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Zhang S, Zhou Z, Wang T, Lu A. Design, Synthesis, and Antifungal Activities of Phenylpyrrole Analogues Based on Alkaloid Lycogalic Acid. Molecules 2024; 29:3150. [PMID: 38999100 PMCID: PMC11243374 DOI: 10.3390/molecules29133150] [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: 06/07/2024] [Revised: 06/26/2024] [Accepted: 06/30/2024] [Indexed: 07/14/2024] Open
Abstract
Plant diseases caused by pathogenic fungi seriously affect the yield and quality of crops, cause huge economic losses, and pose a considerable threat to global food security. Phenylpyrrole analogues were designed and synthesized based on alkaloid lycogalic acid. All target compounds were characterized by 1H NMR, 13C NMR, and HRMS. Their antifungal activities against seven kinds of phytopathogenic fungi were evaluated. The results revealed that most compounds had broad-spectrum fungicidal activities at 50 μg/mL; 14 compounds displayed more than 60% fungicidal activities against Rhizoctonia cerealis and Sclerotinia sclerotiorum, and in particular, the fungicidal activities of compounds 8g and 8h against Rhizoctonia cerealis were more than 90%, which could be further developed as lead agents for water-soluble fungicides. The molecular docking results indicate that compounds 8g and 8h can interact with 14α-demethylase (RcCYP51) through hydrogen bonding with strong affinity.
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Affiliation(s)
- Shuaiheng Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China;
| | - Zhenghong Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China;
| | - Tienan Wang
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde 067000, China
| | - Aidang Lu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China;
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2
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Félix C, Meneses R, Gonçalves MFM, Duarte AS, Jorrín-Novo JV, van de Peer Y, Deforce D, Van Nieuwerburgh F, Alves A, Esteves AC. How temperature modulates the expression of pathogenesis-related molecules of the cross-kingdom pathogen Lasiodiplodia hormozganensis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171917. [PMID: 38580127 DOI: 10.1016/j.scitotenv.2024.171917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024]
Abstract
Lasiodiplodia hormozganensis, initially recognized as a fungal plant pathogen, is recognized now acknowledged as a potential threat to humans. However, our understanding of the pathogenesis mechanisms of Lasiodiplodia species remains limited, and the impact of temperature on its pathogenicity is unclear. This study aims to elucidate the effects of temperature on the biology of L. hormozganensis, focusing on the expression of pathogenesis-related molecules and its ability to function as a cross-kingdom pathogen. We conducted experiments at two different temperatures, 25 and 37 °C, analyzing the proteome and transcriptome of L. hormozganensis. Using strain CBS339.90, initially identified as L. theobromae but confirmed through ITS and tef1-α sequence analysis to be L. hormozganensis, we aimed to understand the fungus's protein expression under varying temperature conditions. Results from the functional analysis of the secretome at 25 °C showed a noteworthy presence of proteins related to carbohydrate metabolism, catabolism, plant cell wall degradation, and pathogenesis. However, when grown at 37 °C, the fungus exhibited an increased production of stress response and pathogenesis-related proteins. Our findings identified various pathways crucial for pathogenesis in both plants and humans, suggesting that L. hormozganensis possesses the genetic foundation to infect both hosts. Specific pathogenesis-related proteins, including the phytotoxin snodprot1, aspartic protease aspergillopepsin, and virulence protein SSD1, were also identified. Concluding, we propose a possible mechanism of how L. hormozganensis adapts to different temperatures. The shift in temperature results in the expression of genes that favor human related pathogenesis molecules.
