resource, including lipoproteins, differentially expressed and membrane-localized proteins, novel start sites and wrongly annotated pseudogenes. Most novelties were confirmed by targeted, parallel reaction monitoring mass spectrometry, including unique ORFs and single amino acid variations (SAAVs) identified in a re-sequenced laboratory strain that are not present in its reference genome. We demonstrate the general applicability of our strategy for genomes with varying GC content and distinct taxonomic origin. We release iPtgxDBs for B. henselae, Bradyrhizobium diazoefficiens and Escherichia coli and the software to generate both proteogenomics search databases and integrated annotation files that can be viewed in a genome browser for any prokaryote.
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Affiliation(s)
- Ulrich Omasits
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland.,Department of Health Sciences and Technology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Damianos Melidis
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Marc Bourqui
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Olga Nikolayeva
- Institute for Molecular Life Sciences & SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Andrea Patrignani
- Functional Genomics Center Zurich, ETH & UZH Zurich, CH-8057 Zurich, Switzerland
| | | | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Mark D Robinson
- Institute for Molecular Life Sciences & SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
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