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Regolo L, Giampieri F, Battino M, Armas Diaz Y, Mezzetti B, Elexpuru-Zabaleta M, Mazas C, Tutusaus K, Mazzoni L. From by-products to new application opportunities: the enhancement of the leaves deriving from the fruit plants for new potential healthy products. Front Nutr 2024; 11:1083759. [PMID: 38895662 PMCID: PMC11184148 DOI: 10.3389/fnut.2024.1083759] [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: 10/29/2022] [Accepted: 05/03/2024] [Indexed: 06/21/2024] Open
Abstract
In the last decades, the world population and demand for any kind of product have grown exponentially. The rhythm of production to satisfy the request of the population has become unsustainable and the concept of the linear economy, introduced after the Industrial Revolution, has been replaced by a new economic approach, the circular economy. In this new economic model, the concept of "the end of life" is substituted by the concept of restoration, providing a new life to many industrial wastes. Leaves are a by-product of several agricultural cultivations. In recent years, the scientific interest regarding leaf biochemical composition grew, recording that plant leaves may be considered an alternative source of bioactive substances. Plant leaves' main bioactive compounds are similar to those in fruits, i.e., phenolic acids and esters, flavonols, anthocyanins, and procyanidins. Bioactive compounds can positively influence human health; in fact, it is no coincidence that the leaves were used by our ancestors as a natural remedy for various pathological conditions. Therefore, leaves can be exploited to manufacture many products in food (e.g., being incorporated in food formulations as natural antioxidants, or used to create edible coatings or films for food packaging), cosmetic and pharmaceutical industries (e.g., promising ingredients in anti-aging cosmetics such as oils, serums, dermatological creams, bath gels, and other products). This review focuses on the leaves' main bioactive compounds and their beneficial health effects, indicating their applications until today to enhance them as a harvesting by-product and highlight their possible reuse for new potential healthy products.
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Affiliation(s)
- Lucia Regolo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali – Università Politecnica delle Marche, Ancona, Italy
| | - Francesca Giampieri
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Santander, Spain
- Department of Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Maurizio Battino
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Santander, Spain
- Department of Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
- International Joint Research Laboratory of Intelligent Agriculture and Agri-Product Processing, Jiangsu University, Zhenjiang, China
| | - Yasmany Armas Diaz
- Department of Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Bruno Mezzetti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali – Università Politecnica delle Marche, Ancona, Italy
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Santander, Spain
| | - Maria Elexpuru-Zabaleta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Santander, Spain
| | - Cristina Mazas
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Santander, Spain
- Universidad Internacional Iberoamericana, Campeche, Mexico
| | - Kilian Tutusaus
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Santander, Spain
- Research Center for Foods, Nutritional Biochemistry and Health, Universidade Internacional do Cuanza, Cuito, Angola
| | - Luca Mazzoni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali – Università Politecnica delle Marche, Ancona, Italy
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González Y, Martínez-Soto D, de Los Santos-Villalobos S, Garcia-Marin LE, Juarez-Moreno K, Castro-Longoria E. Potential application of a fungal co-culture crude extract for the conservation of post-harvest fruits. Braz J Microbiol 2024; 55:1679-1691. [PMID: 38393617 PMCID: PMC11153422 DOI: 10.1007/s42770-024-01274-5] [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: 11/13/2023] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Fungal plant pathogens are responsible for serious losses in many economically important crop species worldwide. Due to the use of fungicides and the fungi genome plasticity, multi-drug resistant strains are emerging as a new generation of pathogens, causing an expansive range of superficial and systemic plant infections, or new opportunistic fungal pathogens for humans. The group of antagonistic fungi Trichoderma spp. has been widely used to enhance plant growth and for the control of different pathogens affecting crops. Although Neurospora crassa is not a mycoparasitic fungus, its secretion of secondary metabolites with antimicrobial activity has been described. In this work, the effect of crude extract of the monoculture of Trichoderma asperellum T8a or the co-culture with N. crassa as an inhibitory treatment against the fungal pathogens Botrytis cinerea and Fusarium solani was evaluated. The findings demonstrate that the secondary metabolites contained in the T. asperellum crude extract have a clear fungistatic activity against B. cinerea and F. solani. Interestingly, this fungistatic activity highly increases when T. asperellum is co-cultivated with the non-pathogenic fungus N. crassa. Moreover, the co-culture crude extract also showed antifungal activity on post-harvest fruits, and no toxic effects on Murine fibroblast L929 (CCL-1) and murine macrophages RAW 264.7 (TIB-71) were observed. All these results together are solid evidence of the potential of the co-culture crude extract of T. asperellum and N. crassa, as an antifungal agent against phytopathogenic fungi, or post-harvest fruits during the transportation or commercialization time.
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Affiliation(s)
- Yael González
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - Domingo Martínez-Soto
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | | | - Luis E Garcia-Marin
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - Karla Juarez-Moreno
- Center for Applied Physics and Advanced Technology, UNAM. Blvd. Juriquilla 3001, Juriquilla La Mesa, 76230, Juriquilla, Queretaro, Mexico
| | - Ernestina Castro-Longoria
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico.
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Amaral DT, Bonatelli IAS, Romeiro-Brito M, Telhe MC, Moraes EM, Zappi DC, Taylor NP, Franco FF. Comparative transcriptome analysis reveals lineage- and environment-specific adaptations in cacti from the Brazilian Atlantic Forest. PLANTA 2024; 260:4. [PMID: 38775846 DOI: 10.1007/s00425-024-04442-x] [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: 01/24/2024] [Accepted: 05/14/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION Natural selection influenced adaptive divergence between Cereus fernambucensis and Cereus insularis, revealing key genes governing abiotic stress responses and supporting neoteny in C. insularis. Uncovering the molecular mechanisms driving adaptive divergence in traits related to habitat adaptation remains a central challenge. In this study, we focused on the cactus clade, which includes Cereus sericifer F.Ritter, Cereus fernambucensis Lem., and Cereus insularis Hemsley. These allopatric species inhabit distinct relatively drier regions within the Brazilian Atlantic Forest, each facing unique abiotic conditions. We leveraged whole transcriptome data and abiotic variables datasets to explore lineage-specific and environment-specific adaptations in these species. Employing comparative phylogenetic methods, we identified genes under positive selection (PSG) and examined their association with non-synonymous genetic variants and abiotic attributes through a PhyloGWAS approach. Our analysis unveiled signatures of selection in all studied lineages, with C. fernambucensis northern populations and C. insularis showing the most PSGs. These PSGs predominantly govern abiotic stress regulation, encompassing heat tolerance, UV stress response, and soil salinity adaptation. Our exclusive observation of gene expression tied to early developmental stages in C. insularis supports the hypothesis of neoteny in this species. We also identified genes associated with abiotic variables in independent lineages, suggesting their role as environmental filters on genetic diversity. Overall, our findings suggest that natural selection played a pivotal role in the geographic range of these species in response to environmental and biogeographic transitions.
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Affiliation(s)
- Danilo T Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Monique Romeiro-Brito
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Milena C Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Daniela Cristina Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), Brasília, Brazil
| | - Nigel Paul Taylor
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Fernando F Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil.
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Boruta T, Ścigaczewska A, Bizukojć M. Investigating the Stirred Tank Bioreactor Co-Cultures of the Secondary Metabolite Producers Streptomyces noursei and Penicillium rubens. Biomolecules 2023; 13:1748. [PMID: 38136619 PMCID: PMC10742013 DOI: 10.3390/biom13121748] [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: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The stirred tank bioreactor co-cultures of the filamentous fungus Penicillium rubens and actinomycete Streptomyces noursei were studied with regard to secondary metabolite (SM) production, sugar consumption, and dissolved oxygen levels. In addition to the quantitative analysis of penicillin G and nystatin A1, the broad repertoire of 22 putatively identified products was semi-quantitatively evaluated with the use of UPLC-MS. Three co-cultivation variants differing with respect to the co-culture initiation method (i.e., the simultaneous inoculation of P. rubens and S. noursei and the 24 or 48 h inoculation delay of S. noursei relative to P. rubens) were investigated. All the co-cultures were carried out in parallel with the corresponding monoculture controls. Even though S. noursei showed the tendency to outperform P. rubens and inhibit the production of fungal secondary metabolites, the approach of simultaneous inoculation was effective in terms of enhancing the production of some S. noursei SMs, namely desferrioxamine E, deshydroxynocardamine, and argvalin. S. noursei displayed the capability of adaptation and SM production even after being inoculated into the 24 or 48 h culture of P. rubens. Interestingly, S. noursei turned out to be more efficient in terms of secondary metabolite production when its inoculation time relative to P. rubens was delayed by 48 h rather than by 24 h. The study demonstrated that the prolongation of inoculation delays can be beneficial for production-related performance in some co-culture systems.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005 Łódź, Poland; (A.Ś.); (M.B.)
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Wu X, Yang Y, Zhang H. Microbial fortification of pharmacological metabolites in medicinal plants. Comput Struct Biotechnol J 2023; 21:5066-5072. [PMID: 37867972 PMCID: PMC10589376 DOI: 10.1016/j.csbj.2023.10.024] [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: 07/08/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023] Open
Abstract
Medicinal plants are rich in secondary metabolites with beneficial pharmacological effects. The production of plant secondary metabolites is subjected to the influences by environmental factors including the plant-associated microbiome, which is crucial to the host's fitness and survival. As a result, research interests are increasing in exploiting microbial capacities for enhancing plant production of pharmacological metabolites. A growing body of recent research provides accumulating evidence in support of developing microbe-based tools for achieving this objective. This mini review presents brief summaries of recent studies on medicinal plants that demonstrate microbe-augmented production of pharmacological terpenoids, polyphenols, and alkaloids, followed by discussions on some key questions beyond the promising observations. Explicit molecular insights into the underlying mechanisms will enhance microbial applications for metabolic fortification in medicinal plants.