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Affiliation(s)
- Carina Félix
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Present address: MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Portugal
| | - Rodrigo Meneses
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052, Belgium
| | - Micael F M Gonçalves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana S Duarte
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Faculty of Dental Medicine, Estrada da Circunvalação, 3504-505, Viseu, Portugal
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Córdoba, Spain
| | - Yves van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Artur Alves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana C Esteves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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3
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Ruan Z, Jiao J, Zhao J, Liu J, Liang C, Yang X, Sun Y, Tang G, Li P. Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash. BMC Genomics 2024; 25:502. [PMID: 38773367 PMCID: PMC11110190 DOI: 10.1186/s12864-024-10424-w] [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: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker. RESULTS In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family. CONCLUSION This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
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Affiliation(s)
- Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiahui Jiao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiaxue Liu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chaoqiong Liang
- Shaanxi Academy of Forestry, Xi'an, Shaanxi, 710082, People's Republic of China
| | - Xia Yang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Sun
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Shi T, Sun X, Yuan Q, Wang J, Shen X. Exploring the role of flavin-dependent monooxygenases in the biosynthesis of aromatic compounds. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:46. [PMID: 38520003 PMCID: PMC10958861 DOI: 10.1186/s13068-024-02490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024]
Abstract
Hydroxylated aromatic compounds exhibit exceptional biological activities. In the biosynthesis of these compounds, three types of hydroxylases are commonly employed: cytochrome P450 (CYP450), pterin-dependent monooxygenase (PDM), and flavin-dependent monooxygenase (FDM). Among these, FDM is a preferred choice due to its small molecular weight, stable expression in both prokaryotic and eukaryotic fermentation systems, and a relatively high concentration of necessary cofactors. However, the catalytic efficiency of many FDMs falls short of meeting the demands of large-scale production. Additionally, challenges arise from the limited availability of cofactors and compatibility issues among enzyme components. Recently, significant progress has been achieved in improving its catalytic efficiency, but have not yet detailed and informative viewed so far. Therefore, this review emphasizes the advancements in FDMs for the biosynthesis of hydroxylated aromatic compounds and presents a summary of three strategies aimed at enhancing their catalytic efficiency: (a) Developing efficient enzyme mutants through protein engineering; (b) enhancing the supply and rapid circulation of critical cofactors; (c) facilitating cofactors delivery for enhancing FDMs catalytic efficiency. Furthermore, the current challenges and further perspectives on improving catalytic efficiency of FDMs are also discussed.
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Affiliation(s)
- Tong Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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Garcia JF, Morales-Cruz A, Cochetel N, Minio A, Figueroa-Balderas R, Rolshausen PE, Baumgartner K, Cantu D. Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:127-142. [PMID: 37934016 DOI: 10.1094/mpmi-09-23-0129-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, U.S.A
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, U.S.A
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Davis, CA, U.S.A
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- Genome Center, University of California, Davis, Davis, CA, U.S.A
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6
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Ma JX, Wang H, Jin C, Ye YF, Tang LX, Si J, Song J. Whole genome sequencing and annotation of Daedaleopsis sinensis, a wood-decaying fungus significantly degrading lignocellulose. Front Bioeng Biotechnol 2024; 11:1325088. [PMID: 38292304 PMCID: PMC10826855 DOI: 10.3389/fbioe.2023.1325088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/15/2023] [Indexed: 02/01/2024] Open
Abstract
Daedaleopsis sinensis is a fungus that grows on wood and secretes a series of enzymes to degrade cellulose, hemicellulose, and lignin and cause wood rot decay. Wood-decaying fungi have ecological, economic, edible, and medicinal functions. Furthermore, the use of microorganisms to biodegrade lignocellulose has high application value. Genome sequencing has allowed microorganisms to be analyzed from the aspects of genome characteristics, genome function annotation, metabolic pathways, and comparative genomics. Subsequently, the relevant information regarding lignocellulosic degradation has been mined by bioinformatics. Here, we sequenced and analyzed the genome of D. sinensis for the first time. A 51.67-Mb genome sequence was assembled to 24 contigs, which led to the prediction of 12,153 protein-coding genes. Kyoto Encyclopedia of Genes and Genomes database analysis of the D. sinensis data revealed that 3,831 genes are involved in almost 120 metabolic pathways. According to the Carbohydrate-Active Enzyme database, 481 enzymes are found in D. sinensis, of which glycoside hydrolases are the most abundant. The genome sequence of D. sinensis provides insights into its lignocellulosic degradation and subsequent applications.