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Affiliation(s)
- Xiaoxuan Wu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Yang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- Nanchang Institute of Industrial Innovation, Chinese Academy of Sciences, Nanchang 330224, China
- Jiangxi Center for Innovation and Incubation of Industrial Technologies, Chinese Academy of Sciences, Nanchang 330200, China
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Dongmo KJJ, Tali MBT, Fongang YSF, Taguimjeu PLKT, Kagho DUK, Bitchagno GT, Lenta BN, Boyom FF, Sewald N, Ngouela SA. In vitro antiplasmodial activity and toxicological profile of extracts, fractions and chemical constituents of leaves and stem bark from Dacryodes edulis (Burseraceae). BMC Complement Med Ther 2023; 23:211. [PMID: 37370061 DOI: 10.1186/s12906-023-03957-2] [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: 10/21/2022] [Accepted: 04/12/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Dacryodes edulis is a plant that belongs to the Burseraceae family. It is widely used traditionally alone or in association with other plants in Cameroonian folk medicine to cure wounds, fever, headaches, and malaria. The aim of this work was to investigate the leaves and stem bark of D. edulis with an emphasis on the antiplasmodial and cytotoxic effects of extracts, fractions, and isolated compounds. METHODS Extracts, fractions, and some isolated compounds were subjected to antiplasmodial activity screening in vitro against chloroquine-sensitive 3D7 and multidrug resistant Dd2 strains of Plasmodium falciparum using a SyBr Green fluorescence-based assay. The cytotoxicity of active extracts, fractions, and compounds was tested against mammalian Raw cell lines using an in vitro resazurin-based viability assay. The structures of the compounds were determined based on their NMR and MS data. The in vivo toxicity using female BALB/c mice was performed on the most active extract according to the protocol of OECD (2002), guideline 423. RESULTS The hydroethanolic extract from the leaves of D. edulis displayed good antiplasmodial activity with IC50 values of 3.10 and 3.56 μg/mL respectively on sensitive (3D7) and multiresistant (Dd2) strains of P. falciparum. Of the sixteen compounds isolated, 3,3',4-tri-O-methylellagic acid (4) exhibited the highest antiplasmodial activity against PfDd2 strains with an IC50 value of 0.63 μg/mL. All extracts, fractions, and isolated compounds demonstrated no cytotoxicity against Raw cell lines with CC50 > 250 μg/mL. In addition, the most active extract on both strains of P. falciparum was nontoxic in vivo, with a LD50 greater than 2000 and 5000 mg/kg. A phytochemical investigation of the stem bark and leaves of D. edulis afforded sixteen compounds, including two xanthones (1-2), three ellagic acid derivatives (3-5), one phenolic compound (6), one depside (7), one triglyceride (8), one auranthiamide acetate (9), one gallic acid derivative (10), four triterpenoids (11-14), and two steroids (15-16). Compounds 1, 2, 5, 7, 8, and 9 were herein reported for the first time from the Burseraceae family. CONCLUSION This work highlights the good in vitro antiplasmodial potency of the hydroethanolic extract of the leaves of this plant and that of two isolated constituents (3,3',4-tri-O-methylellagic acid and ethylgallate) from the plant. These biological results support the use of D. edulis in traditional medicine against malaria.
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Affiliation(s)
- Kevine Johane Jumeta Dongmo
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Mariscal Brice Tchatat Tali
- Antimicrobial and Biocontrol Agents Unit, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | | | | | - Donald Ulrich Kenou Kagho
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | | | - Bruno Ndjakou Lenta
- Department of Chemistry, Higher Teacher Training College, University of Yaoundé I, P.O. Box 47, Yaoundé, Cameroon
| | - Fabrice Fekam Boyom
- Antimicrobial and Biocontrol Agents Unit, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Norbert Sewald
- Department of Chemistry, Bielefeld University, P.O. Box 100131, 33501, Bielefeld, Germany
| | - Silvère Augustin Ngouela
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon.
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De la Cruz-Rodríguez Y, Adrián-López J, Martínez-López J, Neri-Márquez BI, García-Pineda E, Alvarado-Gutiérrez A, Fraire-Velázquez S. Biosynthetic Gene Clusters in Sequenced Genomes of Four Contrasting Rhizobacteria in Phytopathogen Inhibition and Interaction with Capsicum annuum Roots. Microbiol Spectr 2023; 11:e0307222. [PMID: 37222590 PMCID: PMC10269915 DOI: 10.1128/spectrum.03072-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Through screening of rhizobacteria, species that effectively suppress phytopathogens and/or promote plant growth are found. Genome sequencing is a crucial step in obtaining a complete characterization of microorganisms for biotechnological applications. This study aimed to sequence the genomes of four rhizobacteria that differ in their inhibition of four root pathogens and in their interaction with chili pepper roots to identify the species and analyze differences in the biosynthetic gene clusters (BGCs) for antibiotic metabolites and to determine possible phenotype-genotype correlations. Results from sequencing and genome alignment identified two bacteria as Paenibacillus polymyxa, one as Kocuria polaris, and one that was previously sequenced as Bacillus velezensis. Analysis with antiSMASH and PRISM tools showed that B. velezensis 2A-2B, the strain with the best performance of referred characteristics, had 13 BGCs, including those related to surfactin, fengycin, and macrolactin, not shared with the other bacteria, whereas P. polymyxa 2A-2A and 3A-25AI, with up to 31 BGCs, showed lower pathogen inhibition and plant hostility; K. polaris showed the least antifungal capacity. P. polymyxa and B. velezensis had the highest number of BGCs for nonribosomal peptides and polyketides. In conclusion, the 13 BGCs in the genome of B. velezensis 2A-2B that were not present in the other bacteria could explain its effective antifungal capacity and could also contribute to its friendly interaction with chili pepper roots. The high number of other BGCs for nonribosomal peptides and polyketide shared by the four bacteria contributed much less to phenotypic differences. IMPORTANCE To advance the characterization of a microorganism as a biocontrol agent against phytopathogens, it is highly recommended to analyze the potential of the profile of secondary metabolites as antibiotics that it produces to counteract pathogens. Some specific metabolites have positive impacts in plants. By analyzing sequenced genomes with bioinformatic tools, such as antiSMASH and PRISM, outstanding bacterial strains with high potential to inhibit phytopathogens and/or promote plant growth can be quickly selected to confirm and expand our knowledge of BGCs of great value in phytopathology.
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Affiliation(s)
- Yumiko De la Cruz-Rodríguez
- Lab. Biología Integrativa de Plantas y Microorganismos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Jesús Adrián-López
- Lab. MicroRNAs y Cáncer, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Jazmín Martínez-López
- Lab. Biología Integrativa de Plantas y Microorganismos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Bibiana Itzel Neri-Márquez
- Lab. Biología Integrativa de Plantas y Microorganismos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | | | - Alejandro Alvarado-Gutiérrez
- Lab. Biología Integrativa de Plantas y Microorganismos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Saúl Fraire-Velázquez
- Lab. Biología Integrativa de Plantas y Microorganismos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
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Atoum D, Fernandez-Pastor I, Young L, Edrada-Ebel R. Use of Multivariate Analysis to Unravel the Differences between Two Chamomile Varieties and Their Anticancer and Antioxidant Activities. PLANTS (BASEL, SWITZERLAND) 2023; 12:2297. [PMID: 37375922 DOI: 10.3390/plants12122297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Plants from the Asteraceae family were commonly used to treat various diseases. The metabolomic profile of this family consisted of bioactive flavonoids and other phenolics. Chamomile is a member of the Asteraceae family. Jordanian and European chamomile are two varieties of Matricaria chamomilla (German chamomile), which were grown under different environmental conditions, were studied. Many examples of plant varieties with significant distinction in the secondary metabolite they afford have been described in the literature. Multivariate statistical analysis was employed to measure the depth of this variation in two chamomile varieties. METHODS From both types, crude extracts were prepared using solvents of different polarities and tested for their biological activity. The semipolar fraction of the European variety showed anticancer and antioxidant activity. Meanwhile, the semipolar fraction of the Jordanian type exhibited only antioxidant activity. Both extracts were fractionated, and then the biological activity was again assayed. RESULTS European and Jordanian chamomile fractions produced dicaffeoylquinic acid isomers exhibiting antioxidant capability. Additionally, Z-glucoferulic acid was produced from the European chamomile, demonstrating antioxidant activity. The European samples afforded two major compounds, chrysosplenetin and apigenin, that displayed anticancer activity. CONCLUSIONS Different environmental conditions between Jordanian and European chamomile affected the type of isolated compounds. Structure elucidation was performed with HPLC-MS coupled with dereplication techniques and 2D NMR experiments.
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Affiliation(s)
- Dana Atoum
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Ignacio Fernandez-Pastor
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Louise Young
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
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Yu W, Pei R, Zhou J, Zeng B, Tu Y, He B. Molecular regulation of fungal secondary metabolism. World J Microbiol Biotechnol 2023; 39:204. [PMID: 37209190 DOI: 10.1007/s11274-023-03649-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
Many bioactive secondary metabolites synthesized by fungi have important applications in many fields, such as agriculture, food, medical and others. The biosynthesis of secondary metabolites is a complex process involving a variety of enzymes and transcription factors, which are regulated at different levels. In this review, we describe our current understanding on molecular regulation of fungal secondary metabolite biosynthesis, such as environmental signal regulation, transcriptional regulation and epigenetic regulation. The effects of transcription factors on the secondary metabolites produced by fungi were mainly introduced. It was also discussed that new secondary metabolites could be found in fungi and the production of secondary metabolites could be improved. We also highlight the importance of understanding the molecular regulation mechanisms to activate silent secondary metabolites and uncover their physiological and ecological functions. By comprehensively understanding the regulatory mechanisms involved in secondary metabolite biosynthesis, we can develop strategies to improve the production of these compounds and maximize their potential benefits.
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Affiliation(s)
- Wenbin Yu
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Rongqiang Pei
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Jingyi Zhou
- Zhanjiang Preschool Education College, Zhanjiang, 524084, Guangdong, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518000, Guangdong, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China.
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China.
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Subirats J, Sharpe H, Santoro D, Topp E. Modeling Antibiotic Concentrations in the Vicinity of Antibiotic-Producing Bacteria at the Micron Scale. Appl Environ Microbiol 2023; 89:e0026123. [PMID: 36975795 PMCID: PMC10132100 DOI: 10.1128/aem.00261-23] [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: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
It is generally thought that antibiotics confer upon the producing bacteria the ability to inhibit or kill neighboring microorganisms, thereby providing the producer with a significant competitive advantage. Were this to be the case, the concentrations of emitted antibiotics in the vicinity of producing bacteria might be expected to fall within the ranges of MICs that are documented for a number of bacteria. Furthermore, antibiotic concentrations that bacteria are punctually or chronically exposed to in environments harboring antibiotic-producing bacteria might fall within the range of minimum selective concentrations (MSCs) that confer a fitness advantage to bacteria carrying acquired antibiotic resistance genes. There are, to our knowledge, no available in situ measured antibiotic concentrations in the biofilm environments that bacteria typically live in. The objective of the present study was to use a modeling approach to estimate the antibiotic concentrations that might accumulate in the vicinity of bacteria that are producing an antibiotic. Fick's law was used to model antibiotic diffusion using a series of key assumptions. The concentrations of antibiotics within a few microns of single producing cells could not reach MSC (8 to 16 μg/L) or MIC (500 μg/L) values, whereas the concentrations around aggregates of a thousand cells could reach these concentrations. The model outputs suggest that single cells could not produce an antibiotic at a rate sufficient to achieve a bioactive concentration in the vicinity, whereas a group of cells, each producing the antibiotic, could do so. IMPORTANCE It is generally assumed that a natural function of antibiotics is to provide their producers with a competitive advantage. If this were the case, sensitive organisms in proximity to producers would be exposed to inhibitory concentrations. The widespread detection of antibiotic resistance genes in pristine environments suggests that bacteria are indeed exposed to inhibitory antibiotic concentrations in the natural world. Here, a model using Fick's law was used to estimate potential antibiotic concentrations in the space surrounding producing cells at the micron scale. Key assumptions were that per-cell production rates drawn from the pharmaceutical manufacturing industry are applicable in situ, that production rates were constant, and that produced antibiotics are stable. The model outputs indicate that antibiotic concentrations in proximity to aggregates of a thousand cells can indeed be in the minimum inhibitory or minimum selective concentration range.