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Affiliation(s)
- Jin-Xin Ma
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hao Wang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Can Jin
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Fan Ye
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lu-Xin Tang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jie Song
- Department of Horticulture and Food, Guangdong Eco-Engineering Polytechnic, Guangzhou, China
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Ortiz-Álvarez J, Becerra S, Baroncelli R, Hernández-Rodríguez C, Sukno SA, Thon MR. Evolutionary history of the cytochrome P450s from Colletotrichum species and prediction of their putative functional roles during host-pathogen interactions. BMC Genomics 2024; 25:56. [PMID: 38216891 PMCID: PMC10785452 DOI: 10.1186/s12864-023-09858-5] [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: 08/20/2023] [Accepted: 11/29/2023] [Indexed: 01/14/2024] Open
Abstract
The genomes of species belonging to the genus Colletotrichum harbor a substantial number of cytochrome P450 monooxygenases (CYPs) encoded by a broad diversity of gene families. However, the biological role of their CYP complement (CYPome) has not been elucidated. Here, we investigated the putative evolutionary scenarios that occurred during the evolution of the CYPome belonging to the Colletotrichum Graminicola species complex (s.c.) and their biological implications. The study revealed that most of the CYPome gene families belonging to the Graminicola s.c. experienced gene contractions. The reductive evolution resulted in species restricted CYPs are predominant in each CYPome of members from the Graminicola s.c., whereas only 18 families are absolutely conserved among these species. However, members of CYP families displayed a notably different phylogenetic relationship at the tertiary structure level, suggesting a putative convergent evolution scenario. Most of the CYP enzymes of the Graminicola s.c. share redundant functions in secondary metabolite biosynthesis and xenobiotic metabolism. Hence, this current work suggests that the presence of a broad CYPome in the genus Colletotrichum plays a critical role in the optimization of the colonization capability and virulence.
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Affiliation(s)
- Jossue Ortiz-Álvarez
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain
- Present Address: Programa "Investigadoras e Investigadores por México" Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT), Mexico City, México
| | - Sioly Becerra
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain
| | - Riccardo Baroncelli
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico, México
| | - Serenella A Sukno
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain.
| | - Michael R Thon
- Institute for Agrobiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Salamanca, Spain.
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8
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Jin C, Ma JX, Wang H, Tang LX, Ye YF, Li X, Si J. First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution. Front Cell Infect Microbiol 2024; 13:1325418. [PMID: 38264724 PMCID: PMC10803629 DOI: 10.3389/fcimb.2023.1325418] [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: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Sanghuangporus, also known as "Sanghuang" in China, is a well-known genus of traditional Chinese medicinal macrofungi. To make more effective use of Sanghuangporus resources, we completed the first genome assembly and annotation of a monokaryon strain of S. weigelae in the present study. A 33.96-Mb genome sequence was assembled as 13 contigs, leading to prediction of 9377 protein-coding genes. Phylogenetic and average nucleotide identity analyses indicated that the S. weigelae genome is closely related to those of other Sanghuangporus species in evolutionary tree, which clustered in one clade. Collinearity analysis revealed a high level of collinearity of S. weigelae with S. baumii, S. vaninii, and S. sanghuang. Biosynthesis pathways potentially involved in medicinal properties, including terpenoid and polysaccharide synthesis, were identified in S. weigelae, while polysaccharides were identified as the main medicinal metabolites in S. weigelae, with flavonoids more important in Sanghuangporus than other medicinal mushroom groups. Genes encoding 332 carbohydrate-active enzymes were identified in the S. weigelae genome, including major glycoside hydrolases and glycosyltransferases predicted, revealing the robust lignocellulose degradation capacity of S. weigelae. Further, 130 genes, clustered in seven classes were annotated to encode cytochromes P450 in the S. weigelae genome. Overall, our results reveal the remarkably medicinal capacity of S. weigelae and provide new insights that will inform the study of evolution and medicinal application of S. weigelae. The data are a reference resource for the formulation of scientific and rational ecological protection policies for Sanghuangporus species.
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Affiliation(s)
| | | | | | | | | | | | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Kollerov V, Tarlachkov S, Shutov A, Kazantsev A, Donova M. Identification of a Gene Encoding a New Fungal Steroid 7-Hydroxylase and Its Functional Characterization in Pichia pastoris Yeast. Int J Mol Sci 2023; 24:17256. [PMID: 38139084 PMCID: PMC10744122 DOI: 10.3390/ijms242417256] [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: 10/30/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The hydroxylation of steroids in the C7β position is one of the rare reactions that allow the production of value-added precursors in the synthesis of ursodeoxycholic acid and other pharmaceuticals. Recently, we discovered this activity in the ascomycete Curvularia sp. VKM F-3040. In this study, the novel gene of 7-hydroxylase (P450cur) was identified as being heterologously expressed and functionally characterized in Pichia pastoris. Transcriptome data mining and differential expression analysis revealed that 12 putative genes in Curvularia sp. mycelia significantly increased their expression in response to dehydroepiandrosterone (DHEA). The transcriptional level of the most up-regulated cytochrome P450cur gene was increased more than 300-fold. A two-gene construct with a candidate P450cur gene and the gene of its natural redox partner, NADPH-cytochrome P450 reductase (CPR), which is interconnected by a T2A element, was created. Using this construct, recombinant P. pastoris strains co-expressing fungal P450cur and CPR genes were obtained. The functional activity of the recombinant P450cur was studied in vivo during the bioconversion of androstane steroids. The fungal 7-monooxygenase predominantly catalyzed the 7β-hydroxylation of androstadienedione (ADD), DHEA, and androstenediol, whereas 1-dehydrotestosterone was hydroxylated by P450cur mainly at the C7-Hα position. To our knowledge, this is the first report of a recombinant yeast capable of catalyzing the 7α/β-hydroxylation of ADD and DHEA.