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Affiliation(s)
- Jessica Subirats
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Hannah Sharpe
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Domenico Santoro
- USP Technologies, London, Ontario, Canada
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, Ontario, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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11
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Busi SB, de Nies L, Pramateftaki P, Bourquin M, Kohler TJ, Ezzat L, Fodelianakis S, Michoud G, Peter H, Styllas M, Tolosano M, De Staercke V, Schön M, Galata V, Wilmes P, Battin T. Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters. Microbiol Spectr 2023; 11:e0406922. [PMID: 36688698 PMCID: PMC9927545 DOI: 10.1128/spectrum.04069-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.
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Affiliation(s)
- Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paraskevi Pramateftaki
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Massimo Bourquin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tyler J. Kohler
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Leïla Ezzat
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Michail Styllas
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Tolosano
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vincent De Staercke
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martina Schön
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Valentina Galata
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tom Battin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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12
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Rehm K, Vollenweider V, Kümmerli R, Bigler L. Rapid identification of pyoverdines of fluorescent Pseudomonas spp. by UHPLC-IM-MS. Biometals 2023; 36:19-34. [PMID: 36261676 PMCID: PMC9925543 DOI: 10.1007/s10534-022-00454-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/26/2022] [Indexed: 11/02/2022]
Abstract
Siderophores are iron-chelating molecules produced by bacteria and other microbes. They are involved with virulence in infections and play key roles in bacterial community assembly and as plant protectants due to their pathogen control properties. Although assays exist to screen whether newly isolated bacteria can produce siderophores, the chemical structures of many of these bio-active molecules remain unidentified due to the lack of rapid analytical procedures. An important group of siderophores are pyoverdines. They consist of a structurally diverse group of chromopeptides, whose amino acid sequence is characteristic for the fluorescent Pseudomonas species that secrets them. Although over 60 pyoverdine structures have been described so far, their characterization is cumbersome and several methods (isoelectrofocusing, iron uptake measurement, mass determination) are typically combined as ambiguous results are often achieved by a single method. Those additional experiments consume valuable time and resources and prevent high-throughput analysis. In this work, we present a new pyoverdine characterisation option by recording their collision cross sections (CCS) using trapped ion mobility spectrometry. This can be done simultaneously in combination with UHPLC and high-resolution MS resulting in a rapid identification of pyoverdines. The high specificity of CCS values is presented for 17 pyoverdines secreted by different Pseudomonas strains. The pyoverdine mass determination by full scan MS was supported by fragments obtained from broadband collision induced dissociation (bbCID). As iron contaminations in laboratories are not uncommon, CCS values of ferripyoverdines were also evaluated. Thereby, unusual and highly characteristic ion mobility patterns were obtained that are suitable as an alternative identification marker.
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Affiliation(s)
- Karoline Rehm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Vera Vollenweider
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
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13
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Elhamouly NA, Hewedy OA, Zaitoon A, Miraples A, Elshorbagy OT, Hussien S, El-Tahan A, Peng D. The hidden power of secondary metabolites in plant-fungi interactions and sustainable phytoremediation. FRONTIERS IN PLANT SCIENCE 2022; 13:1044896. [PMID: 36578344 PMCID: PMC9790997 DOI: 10.3389/fpls.2022.1044896] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
The global environment is dominated by various small exotic substances, known as secondary metabolites, produced by plants and microorganisms. Plants and fungi are particularly plentiful sources of these molecules, whose physiological functions, in many cases, remain a mystery. Fungal secondary metabolites (SM) are a diverse group of substances that exhibit a wide range of chemical properties and generally fall into one of four main family groups: Terpenoids, polyketides, non-ribosomal peptides, or a combination of the latter two. They are incredibly varied in their functions and are often related to the increased fitness of the respective fungus in its environment, often competing with other microbes or interacting with plant species. Several of these metabolites have essential roles in the biological control of plant diseases by various beneficial microorganisms used for crop protection and biofertilization worldwide. Besides direct toxic effects against phytopathogens, natural metabolites can promote root and shoot development and/or disease resistance by activating host systemic defenses. The ability of these microorganisms to synthesize and store biologically active metabolites that are a potent source of novel natural compounds beneficial for agriculture is becoming a top priority for SM fungi research. In this review, we will discuss fungal-plant secondary metabolites with antifungal properties and the role of signaling molecules in induced and acquired systemic resistance activities. Additionally, fungal secondary metabolites mimic plant promotion molecules such as auxins, gibberellins, and abscisic acid, which modulate plant growth under biotic stress. Moreover, we will present a new trend regarding phytoremediation applications using fungal secondary metabolites to achieve sustainable food production and microbial diversity in an eco-friendly environment.
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Affiliation(s)
- Neveen Atta Elhamouly
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Botany, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt
| | - Omar A. Hewedy
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Amr Zaitoon
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Angelica Miraples
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Omnia T. Elshorbagy
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Suzan Hussien
- Botany Department Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Amira El-Tahan
- Plant Production Department, Arid Lands Cultivation Research Institute, the City of Scientific Research and Technological Applications, City of Scientific Research and Technological Applications (SRTA-City), Borg El Arab, Alexandria, Egypt
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Chowdhury A, Bandyopadhyay A. Compelling Cyclic Peptide Scaffolds for Antitubercular Action: An Account (2011-21) of the Natural Source. Curr Protein Pept Sci 2022; 23:823-836. [PMID: 36200246 DOI: 10.2174/1389203723666220930111259] [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: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/20/2023]
Abstract
Natural cyclic peptide scaffolds are indispensable in medicinal chemistry, chemical biology, and drug discovery platforms due to their chemical diversity, structural integrity, proteolytic stability and biocompatibility. Historically, their isolation and profound understanding of target engagement have been identified as lead pharmacophore discovery. Natural cyclic peptides are the largest class of pharmacologically active scaffold, in which most show activity against drug-resistant Mycobacterium tuberculosis (Mtb). Nevertheless, eight recently discovered cyclic peptide scaffolds exhibit promising antitubercular activity among numerous naturally occurring antitubercular peptides, and they are amenable scaffolds to drug development. We examined their biological origin, scaffolds, isolations, chemical synthesis, and reasons for biological actions against Mtb. Understanding these peptide scaffold details will further allow synthetic and medicinal chemists to develop novel peptide therapeutics against tuberculosis-infected deadly diseases. This review emphasizes these cyclic peptides' in vitro and in vivo activity profiles, including their structural and chemical features.
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Affiliation(s)
- Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
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15
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Santamaria G, Liao C, Lindberg C, Chen Y, Wang Z, Rhee K, Pinto FR, Yan J, Xavier JB. Evolution and regulation of microbial secondary metabolism. eLife 2022; 11:e76119. [PMID: 36409069 PMCID: PMC9708071 DOI: 10.7554/elife.76119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large populations that collectively secrete massive amounts of secondary metabolites and alter their environment. Yet, the conditions favoring secondary metabolism despite the potential costs for primary metabolism remain unclear. Here we investigated the biosurfactants that the bacterium Pseudomonas aeruginosa makes and secretes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that the ability to make surfactants from glycerol varies inconsistently across the phylogenetic tree; instead, lineages that lost this ability are also worse at reducing the oxidative stress of primary metabolism on glycerol. Experiments with different carbon sources support a link with oxidative stress that explains the inconsistent distribution across the P. aeruginosa phylogeny and suggests a general principle: P. aeruginosa lineages produce surfactants if they can reduce the oxidative stress produced by primary metabolism and have excess resources, beyond their primary needs, to afford secondary metabolism. These results add a new layer to the regulation of a secondary metabolite unessential for primary metabolism but important to change physical properties of the environments surrounding bacterial populations.
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Affiliation(s)
- Guillem Santamaria
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Chloe Lindberg
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Zhe Wang
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Francisco Rodrigues Pinto
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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16
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Ngashangva N, Mukherjee PK, Sharma C, Kalita MC, Sarangthem I. Integrated genomics and proteomics analysis of Paenibacillus peoriae IBSD35 and insights into its antimicrobial characteristics. Sci Rep 2022; 12:18861. [PMID: 36344671 PMCID: PMC9640621 DOI: 10.1038/s41598-022-23613-y] [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: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial peptides offer the characteristics to counter AMR because the resistance development is low or no resistance. Antimicrobial peptides from Paenibacillus peoriae IBSD35 cell-free supernatant were salted out and purified using chromatography and characterized with liquid chromatography-tandem-mass spectrometry. The extract has shown a high and broad spectrum of antimicrobial activity. Combining the strain IBSD35 genome sequence with its proteomic data enabled the prediction of biosynthetic gene clusters by connecting the peptide from LC-MS/MS data to the gene that encode. Antimicrobial peptide databases offered a platform for the effective search, prediction, and design of AMPs and expanded the studies on their isolation, structure elucidation, biological evaluation, and pathway engineering. The genome-based taxonomy and comparisons have shown that P. peoriae IBSD35 is closely related to Paenibacillus peoriae FSL J3-0120. P. peoriae IBSD35 harbored endophytic trait genes and nonribosomal peptide synthases biosynthetic gene clusters. The comparative genomics revealed evolutionary insights and facilitated the discovery of novel SMs using proteomics from the extract of P. peoriae IBSD35. It will increase the potential to find novel bio-molecules to counter AMR.
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Affiliation(s)
- Ng Ngashangva
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Pulok K. Mukherjee
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Chandradev Sharma
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Mohan C. Kalita
- grid.411779.d0000 0001 2109 4622Department of Biotechnology, Gauhati University, Jalukbari, Guwahati, Assam 781014 India
| | - Indira Sarangthem
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
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17
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Meng L, Zhou R, Lin J, Zang X, Wang Q, Wang P, Wang L, Li Z, Wang W. Transcriptome and metabolome analyses reveal transcription factors regulating ganoderic acid biosynthesis in Ganoderma lucidum development. Front Microbiol 2022; 13:956421. [PMID: 35992655 PMCID: PMC9386254 DOI: 10.3389/fmicb.2022.956421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Ganoderma lucidum is an important medicinal fungus in Asian countries. Ganoderic acid (GA) is the major variety of bioactive and medicative components in G. lucidum. Biosynthesis of secondary metabolites is usually associated with cell differentiation and development. However, the mechanism underlying these phenomena remain unclear. Transcription factors play an essential regulatory role in the signal transduction pathway, owing to the fact that they represent the major link between signal transduction and expression of target genes. In the present study, we performed transcriptome and metabolome analyses to identify transcription factors involved in GA biosynthesis during development of G. lucidum. Transcriptome data revealed differentially expressed genes between mycelia and primordia, as well as between mycelia and the fruiting body. Results from gene ontology enrichment analysis and metabolome analyses suggested that GAs and flavonoids biosynthetic process significantly changed during fungal development. The analysis of predicted occurrences of DNA-binding domains revealed a set of 53 potential transcription factor families in G. lucidum. Notably, we found homeobox transcription factor and velvet family protein played important role in GA biosynthesis. Combined with previous studies, we provided a model diagram of transcription factors involved in GA biosynthesis during fruiting body formation. Collectively, these results are expected to enhance our understanding into the mechanisms underlying secondary metabolite biosynthesis and development in fungi.
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18
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Link Between Antibiotic Persistence and Antibiotic Resistance in Bacterial Pathogens. Front Cell Infect Microbiol 2022; 12:900848. [PMID: 35928205 PMCID: PMC9343593 DOI: 10.3389/fcimb.2022.900848] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022] Open
Abstract
Both, antibiotic persistence and antibiotic resistance characterize phenotypes of survival in which a bacterial cell becomes insensitive to one (or even) more antibiotic(s). However, the molecular basis for these two antibiotic-tolerant phenotypes is fundamentally different. Whereas antibiotic resistance is genetically determined and hence represents a rather stable phenotype, antibiotic persistence marks a transient physiological state triggered by various stress-inducing conditions that switches back to the original antibiotic sensitive state once the environmental situation improves. The molecular basics of antibiotic resistance are in principle well understood. This is not the case for antibiotic persistence. Under all culture conditions, there is a stochastically formed, subpopulation of persister cells in bacterial populations, the size of which depends on the culture conditions. The proportion of persisters in a bacterial population increases under different stress conditions, including treatment with bactericidal antibiotics (BCAs). Various models have been proposed to explain the formation of persistence in bacteria. We recently hypothesized that all physiological culture conditions leading to persistence converge in the inability of the bacteria to re-initiate a new round of DNA replication caused by an insufficient level of the initiator complex ATP-DnaA and hence by the lack of formation of a functional orisome. Here, we extend this hypothesis by proposing that in this persistence state the bacteria become more susceptible to mutation-based antibiotic resistance provided they are equipped with error-prone DNA repair functions. This is - in our opinion - in particular the case when such bacterial populations are exposed to BCAs.
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Affiliation(s)
- Wolfgang Eisenreich
- Bavarian NMR Center – Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
- *Correspondence: Wolfgang Eisenreich,
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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19
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Ethnobotanical Uses, Phytochemistry, Toxicology, and Pharmacological Properties of Euphorbia neriifolia Linn. against Infectious Diseases: A Comprehensive Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144374. [PMID: 35889247 PMCID: PMC9319654 DOI: 10.3390/molecules27144374] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 02/08/2023]
Abstract
Medicinal plants have considerable potential as antimicrobial agents due to the presence of secondary metabolites. This comprehensive overview aims to summarize the classification, morphology, and ethnobotanical uses of Euphorbia neriifolia L. and its derived phytochemicals with the recent updates on the pharmacological properties against emerging infectious diseases, mainly focusing on bacterial, viral, fungal, and parasitic infections. The data were collected from electronic databases, including Google Scholar, PubMed, Semantic Scholar, ScienceDirect, and SpringerLink by utilizing several keywords like 'Euphorbia neriifolia', 'phytoconstituents', 'traditional uses', 'ethnopharmacological uses', 'infectious diseases', 'molecular mechanisms', 'COVID-19', 'bacterial infection', 'viral infection', etc. The results related to the antimicrobial actions of these plant extracts and their derived phytochemicals were carefully reviewed and summarized. Euphol, monohydroxy triterpene, nerifoliol, taraxerol, β-amyrin, glut-5-(10)-en-1-one, neriifolione, and cycloartenol are the leading secondary metabolites reported in phytochemical investigations. These chemicals have been shown to possess a wide spectrum of biological functions. Different extracts of E. neriifolia exerted antimicrobial activities against various pathogens to different extents. Moreover, major phytoconstituents present in this plant, such as quercetin, rutin, friedelin, taraxerol, epitaraxerol, taraxeryl acetate, 3β-friedelanol, 3β-acetoxy friedelane, 3β-simiarenol, afzelin, 24-methylene cycloarenol, ingenol triacetate, and β-amyrin, showed significant antimicrobial activities against various pathogens that are responsible for emerging infectious diseases. This plant and the phytoconstituents, such as flavonoids, monoterpenoids, diterpenoids, triterpenoids, and alkaloids, have been found to have significant antimicrobial properties. The current evidence suggests that they might be used as leads in the development of more effective drugs to treat emerging infectious diseases, including the 2019 coronavirus disease (COVID-19).
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20
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Antioxidant, Antidiabetic, and Antibacterial Potentials and Chemical Composition of Salvia officinalis and Mentha suaveolens Grown Wild in Morocco. Adv Pharmacol Pharm Sci 2022; 2022:2844880. [PMID: 35755940 PMCID: PMC9217590 DOI: 10.1155/2022/2844880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 12/18/2022] Open
Abstract
This work evaluated in vitro antioxidant, antidiabetic, and antibacterial properties of Salvia officinalis (S. officinalis) and Mentha suaveolens (M. suaveolens) essential oils (EO). The EOs were extracted, and their chemical composition was determined using GC-MS analysis. The in vitro antioxidant, antidiabetic, and antibacterial activities of S. officinalis and M. suaveolens EO were shown to be remarkable. Furthermore, S. officinalis EO demonstrated better antioxidant findings (using DPPH, ABTS, and FRAP test) than M. suaveolens EO (p < 0.5). There were no significant differences in the inhibitory effects of the EOs on α-amylase and α-glucosidase activities in the antidiabetic assays. All of the examined bacterial strains (10 different strains), with the exception of P. aeruginosa, demonstrated significant sensitivity to the tested EOs, with M. suaveolens EO exhibiting better activity than S. officinalis EO. Thus, the research indicated that EO from these two medicinal plants has considerable potential for application in the formulation of antibacterial, antioxidant, and antidiabetic pharmaceuticals. However, more research studies are required to interpret the pharmacologic action of the studied EOs and their principal constituents and to confirm their safety.
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Production and Functionalities of Specialized Metabolites from Different Organic Sources. Metabolites 2022; 12:metabo12060534. [PMID: 35736468 PMCID: PMC9228302 DOI: 10.3390/metabo12060534] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Medicinal plants are rich sources of specialized metabolites that are of great importance to plants, animals, and humans. The usefulness of active biological compounds cuts across different fields, such as agriculture, forestry, food processing and packaging, biofuels, biocatalysts, and environmental remediation. In recent years, research has shifted toward the use of microbes, especially endophytes (bacteria, fungi, and viruses), and the combination of these organisms with other alternatives to optimize the production and regulation of these compounds. This review reinforces the production of specialized metabolites, especially by plants and microorganisms, and the effectiveness of microorganisms in increasing the production/concentration of these compounds in plants. The study also highlights the functions of these compounds in plants and their applications in various fields. New research areas that should be explored to produce and regulate these compounds, especially in plants and microbes, have been identified. Methods involving molecular studies are yet to be fully explored, and next-generation sequencing possesses an interesting and reliable approach.
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22
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Lateral flow immunoassay for small-molecules detection in phytoproducts: a review. J Nat Med 2022; 76:521-545. [PMID: 35171397 PMCID: PMC9165253 DOI: 10.1007/s11418-022-01605-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/29/2022] [Indexed: 11/10/2022]
Abstract
Phytoproducts are involved in various fields of industry. Small-molecule (Mw < 900 Da) organic compounds can be used to indicate the quality of plant samples in the perspective of efficacy by measuring the necessary secondary metabolites and in the perspective of safety by measuring the adulterant level of toxic compounds. The development of reliable detection methods for these compounds in such a complicated matrix is challenging. The lateral flow immunoassay (LFA) is one of the immunoassays well-known for its simplicity, portability, and rapidity. In this review, the general principle, components, format, and application of the LFA for phytoproducts are discussed.
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Phonghanpot S, Jarintanan F. Secondary Metabolism Gene Diversity and Cocultivation toward Isolation and Identification of Potent Bioactive Compounds Producing Bacterial Strains from Thailand's Natural Resources. SCIENTIFICA 2022; 2022:2827831. [PMID: 35677864 PMCID: PMC9168185 DOI: 10.1155/2022/2827831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/29/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Thailand was proposed to be rich unexplored source of microorganisms, especially bacterial strains. There should be bacteria with high secondary metabolite production potential in the natural resources that are still unidentified. Moreover, they might not produce secondary metabolites in standard laboratory culture condition after isolation, in which coculture condition would help us pursuing the bacteria to produce bioactive metabolites. Here, we aimed to identify new bacterial strains with high secondary metabolite production potential from Thailand's natural resources. To achieve the goal, we performed bacteria isolation, phylogenetic analysis, degenerate PCR of secondary metabolism genes, cocultivation, antibacterial analysis, and HPLC chemical profiling. We isolated distinct 40 bacterial strains, which have over 98% 16S rRNA sequence similarity with known species. There were 22, 31, and 29 strains giving positive PCR amplification of NRPS, PKS, and TPS genes, respectively. Among them, Bacillus licheniformis RSUCC0101 had the highest number of PCR products, 26. In standard single culture condition, crude extracts prepared from Bacillus safensis RSUCC0021 and Bacillus amyloliquefaciens RSUCC0282 could inhibit the growth of Staphylococcus aureus ATCC25923. Furthermore, the cocultivation and HPLC analyses showed that the extracts prepared from 3 pairs of culture between Staphylococcus sp. RSUCC0020, Micrococcus luteus RSUCC0053, Staphylococcus sp. RSUCC0087, and Staphylococcus pasteuri RSUCC0090 could inhibit the growth of Staphylococcus aureus ATCC25923 and produced distinct chemical profiles from their single culture condition. Our study led to the isolation and identification of several promising bacterial strains for production of secondary metabolites that might be useful in biomedical applications.
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Affiliation(s)
- Suranat Phonghanpot
- Biochemistry Unit, Department of Biomedical Science, Faculty of Sciences, Rangsit University, 52/347 Muang Ake, Phaholyothin Road, Lak Hok, Muang, Pathum Thani 12000, Thailand
| | - Faongchat Jarintanan
- Faculty of Medical Technology, Rangsit University, 52/347 Muang Ake, Phaholyothin Road, Lak Hok, Muang, Pathum Thani 12000, Thailand
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Sharma G, Curtis PD. The Impacts of Microgravity on Bacterial Metabolism. Life (Basel) 2022; 12:life12060774. [PMID: 35743807 PMCID: PMC9225508 DOI: 10.3390/life12060774] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/15/2022] Open
Abstract
The inside of a space-faring vehicle provides a set of conditions unlike anything experienced by bacteria on Earth. The low-shear, diffusion-limited microenvironment with accompanying high levels of ionizing radiation create high stress in bacterial cells, and results in many physiological adaptations. This review gives an overview of the effect spaceflight in general, and real or simulated microgravity in particular, has on primary and secondary metabolism. Some broad trends in primary metabolic responses can be identified. These include increases in carbohydrate metabolism, changes in carbon substrate utilization range, and changes in amino acid metabolism that reflect increased oxidative stress. However, another important trend is that there is no universal bacterial response to microgravity, as different bacteria often have contradictory responses to the same stress. This is exemplified in many of the observed secondary metabolite responses where secondary metabolites may have increased, decreased, or unchanged production in microgravity. Different secondary metabolites in the same organism can even show drastically different production responses. Microgravity can also impact the production profile and localization of secondary metabolites. The inconsistency of bacterial responses to real or simulated microgravity underscores the importance of further research in this area to better understand how microbes can impact the people and systems aboard spacecraft.