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Affiliation(s)
- Vyacheslav Kollerov
- Federal Research Center «Pushchino Center for Biological Research of the Russian Academy of Sciences», G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, 142290 Pushchino, Russia; (S.T.); (A.S.); (M.D.)
| | - Sergey Tarlachkov
- Federal Research Center «Pushchino Center for Biological Research of the Russian Academy of Sciences», G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, 142290 Pushchino, Russia; (S.T.); (A.S.); (M.D.)
| | - Andrei Shutov
- Federal Research Center «Pushchino Center for Biological Research of the Russian Academy of Sciences», G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, 142290 Pushchino, Russia; (S.T.); (A.S.); (M.D.)
| | - Alexey Kazantsev
- Chemical Department, Moscow State University, GSP-1, Leninskiye Gori, 1, 119991 Moscow, Russia;
| | - Marina Donova
- Federal Research Center «Pushchino Center for Biological Research of the Russian Academy of Sciences», G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, 142290 Pushchino, Russia; (S.T.); (A.S.); (M.D.)
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10
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Yu J, Kong L, Fan S, Li M, Li J. Genomic Characterization of the Mycoparasite Pestalotiopsis sp. Strain cr013 from Cronartium ribicola. Pol J Microbiol 2023; 72:433-442. [PMID: 38095159 PMCID: PMC10725163 DOI: 10.33073/pjm-2023-041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/24/2023] [Indexed: 12/17/2023] Open
Abstract
The Pestalotiopsis sp. strain cr013 is a mycoparasite of Cronartium ribicola, a potential biocontrol fungus for Armand pine (Pinus armandii) blister rust. A previous study showed that the strain cr013 has great potential to produce new compounds. However, there has been no report of the whole-genome sequence of the mycoparasite Pestalotiopsis sp. In this study, the BGISEQ-500 and Oxford Nanopore GridION X5 sequencing platforms were used to sequence the strain cr013 isolates and assemble the reads to obtain the complete genome. We first report the whole-genome information of the mycoparasite Pestalotiopsis sp. strain cr013 (GenBank accession number: JACFXT010000000, BioProject ID: PRJNA647543, BioSample ID: SAMN15589943), and the genomic components and gene functions related to the mycoparasitism process were analyzed. This study provides a theoretical basis for understanding the lifestyle strategy of the mycoparasite Pestalotiopsis sp. and reveals the mechanisms underlying secondary metabolite diversity in the strain cr013.
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Affiliation(s)
- Jinde Yu
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Lei Kong
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Shichang Fan
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Mingjiao Li
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Jing Li
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
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Welgemoed T, Duong TA, Barnes I, Stukenbrock EH, Berger DK. Population genomic analyses suggest recent dispersal events of the pathogen Cercospora zeina into East and Southern African maize cropping systems. G3 (BETHESDA, MD.) 2023; 13:jkad214. [PMID: 37738420 PMCID: PMC10627275 DOI: 10.1093/g3journal/jkad214] [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: 08/03/2023] [Revised: 08/03/2023] [Accepted: 09/06/2023] [Indexed: 09/24/2023]
Abstract
A serious factor hampering global maize production is gray leaf spot disease. Cercospora zeina is one of the causative pathogens, but population genomics analysis of C. zeina is lacking. We conducted whole-genome Illumina sequencing of a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe, and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the C. zeina isolates was done by (1) de novo assembly of the reads with SPAdes, (2) annotation with BRAKER, and (3) protein clustering with OrthoFinder. A published long-read assembly of C. zeina (CMW25467) from Zambia was included and annotated using the same pipeline. This analysis revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. Accessory gene content was largely shared between isolates from all countries, with a few genes unique to populations from Southern Africa (32) or East Africa (6). There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). PCA, ADMIXTURE, and phylogenetic analysis using a neighbor-net network indicated a population structure with a geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, possibly from 2 regional founder populations, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa.