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De Miccolis Angelini RM, Landi L, Raguseo C, Pollastro S, Faretra F, Romanazzi G. Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa. Front Microbiol 2022; 13:854852. [PMID: 35356516 PMCID: PMC8959702 DOI: 10.3389/fmicb.2022.854852] [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: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.
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Affiliation(s)
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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Park JC, Yoo Y, Lim H, Yun S, Win KTYS, Kim KM, Lee GS, Cho MH, Lee TH, Sano H, Lee SW. Intracellular Ca 2+ accumulation triggered by caffeine provokes resistance against a broad range of biotic stress in rice. PLANT, CELL & ENVIRONMENT 2022; 45:1049-1064. [PMID: 35098547 DOI: 10.1111/pce.14273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
Chemical pesticides are still frequently overused to diminish such crop loss caused by biotic stress despite the threat to humans and the environment. Thus, it is urgent to find safer and more effective defense strategies. In this study, we report that caffeine, implanted through a transgenic approach, enhances resistance against variable biotic stresses in rice without fitness cost. Caffeine-producing rice (CPR) was generated by introducing three N-methyltransferase genes involved in the biosynthesis of caffeine in coffee plants. The CPR plants have no differences in morphology and growth compared to their wild-type counterparts, but they show strongly enhanced resistance to both bacterial leaf blight, rice blast, and attack of white-backed planthoppers. Caffeine acts as a repellent agent against rice pathogens. Moreover, caffeine triggers a series of Ca2+ signalling-like processes to synthesize salicylic acid (SA), a hormone associated with plant resistance. In CPR, phosphodiesterase was inhibited by caffeine, cAMP and cGMP increased, intracellular Ca2+ increased, phenylalanine lyase (PAL) was activated by OsCPK1, and SA synthesis was activated. This finding is a novel strategy to improve resistance against the biotic stresses of crops with a special type of defense inducer.
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Affiliation(s)
- Jong-Chan Park
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Youngchul Yoo
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Hyemin Lim
- Forest Bioresources Department, National Institute of Forest Science, Suwon-si, Gyeonggi-do, Korea
| | - Sopheap Yun
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, Republic of Korea
| | - Kay Tha Ye Soe Win
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, Republic of Korea
| | - Gang-Seob Lee
- Genomics Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Man-Ho Cho
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Tae Hoon Lee
- Department of Applied Chemistry, Kyung Hee University, Yongin, Republic of Korea
| | - Hiroshi Sano
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Nara, Japan
| | - Sang-Won Lee
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
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A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications. Int J Mol Sci 2022; 23:ijms23063135. [PMID: 35328559 PMCID: PMC8954581 DOI: 10.3390/ijms23063135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 03/11/2022] [Indexed: 12/20/2022] Open
Abstract
The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain's genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.
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28
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Perry EK, Meirelles LA, Newman DK. From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance. Nat Rev Microbiol 2022; 20:129-142. [PMID: 34531577 PMCID: PMC8857043 DOI: 10.1038/s41579-021-00620-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Secondary metabolites profoundly affect microbial physiology, metabolism and stress responses. Increasing evidence suggests that these molecules can modulate microbial susceptibility to commonly used antibiotics; however, secondary metabolites are typically excluded from standard antimicrobial susceptibility assays. This may in part account for why infections by diverse opportunistic bacteria that produce secondary metabolites often exhibit discrepancies between clinical antimicrobial susceptibility testing results and clinical treatment outcomes. In this Review, we explore which types of secondary metabolite alter antimicrobial susceptibility, as well as how and why this phenomenon occurs. We discuss examples of molecules that opportunistic and enteric pathogens either generate themselves or are exposed to from their neighbours, and the nuanced impacts these molecules can have on tolerance and resistance to certain antibiotics.
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Affiliation(s)
- Elena K Perry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lucas A Meirelles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
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29
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Characterization and Valorization of the Agricultural Waste Obtained from Lavandula Steam Distillation for Its Reuse in the Food and Pharmaceutical Fields. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051613. [PMID: 35268713 PMCID: PMC8911589 DOI: 10.3390/molecules27051613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023]
Abstract
The main focus of the current research was the characterization of the by-products from the steam distillation of Lavandula angustifolia Mill. (LA) and Lavandula x intermedia Emeric ex Loisel (LI) aerial parts, as they are important sources of bioactive compounds suitable for several applications in the food, cosmetic, and pharmaceutical industries. The oil-exhausted biomasses were extracted and the total polyphenol and flavonoid contents were, respectively, 19.22 ± 4.16 and 1.56 ± 0.21 mg/g for LA extract and 17.06 ± 3.31 and 1.41 ± 0.10 mg/g for LI extract. The qualitative analysis by liquid chromatography-electrospray tandem mass spectrometry (HPLC-ESI-MS) revealed that both the extracts were rich in phenolic acids and glycosylated flavonoids. The extracts exhibited radical scavenging, chelating, reducing activities, and inhibitory capacities on acetylcholinesterase and tyrosinase. The IC50 values against acetylcholinesterase and tyrosinase were, respectively, 5.35 ± 0.47 and 5.26 ± 0.02 mg/mL for LA, and 6.67 ± 0.12 and 6.56 ± 0.16 mg/mL for LI extracts. In conclusion, the oil-exhausted biomasses demonstrated to represent important sources of bioactive compounds, suitable for several applications in the food, cosmetic, and pharmaceutical industries.
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Prevalence and correlates of phenazine resistance in culturable bacteria from a dryland wheat field. Appl Environ Microbiol 2022; 88:e0232021. [PMID: 35138927 DOI: 10.1128/aem.02320-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phenazines are a class of bacterially-produced redox-active natural antibiotics that have demonstrated potential as a sustainable alternative to traditional pesticides for the biocontrol of fungal crop diseases. However, the prevalence of bacterial resistance to agriculturally-relevant phenazines is poorly understood, limiting both the understanding of how these molecules might shape rhizosphere bacterial communities and the ability to perform risk assessment for off-target effects. Here, we describe profiles of susceptibility to the antifungal agent phenazine-1-carboxylic acid (PCA) across more than 100 bacterial strains isolated from a wheat field where PCA producers are indigenous and abundant. We find that Gram-positive bacteria are typically more sensitive to PCA than Gram-negative bacteria, but that there is also significant variability in susceptibility both within and across phyla. Phenazine-resistant strains are more likely to be isolated from the wheat rhizosphere, where PCA producers are also more abundant, compared to bulk soil. Furthermore, PCA toxicity is pH-dependent for most susceptible strains and broadly correlates with PCA reduction rates, suggesting that uptake and redox-cycling are important determinants of phenazine toxicity. Our results shed light on which classes of bacteria are most likely to be susceptible to phenazine toxicity in acidic or neutral soils. In addition, the taxonomic and phenotypic diversity of our strain collection represents a valuable resource for future studies on the role of natural antibiotics in shaping wheat rhizosphere communities. Importance Microbial communities contribute to crop health in important ways. For example, phenazine metabolites are a class of redox-active molecules made by diverse soil bacteria that underpin the biocontrol of wheat and other crops. Their physiological functions are nuanced: in some contexts they are toxic, in others, beneficial. While much is known about phenazine production and the effect of phenazines on producing strains, our ability to predict how phenazines might shape the composition of environmental microbial communities is poorly constrained; that phenazine prevalence in the rhizosphere is predicted to increase in arid soils as the climate changes provides an impetus for further study. As a step towards gaining a predictive understanding of phenazine-linked microbial ecology, we document the effects of phenazines on diverse bacteria that were co-isolated from a wheat rhizosphere and identify conditions and phenotypes that correlate with how a strain will respond to phenazines.
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31
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Rehm K, Vollenweider V, Kümmerli R, Bigler L. A comprehensive method to elucidate pyoverdines produced by fluorescent Pseudomonas spp. by UHPLC-HR-MS/MS. Anal Bioanal Chem 2022; 414:2671-2685. [PMID: 35084507 PMCID: PMC8888394 DOI: 10.1007/s00216-022-03907-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/09/2022] [Accepted: 01/15/2022] [Indexed: 12/01/2022]
Abstract
Microbial secondary metabolites represent a rich source for drug discovery, plant protective agents, and biotechnologically relevant compounds. Among them are siderophores, iron-chelating molecules, that show a great influence on bacterial community assembly and the potential to control pathogen invasions. One of such a siderophore is pyoverdine that is produced by fluorescent Pseudomonas members and consists of different peptide chains specific to each bacterial species. The identification and structural elucidation of such suites of siderophores remain widely underexplored as general high-throughput analytical protocols are missing. Therefore, a dedicated method was established allowing a rapid localization and structural elucidation of pyoverdines. Liquid bacterial culture samples were purified by an easy small-scale solid-phase extraction (SPE). Ultra-high-performance liquid chromatography high-resolution tandem mass spectrometry (UHPLC-HR-MS/MS) separated highly polar pyoverdines and their derivatives. All ion fragmentation (AIF) generated mass spectra containing the characteristic fragments of the biological precursor of pyoverdine, ferribactin. This led to the revelation of the mass of secreted pyoverdines. Targeted MS/MS experiments at multiple collision energies accomplished the full structure elucidation of the pyoverdine peptide chain. A mass calculator and a fragmentation predictor facilitated greatly the interpretation of MS/MS spectra by providing accurate masses for a straightforward comparison of measured and theoretical values. The method was successfully validated using four well-known pyoverdines with various peptide chains. Finally, the applicability was proven by the analysis of 13 unknown pyoverdines secreted by sampled bacterial cultures. Among these, 4 novel pyoverdine peptide chains were discovered and are herein reported for the first time.
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Affiliation(s)
- Karoline Rehm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Vera Vollenweider
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
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Sharma S, Meyer V. The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life. Fungal Biol Biotechnol 2022; 9:1. [PMID: 35012670 PMCID: PMC8744264 DOI: 10.1186/s40694-021-00130-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/12/2021] [Indexed: 12/13/2022] Open
Abstract
Background Biological pigmentation is one of the most intriguing traits of many fungi. It holds significance to scientists, as a sign of biochemical metabolism and organism-environment interaction, and to artists, as the source of natural colors that capture the beauty of the microbial world. Furthermore, the functional roles and aesthetic appeal of biological pigmentation may be a path to inspiring human empathy for microorganisms, which is key to understanding and preserving microbial biodiversity. A project focused on cross-species empathy was initiated and conducted as part of an artist-in-residence program in 2021. The aim of this residency is to bridge the current divide between science and art through interdisciplinary practice focused on fungi. Results The residency resulted in multiple products that are designed for artistic and scientific audiences with the central theme of biological pigmentation in fungi and other microorganisms. The first product is a video artwork that focuses on Aspergillus niger as a model organism that produces melanin pigment in a biosynthetic process similar to that of humans. The growth and morphology of this commonplace organism are displayed through video, photo, animation, and time-lapse footage, inviting the viewer to examine the likenesses and overlaps between humans and fungi. The second product is The Living Color Database, an online compendium of biological colors for scientists, artists, and designers. It links organisms across the tree of life, focusing on fungi, bacteria, and archaea, and the colors they express through biological pigmentation. Each pigment is represented in terms of its chemistry, its related biosynthesis, and its color expressions according to different indices: HEX, RGB, and Pantone. It is available at color.bio. Conclusions As fungal biotechnology continues to mature into new application areas, it is as important as ever that there is human empathy for these organisms to promote the preservation and appreciation of fungal biodiversity. The products presented here provide paths for artists, scientists, and designers to understand microorganisms through the lens of color, promoting interspecies empathy through research, teaching, and practice.
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Affiliation(s)
- Sunanda Sharma
- Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Str. des 17. Juni 135, 10623, Berlin, Germany.
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Str. des 17. Juni 135, 10623, Berlin, Germany.
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González Y, de los Santos-Villalobos S, Castro-Longoria E. Trichoderma Secondary Metabolites Involved in Microbial Inhibition. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Mishra N, Chauhan P, Verma P, Singh SP, Mishra A. Metabolomic Approaches to Study Trichoderma-Plant Interactions. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Toplak M, Teufel R. Three Rings to Rule Them All: How Versatile Flavoenzymes Orchestrate the Structural Diversification of Natural Products. Biochemistry 2021; 61:47-56. [PMID: 34962769 PMCID: PMC8772269 DOI: 10.1021/acs.biochem.1c00763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The structural diversification
of natural products is instrumental
to their versatile bioactivities. In this context, redox tailoring
enzymes are commonly involved in the modification and functionalization
of advanced pathway intermediates en route to the mature natural products.
In recent years, flavoprotein monooxygenases have been shown to mediate
numerous redox tailoring reactions that include not only (aromatic)
hydroxylation, Baeyer–Villiger oxidation, or epoxidation reactions
but also oxygenations that are coupled to extensive remodeling of
the carbon backbone, which are often central to the installment of
the respective pharmacophores. In this Perspective, we will highlight
recent developments and discoveries in the field of flavoenzyme catalysis
in bacterial natural product biosynthesis and illustrate how the flavin
cofactor can be fine-tuned to enable chemo-, regio-, and stereospecific
oxygenations via distinct flavin-C4a-peroxide and flavin-N5-(per)oxide
species. Open questions remain, e.g., regarding the breadth of chemical
reactions enabled particularly by the newly discovered flavin-N5-oxygen
adducts and the role of the protein environment in steering such cascade-like
reactions. Outstanding cases involving different flavin oxygenating
species will be exemplified by the tailoring of bacterial aromatic
polyketides, including enterocin, rubromycins, rishirilides, mithramycin,
anthracyclins, chartreusin, jadomycin, and xantholipin. In addition,
the biosynthesis of tropone natural products, including tropolone
and tropodithietic acid, will be presented, which features a recently
described prototypical flavoprotein dioxygenase that may combine flavin-N5-peroxide
and flavin-N5-oxide chemistry. Finally, structural and mechanistic
features of selected enzymes will be discussed as well as hurdles
for their application in the formation of natural product derivatives
via bioengineering.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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Mahmood MZ, Bibi S, Shahzad M, Fakhar A, Rafique M, Qayyum A. Mechanisms of microbes to combat salinity in soil by producing secondary metabolites. ARABIAN JOURNAL OF GEOSCIENCES 2021. [DOI: 10.1007/s12517-021-09371-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Romsdahl J, Schultzhaus Z, Cuomo CA, Dong H, Abeyratne-Perera H, Hervey WJ, Wang Z. Phenotypic Characterization and Comparative Genomics of the Melanin-Producing Yeast Exophiala lecanii-corni Reveals a Distinct Stress Tolerance Profile and Reduced Ribosomal Genetic Content. J Fungi (Basel) 2021; 7:1078. [PMID: 34947060 PMCID: PMC8709033 DOI: 10.3390/jof7121078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
The black yeast Exophiala lecanii-corni of the order Chaetothyriales is notable for its ability to produce abundant quantities of DHN-melanin. While many other Exophiala species are frequent causal agents of human infection, E. lecanii-corni CBS 102400 lacks the thermotolerance requirements that enable pathogenicity, making it appealing for use in targeted functional studies and biotechnological applications. Here, we report the stress tolerance characteristics of E. lecanii-corni, with an emphasis on the influence of melanin on its resistance to various forms of stress. We find that E. lecanii-corni has a distinct stress tolerance profile that includes variation in resistance to temperature, osmotic, and oxidative stress relative to the extremophilic and pathogenic black yeast Exophiala dermatitidis. Notably, the presence of melanin substantially impacts stress resistance in E. lecanii-corni, while this was not found to be the case in E. dermatitidis. The cellular context, therefore, influences the role of melanin in stress protection. In addition, we present a detailed analysis of the E. lecanii-corni genome, revealing key differences in functional genetic content relative to other ascomycetous species, including a significant decrease in abundance of genes encoding ribosomal proteins. In all, this study provides insight into how genetics and physiology may underlie stress tolerance and enhances understanding of the genetic diversity of black yeasts.
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Affiliation(s)
- Jillian Romsdahl
- National Research Council Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - Zachary Schultzhaus
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
| | - Hong Dong
- Biotechnology Branch, CCDC Army Research Laboratory, Adelphi, MD 20783, USA;
| | - Hashanthi Abeyratne-Perera
- American Society for Engineering Education Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - W. Judson Hervey
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
| | - Zheng Wang
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
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Kaur L, Malhi DS, Cooper R, Kaur M, Sohal HS, Mutreja V, Sharma A. Comprehensive review on ethnobotanical uses, phytochemistry, biological potential and toxicology of Parthenium hysterophorus L.: A journey from noxious weed to a therapeutic medicinal plant. JOURNAL OF ETHNOPHARMACOLOGY 2021; 281:114525. [PMID: 34411657 DOI: 10.1016/j.jep.2021.114525] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/02/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
ETHNO-PHARMACOLOGICAL RELEVANCE Parthenium hysterophorus L. is a noxious weed and a species of flowering plant in the Asteraceae family. It is regarded as the seventh most deadly weed in the world: harmful to both humans and livestock. It is widely known as Congress Grass or Feverfew. Despite its pitfalls, P. hysterophorus bestows medicinal effects. Although prolific in nature and difficult to control, many novel applications of this controversial herb have been discovered as an approach to manage the weed. AIM The current review aims to compile all the ethnobotanical, phytochemistry, biological activities and utilities, clinical studies and toxicity data available on P. hysterophorus and its major chemical constituent parthenin. MATERIALS AND METHODS Extensive literature surveyed Google search, Google scholar, Wiley online library, Elsevier, Springer, Science direct, American Chemical Society, Royal Society of Chemistry and Research Gate. RESULT According to the study, P. hysterophorus is utilized as a traditional medicine throughout Central America and the Caribbean. It can be used to treat skin infections, dermatitis, amoebic dysentery, and as an analgesic in the treatment of muscular rheumatism. The extracts obtained from P. hysterophorus have anti-inflammatory, antioxidant, larvicidal, anti-microbial, insecticidal, hypoglycaemic and anti-cancer activity. CONCLUSION The earlier investigations confirmed that P. hysterophorus has numerous traditional and biological applications. However, the scientific data are limited in clinical and toxicological studies. Therefore, further research is required on clinical and toxicological aspects to understand the complete potential and effects of P. hysterophorus.
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Affiliation(s)
- Loveleen Kaur
- Medicinal and Natural Product Laboratory, Department of Chemistry, University Institute of Sciences, Chandigarh University, Gharuan, Mohali, 140413, India
| | - Dharambeer Singh Malhi
- Medicinal and Natural Product Laboratory, Department of Chemistry, University Institute of Sciences, Chandigarh University, Gharuan, Mohali, 140413, India
| | - Raymond Cooper
- Dept Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | - Manvinder Kaur
- Medicinal and Natural Product Laboratory, Department of Chemistry, University Institute of Sciences, Chandigarh University, Gharuan, Mohali, 140413, India
| | - Harvinder Singh Sohal
- Medicinal and Natural Product Laboratory, Department of Chemistry, University Institute of Sciences, Chandigarh University, Gharuan, Mohali, 140413, India
| | - Vishal Mutreja
- Medicinal and Natural Product Laboratory, Department of Chemistry, University Institute of Sciences, Chandigarh University, Gharuan, Mohali, 140413, India
| | - Ajay Sharma
- Medicinal and Natural Product Laboratory, Department of Chemistry, University Institute of Sciences, Chandigarh University, Gharuan, Mohali, 140413, India.
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Bauman KD, Butler KS, Moore BS, Chekan JR. Genome mining methods to discover bioactive natural products. Nat Prod Rep 2021; 38:2100-2129. [PMID: 34734626 PMCID: PMC8597713 DOI: 10.1039/d1np00032b] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Indexed: 12/22/2022]
Abstract
Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Keelie S Butler
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
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Wannasaksri W, Temviriyanukul P, Aursalung A, Sahasakul Y, Thangsiri S, Inthachat W, On-Nom N, Chupeerach C, Pruesapan K, Charoenkiatkul S, Suttisansanee U. Influence of Plant Origins and Seasonal Variations on Nutritive Values, Phenolics and Antioxidant Activities of Adenia viridiflora Craib., an Endangered Species from Thailand. Foods 2021; 10:foods10112799. [PMID: 34829080 PMCID: PMC8623237 DOI: 10.3390/foods10112799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/31/2022] Open
Abstract
Adenia viridiflora Craib. is an indigenous plant found in Thailand, Cambodia and Vietnam that has become threatened owing to lack of knowledge about its agricultural management. This plant is now rare in the wild and was registered in the Plant Genetic Conservation Project under the initiation of Her Royal Highness Princess Maha Chakri Sirindhorn (RSPG) to promote sustainable conservation and optimally beneficial utilization. A. viridiflora has a long history of utilization as a nutrient-rich source with medicinal properties but scientific evidence of the veracity of these claims is limited. Here, the nutritional compositions, phenolic contents and antioxidant activities of different plant parts (young shoots and old leaves) of A. viridiflora were investigated using plants collected from four areas of Thailand as Kamphaeng Phet (KP), Muang Nakhon Ratchasima (MN), Pakchong Nakhon Ratchasima (PN) and Uthai Thani (UT) at different harvesting periods (March-April, May–June and July–August). Results indicated that young shoots provided higher energy, protein, fat, dietary fiber, phosphorus, sodium, and zinc than old leaves. By contrast, nutrients such as total sugar, vitamin C, carotenoids, potassium, calcium, magnesium, and iron contents were higher in old leaves that also exhibited higher phenolic contents and most antioxidant activities than young shoots. Generally, most nutrients, phenolic contents, and antioxidant activities exhibited no clear trend among different plant origins. The harvesting period of July–August provided a suitable climate for biosynthesis of most nutrients, while high phenolics were mainly found in samples harvested in March–April. No clear trend was observed in the prevalence of antioxidant activities that varied according to assay techniques.
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Affiliation(s)
- Werawat Wannasaksri
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Piya Temviriyanukul
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Amornrat Aursalung
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Yuraporn Sahasakul
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Sirinapa Thangsiri
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Woorawee Inthachat
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Nattira On-Nom
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Chaowanee Chupeerach
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Kanchana Pruesapan
- Plant Varieties Protection Division, Department of Agriculture, Ministry of Agriculture and Cooperatives, Bangkok 10900, Thailand;
| | - Somsri Charoenkiatkul
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
| | - Uthaiwan Suttisansanee
- Institute of Nutrition, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand; (W.W.); (P.T.); (A.A.); (Y.S.); (S.T.); (W.I.); (N.O.-N.); (C.C.); (S.C.)
- Correspondence: ; Tel.: +66-(0)-2800-2380 (ext. 422)
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Lucarini M, Durazzo A, Bernini R, Campo M, Vita C, Souto EB, Lombardi-Boccia G, Ramadan MF, Santini A, Romani A. Fruit Wastes as a Valuable Source of Value-Added Compounds: A Collaborative Perspective. Molecules 2021; 26:6338. [PMID: 34770747 PMCID: PMC8586962 DOI: 10.3390/molecules26216338] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/26/2021] [Accepted: 10/13/2021] [Indexed: 01/06/2023] Open
Abstract
The by-products/wastes from agro-food and in particular the fruit industry represents from one side an issue since they cannot be disposed as such for their impact on the environment but they need to be treated as a waste. However, on the other side, they are a source of bioactive healthy useful compounds which can be recovered and be the starting material for other products in the view of sustainability and a circular economy addressing the global goal of "zero waste" in the environment. An updated view of the state of art of the research on fruit wastes is here given under this perspective. The topic is defined as follows: (i) literature quantitative analysis of fruit waste/by-products, with particular regards to linkage with health; (ii) an updated view of conventional and innovative extraction procedures; (iii) high-value added compounds obtained from fruit waste and associated biological properties; (iv) fruit wastes presence and relevance in updated databases. Nowadays, the investigation of the main components and related bioactivities of fruit wastes is being continuously explored throughout integrated and multidisciplinary approaches towards the exploitation of emerging fields of application which may allow to create economic, environmental, and social value in the design of an eco-friendly approach of the fruit wastes.
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Affiliation(s)
- Massimo Lucarini
- CREA-Research Centre for Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy;
| | - Alessandra Durazzo
- CREA-Research Centre for Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy;
| | - Roberta Bernini
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy;
| | - Margherita Campo
- PHYTOLAB (Pharmaceutical, Cosmetic, Food Supplement Technology and Analysis)-DiSIA, Department of Statistics, Computer Science, Applications “G. Parenti”, University of Florence, Via U. Schiff, 6-50019 Sesto Fiorentino, 50121 Florence, Italy; (M.C.); (A.R.)
| | - Chiara Vita
- QuMAP-PIN S.c.r.l.-Polo Universitario “Città di Prato” Servizi didattici e scientifici per l’Università di Firenze, Piazza Giovanni Ciardi, 25-59100 Prato, Italy;
| | - Eliana B. Souto
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal;
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | | | - Mohamed Fawzy Ramadan
- Agricultural Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt;
- Deanship of Scientific Research, Umm Al-Qura University, Makkah 24231, Saudi Arabia
| | - Antonello Santini
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Annalisa Romani
- PHYTOLAB (Pharmaceutical, Cosmetic, Food Supplement Technology and Analysis)-DiSIA, Department of Statistics, Computer Science, Applications “G. Parenti”, University of Florence, Via U. Schiff, 6-50019 Sesto Fiorentino, 50121 Florence, Italy; (M.C.); (A.R.)
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Sreeram S, Sathishkumar R, Amritha PS. Targeting the ENV spike protein of HIV with naturally occurring compounds: an in-silico study for drug designing. ADVANCES IN TRADITIONAL MEDICINE 2021. [PMCID: PMC8506072 DOI: 10.1007/s13596-021-00617-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Naskar S, Roy C, Ghosh S, Mukhopadhyay A, Hazarika LK, Chaudhuri RK, Roy S, Chakraborti D. Elicitation of biomolecules as host defense arsenals during insect attacks on tea plants (Camellia sinensis (L.) Kuntze). Appl Microbiol Biotechnol 2021; 105:7187-7199. [PMID: 34515843 DOI: 10.1007/s00253-021-11560-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/28/2022]
Abstract
The most consumed and economically important beverage plant, tea (Camellia sinensis), and its pests have coevolved so as to maintain the plant-insect interaction. In this review, findings of different research groups on pest responsive tolerance mechanisms that exist in tea manifested through the production of secondary metabolites and their inducers are presented. The phytochemicals of C. sinensis have been categorized into volatiles, nonvolatiles, enzymes, and phytohormones for convenience. Two types of pests, namely the piercing-sucking pests and chewing pests, are associated with tea. Both the insect groups can trigger the production of those metabolites and inducers through several primary and secondary biosynthetic pathways. These induced biomolecules can act as insect repellents and most of them are associated with lowering the nutrient quality of plant tissue and increasing the indigestibility in the pest's gut. Moreover, some of them also act as predator attractants of particular pests. The herbivore-induced plant volatiles secreted from tea plants during pest infestation were (E)-nerolidol, α-farnesene, (Z)-3-hexenol, (E)-4,8-dimethyl-1,3,7-nonatriene, indole, benzyl nitrile (BN), linalool, and ocimenes. The nonvolatiles like theaflavin and L-theanine were increased in response to the herbivore attack. Simultaneously, S-adenosyl-L-methionine synthase, caffeine synthase activities were affected, whereas flavonoid synthesis and wax formation were elevated. Defense responsive enzymes like peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase, ascorbate peroxidase, and catalase are involved in pest prevention mechanisms. Phytohormones like jasmonic acid, salicylic acid, abscisic acid, and ethylene act as the modulator of the defense system. The objective of this review is to discuss the defensive roles of these metabolites and their inducers against pest infestation in tea with an aim to develop environmentally sustainable pesticides in the future.Key points• Herbivore-induced volatile signals and their effects on neighboring tea plant protection• Stereochemical conversion of volatiles, effects of nonvolatiles, expression of defense-responsive enzymes, and phytohormones due to pest attack• Improved understanding of metabolites for bio-sustainable pesticide development.
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Affiliation(s)
- Sudipta Naskar
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Chitralekha Roy
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Sanatan Ghosh
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Ananda Mukhopadhyay
- Entomology Research Unit, Department of Zoology, University of North Bengal, Siliguri, , Darjeeling, 734013, India
| | | | | | - Somnath Roy
- Department of Entomology, Tocklai Tea Research Institute, Tea Research Association, Jorhat, Assam, 785008, India.
| | - Dipankar Chakraborti
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India.
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Lowe H, Toyang N, Steele B, Bryant J, Ngwa W, Nedamat K. The Current and Potential Application of Medicinal Cannabis Products in Dentistry. Dent J (Basel) 2021; 9:106. [PMID: 34562980 PMCID: PMC8466648 DOI: 10.3390/dj9090106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/10/2021] [Accepted: 08/31/2021] [Indexed: 01/02/2023] Open
Abstract
Oral and dental diseases are a major global burden, the most common non-communicable diseases (NCDs), and may even affect an individual's general quality of life and health. The most prevalent dental and oral health conditions are tooth decay (otherwise referred to as dental caries/cavities), oral cancers, gingivitis, periodontitis, periodontal (gum) disease, Noma, oro-dental trauma, oral manifestations of HIV, sensitive teeth, cracked teeth, broken teeth, and congenital anomalies such as cleft lip and palate. Herbs have been utilized for hundreds of years in traditional Chinese, African and Indian medicine and even in some Western countries, for the treatment of oral and dental conditions including but not limited to dental caries, gingivitis and toothaches, dental pulpitis, halitosis (bad breath), mucositis, sore throat, oral wound infections, and periodontal abscesses. Herbs have also been used as plaque removers (chew sticks), antimicrobials, analgesics, anti-inflammatory agents, and antiseptics. Cannabis sativa L. in particular has been utilized in traditional Asian medicine for tooth-pain management, prevention of dental caries and reduction in gum inflammation. The distribution of cannabinoid (CB) receptors in the mouth suggest that the endocannabinoid system may be a target for the treatment of oral and dental diseases. Most recently, interest has been geared toward the use of Cannabidiol (CBD), one of several secondary metabolites produced by C. sativa L. CBD is a known anti-inflammatory, analgesic, anxiolytic, anti-microbial and anti-cancer agent, and as a result, may have therapeutic potential against conditions such burning mouth syndrome, dental anxiety, gingivitis, and possible oral cancer. Other major secondary metabolites of C. sativa L. such as terpenes and flavonoids also share anti-inflammatory, analgesic, anxiolytic and anti-microbial properties and may also have dental and oral applications. This review will investigate the potential of secondary metabolites of C. sativa L. in the treatment of dental and oral diseases.
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Affiliation(s)
- Henry Lowe
- Biotech R & D Institute, University of the West Indies, Mona 99999, Jamaica; (H.L.); (J.B.)
- Vilotos Pharmaceuticals Inc., Baltimore, MD 21202, USA;
- Flavocure Biotech Inc., Baltimore, MD 21202, USA
- Department of Medicine, University of Maryland Medical School, Baltimore, MD 21202, USA
| | - Ngeh Toyang
- Vilotos Pharmaceuticals Inc., Baltimore, MD 21202, USA;
- Flavocure Biotech Inc., Baltimore, MD 21202, USA
| | - Blair Steele
- Biotech R & D Institute, University of the West Indies, Mona 99999, Jamaica; (H.L.); (J.B.)
| | - Joseph Bryant
- Biotech R & D Institute, University of the West Indies, Mona 99999, Jamaica; (H.L.); (J.B.)
| | - Wilfred Ngwa
- Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA;
- School of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kaveh Nedamat
- Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA 02142, USA;
- Auraleaf Innovations, Toronto, ON M9B 4H6, Canada
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Bano SA, Naz S, Uzair B, Hussain M, Khan MM, Bibi H, Habiba U, Nisa S, Israr M. Detection of microorganisms with antibacterial activities from different industrial wastes and GC-MS analysis of crude microbial extract. BRAZ J BIOL 2021; 83:e245585. [PMID: 34495157 DOI: 10.1590/1519-6984.245585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/30/2021] [Indexed: 11/21/2022] Open
Abstract
Many soil microorganisms' i.e., bacteria and fungi produce secondary metabolites called antibiotics. These are used for the treatment of some of the bacterial, fungal and protozoal diseases of humans. There is a need for isolation of a broad spectrum of antibiotics from microorganisms due to the emergence of antibiotic resistance. In the present study two antibiotic producing bacteria Klebsiella pneumoniae and Bacillus cereus were isolated from pharmaceutical and poultry feed industry of Hattar, Haripur Pakistan. Total 10 waste samples were collected from different industries (Marble, Ghee, Soap, Mineral, Steel, Poultry Feed, Pharmaceutical, Qarshi, Cosmetic and Glass). Thirty-three bacterial strains were isolated from industrial wastes of these ten different industries. Fourteen out of thirty-three bacterial strains exhibited antimicrobial activities against at least one of the test microbes considered in this study including Escherchia coli, Staphylococcus aureus and Salmonella typhi. The bacteria were isolated by standard serial dilution spread plate technique. Morphological characterization of the isolates was done by Gram staining. Nine bacterial isolates out of fourteen were initially identified as B. cereus and five as K. pneumoniae through biochemical characterization. The antibacterial activities were tested by well diffusion method. Maximum number of antibiotic producing bacteria were isolated from pharmaceutical and poultry feed industry based on the results of primary screening, the most potential isolates S9, S19, S20, S22 and S23 were selected for secondary screening. The maximum activity against E. coli and S. aureus was recorded by bacterial isolate S19 i.e zones of inhibition of 6.5mm and 9mm while S20 showed 7.5mm and 6mm zones respectively. Molecular identification was carried out on the basis of 16S rRNA sequence analysis. Finally, the isolates were identified as B. cereus accession number LC538271and K. pneumoniae accession number MT078679. Analysis of bacterial extract S20 through GC-MS indicated the presence of 8 compounds of diverse nature and structure. Present study suggests that wastes of pharmaceutical and poultry feed industry may have antibiotic producing bacteria. These bacteria could be utilized for the production of antibiotics. B. cereus and K. pneumoniae isolated from wastes of poultry feed and pharmaceutical industries have the potential to produce antibiotics and could be used to control the microbial growth.
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Affiliation(s)
- S A Bano
- The University of Haripur, Department of Microbiology, Khyber Pakhtunkhwa, Pakistan
| | - S Naz
- The University of Haripur, Department of Microbiology, Khyber Pakhtunkhwa, Pakistan
| | - B Uzair
- International Islamic University, Department of Biosciences, Islamabad, Pakistan
| | - M Hussain
- The University of Haripur, Department of Forestry and Wild Life, Khyber Pakhtunkhwa, Pakistan
| | - M M Khan
- The University of Haripur, Department of Microbiology, Khyber Pakhtunkhwa, Pakistan
| | - H Bibi
- Agricultural University, Department of Soil and Environmental Sciences, Peshawar, Pakistan
| | - U Habiba
- The University of Haripur, Department of Forestry and Wild Life, Khyber Pakhtunkhwa, Pakistan
| | - S Nisa
- The University of Haripur, Department of Microbiology, Khyber Pakhtunkhwa, Pakistan
| | - M Israr
- The University of Haripur, Department of Biology, Khyber Pakhtunkhwa, Pakistan.,Hebei Normal University Shijiazhuang, College of Life Science, Hebei, PR China
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Chen YH, Chiang PW, Rogozin DY, Degermendzhy AG, Chiu HH, Tang SL. Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach. Commun Biol 2021; 4:996. [PMID: 34426638 PMCID: PMC8382752 DOI: 10.1038/s42003-021-02510-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/01/2021] [Indexed: 11/08/2022] Open
Abstract
Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia.
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Affiliation(s)
- Yu-Hsiang Chen
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Denis Yu Rogozin
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
- Siberian Federal University, Krasnoyarsk, Russia
| | - Andrey G Degermendzhy
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sen-Lin Tang
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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Palmer JM, Wiemann P, Greco C, Chiang YM, Wang CCC, Lindner DL, Keller NP. The sexual spore pigment asperthecin is required for normal ascospore production and protection from UV light in Aspergillus nidulans. J Ind Microbiol Biotechnol 2021; 48:6355442. [PMID: 34415047 PMCID: PMC8762651 DOI: 10.1093/jimb/kuab055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2022]
Abstract
Many fungi develop both asexual and sexual spores that serve as propagules for dissemination and/or recombination of genetic traits. Asexual spores are often heavily pigmented and this pigmentation provides protection from UV light. However, little is known about any purpose pigmentation may serve for sexual spores. The model Ascomycete Aspergillus nidulans produces both green pigmented asexual spores (conidia) and red pigmented sexual spores (ascospores). Here we find that the previously characterized red pigment, asperthecin, is the A. nidulans ascospore pigment. The asperthecin biosynthetic gene cluster is composed of three genes, aptA, aptB, and aptC where deletion of either aptA (encoding a polyketide synthase) or aptB (encoding a thioesterase) yields small, mishappen hyaline ascospores while deletion of aptC (encoding a monooxygenase) yields morphologically normal but purple ascospores. ∆aptA and ∆aptB but not ∆aptC or WT ascospores are extremely sensitive to UV light. We find that two historical ascospore color mutants, clA6 and clB1, possess mutations in aptA and aptB sequences respectively.
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Affiliation(s)
- Jonathan M Palmer
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI 53726, USA
| | - Philipp Wiemann
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Claudio Greco
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yi Ming Chiang
- Departments of Chemistry and Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Clay C C Wang
- Departments of Chemistry and Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI 53726, USA
| | - Nancy P Keller
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Single Cell Protein: A Potential Substitute in Human and Animal Nutrition. SUSTAINABILITY 2021. [DOI: 10.3390/su13169284] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Single cell protein (SCP) is the first product of the fermentation process and has proven to be a good protein alternative. Food competition is becoming more intense as the world’s population continues to grow. Soon, SCP may be able to compensate for a protein deficit. Various global businesses are focusing on SCP production, and the scope of its application is expanding as time and knowledge increases. High quantities of SCP can be produced by microorganisms, such as algae, yeast, fungi and bacteria, due to their fast development rate and the significant level of protein in their chemical structure. Beside proteins, SCP contains carbohydrates, nucleic acids, lipids, minerals, vitamins and several important amino acids. SCP has been an effective substitute for more expensive protein sources such as fish and soybean products. In conclusion, SCP can easily replace traditional protein sources in human and animal feed without detrimental effects. Potential substrate candidates and optimization strategies for SCP production have been extensively studied. This review article focuses on the various aspects of SCP, from its production, using different substrates, player microorganisms and nutritional benefits, to its economic aspects.
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Prashanthi R, G K S, S K, L M. Isolation, characterization, and molecular identification of soil bacteria showing antibacterial activity against human pathogenic bacteria. J Genet Eng Biotechnol 2021; 19:120. [PMID: 34406527 PMCID: PMC8374016 DOI: 10.1186/s43141-021-00219-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 07/28/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The present study dealt with the screening of soil bacteria with antibacterial activity from different locations in Bangalore, India. Antibiotics play the role of self-defense mechanism for the bacteria and are produced as secondary metabolites to protect themselves from other competitive microorganisms. The need for new antibiotics arose as the pathogenic bacteria acquire resistance to various antibiotics meant for treating human diseases. Given the importance of antibiotics of bacterial origin, standard techniques have been used to isolate and characterize the soil bacteria which showed antibacterial activity. RESULTS The isolated bacteria were tested against human pathogenic bacteria like Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae by primary and secondary screening methods. The isolates PR1, PR2, and PR3 were confirmed to have antibacterial activity against S. aureus, E. coli, P. aeruginosa, and K. pneumoniae by both methods. Studies on the effect of filter sterilization, autoclaving, and proteinase K treatment on culture filtrates showed filter sterilization as the best method. The effect of different carbon and nitrogen sources on the antibacterial activity showed that preference by each isolate differed for carbon and nitrogen requirements. The isolates PR1, PR2, and PR3 were identified as Bacillus aryabhattai strain PR-D07, Arthrobacter humicola strain PR-F07, and Neomicrococcus lactis strain PR-F11 through 16S rRNA sequencing. CONCLUSION Findings from this research work are encouraging and could proceed further to applied aspects. Only 3 bacterial isolates out of 263 isolates from soil samples displayed antibacterial activity against human pathogens S. aureus, E. coli, P. aeruginosa, and K. pneumoniae. They were identified as B. aryabhattai, A. humicola, and N. lactis by 16S rRNA studies and all of them are Gram-positive. Each isolate preferred different carbon and nitrogen sources for their enhanced antibacterial activity. Efficacy of the culture filtrates of these isolates was tested by filter sterilization, autoclaving, and proteinase K treatment. Filter-sterilized culture filtrates showed higher antibacterial activity than other treatments. A comparison of the antibacterial activity of culture filtrates and antibiotic streptomycin produced an inhibition zone of 18.5 mm and 15.5 mm respectively. This is the first report on the antibacterial activity of all the 3 bacterial strains (B. aryabhattai strain PR-D07, A. humicola strain PR-F07, and N. lactis strain PR-F11), against all the human pathogens, mentioned earlier. It is also found that the antibiotic factor is proteinaceous as proteinase K considerably reduced the antibacterial activity of the culture filtrates. With the above significant results, these 3 bacteria are considered to be promising candidates for the isolation of new antibacterial agents.
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Affiliation(s)
- R Prashanthi
- Department of Biotechnology and Genetics, M. S. Ramaiah College of Arts, Science and Commerce, Karnataka, 560054, Bengaluru, India.
| | - Shreevatsa G K
- Department of Biotechnology and Genetics, M. S. Ramaiah College of Arts, Science and Commerce, Karnataka, 560054, Bengaluru, India
| | - Krupalini S
- Department of Biotechnology and Genetics, M. S. Ramaiah College of Arts, Science and Commerce, Karnataka, 560054, Bengaluru, India
| | - Manoj L
- Department of Biotechnology and Genetics, M. S. Ramaiah College of Arts, Science and Commerce, Karnataka, 560054, Bengaluru, India
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50
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Al-shaibani MM, Radin Mohamed RMS, Sidik NM, Enshasy HAE, Al-Gheethi A, Noman E, Al-Mekhlafi NA, Zin NM. Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications. Molecules 2021; 26:molecules26154504. [PMID: 34361657 PMCID: PMC8347454 DOI: 10.3390/molecules26154504] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 12/08/2022] Open
Abstract
The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.
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Affiliation(s)
- Muhanna Mohammed Al-shaibani
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
| | - Radin Maya Saphira Radin Mohamed
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Nik Marzuki Sidik
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli 17600, Kelantan, Malaysia
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Hesham Ali El Enshasy
- Institute of Bioproducts Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai 81310, Johor, Malaysia;
- City of Scientific Research and Technology Applications (SRTA), 21934 New Burg Al Arab, Alexandria, Egypt
| | - Adel Al-Gheethi
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Efaq Noman
- Applied Microbiology Department, Faculty of Applied Sciences, Taiz University, Taiz 6803, Yemen;
| | - Nabil Ali Al-Mekhlafi
- Atta-ur-Rahman Institute for Natural Product Discovery, UiTM, Puncak Alam Campus, Bandar Puncak Alam 42300, Selangor, Malaysia;
- Biochemical Technology Program, Department of Chemistry Faculty of Applied Science, Thamar University, Thamar P.O. Box 87246, Yemen
| | - Noraziah Mohamad Zin
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
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