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Affiliation(s)
- Tanya Welgemoed
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-11, Kiel 24118, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön 24306, Germany
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
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12
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Mlambo G, Padayachee T, Nelson DR, Syed K. Genome-Wide Analysis of the Cytochrome P450 Monooxygenases in the Lichenized Fungi of the Class Lecanoromycetes. Microorganisms 2023; 11:2590. [PMID: 37894248 PMCID: PMC10608907 DOI: 10.3390/microorganisms11102590] [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: 08/18/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Lichens are unique organisms that exhibit a permanent symbiosis between fungi and algae or fungi and photosynthetic bacteria. Lichens have been found to produce biotechnologically valuable secondary metabolites. A handful of studies showed that tailoring enzymes such as cytochrome P450 monooxygenases (CYPs/P450s) play a key role in synthesizing these metabolites. Despite the critical role of P450s in the biosynthesis of secondary metabolites, the systematic analysis of P450s in lichens has yet to be reported. This study is aimed to address this research gap. A genome-wide analysis of P450s in five lichens from the fungal class Lecanoromycetes revealed the presence of 434 P450s that are grouped into 178 P450 families and 345 P450 subfamilies. The study indicated that none of the P450 families bloomed, and 15 P450 families were conserved in all five Lecanoromycetes. Lecanoromycetes have more P450s and higher P450 family diversity compared to Pezizomycetes. A total of 73 P450s were found to be part of secondary metabolite gene clusters, indicating their potential involvement in the biosynthesis of secondary metabolites. Annotation of P450s revealed that CYP682BG1 and CYP682BG2 from Cladonia grayi and Pseudevernia furfuracea (physodic acid chemotype) are involved in the synthesis of grayanic acid and physodic acid, CYP65FQ2 from Stereocaulon alpinum is involved in the synthesis of atranorin, and CYP6309A2 from Cladonia uncialis is involved in the synthesis of usnic acid. This study serves as a reference for future annotation of P450s in lichens.
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Affiliation(s)
- Gugulethu Mlambo
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Vulindlela, KwaDlangezwa 3886, South Africa; (G.M.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Vulindlela, KwaDlangezwa 3886, South Africa; (G.M.); (T.P.)
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Vulindlela, KwaDlangezwa 3886, South Africa; (G.M.); (T.P.)
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13
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Subban K, Kempken F. Insights into Taxol® biosynthesis by endophytic fungi. Appl Microbiol Biotechnol 2023; 107:6151-6162. [PMID: 37606790 PMCID: PMC10560151 DOI: 10.1007/s00253-023-12713-y] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/23/2023]
Abstract
There have been two hundred reports that endophytic fungi produce Taxol®, but its production yield is often rather low. Although considerable efforts have been made to increase Taxol/taxanes production in fungi by manipulating cocultures, mutagenesis, genome shuffles, and gene overexpression, little is known about the molecular signatures of Taxol biosynthesis and its regulation. It is known that some fungi have orthologs of the Taxol biosynthetic pathway, but the overall architecture of this pathway is unknown. A biosynthetic putative gene homology approach, combined with genomics and transcriptomics analysis, revealed that a few genes for metabolite residues may be located on dispensable chromosomes. This review explores a number of crucial topics (i) finding biosynthetic pathway genes using precursors, elicitors, and inhibitors; (ii) orthologs of the Taxol biosynthetic pathway for rate-limiting genes/enzymes; and (iii) genomics and transcriptomics can be used to accurately predict biosynthetic putative genes and regulators. This provides promising targets for future genetic engineering approaches to produce fungal Taxol and precursors. KEY POINTS: • A recent trend in predicting Taxol biosynthetic pathway from endophytic fungi. • Understanding the Taxol biosynthetic pathway and related enzymes in fungi. • The genetic evidence and formation of taxane from endophytic fungi.
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Affiliation(s)
- Kamalraj Subban
- Department of Genetics & Molecular Biology in Botany, Botanical Institute and Botanical Garden, Christian-Albrecht University of Kiel, Olshausenstraße 40, 24098, Kiel, Germany
| | - Frank Kempken
- Department of Genetics & Molecular Biology in Botany, Botanical Institute and Botanical Garden, Christian-Albrecht University of Kiel, Olshausenstraße 40, 24098, Kiel, Germany.
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Tseng WS, Lee MJ, Wu JA, Kuo SL, Chang SL, Huang SJ, Liu CT. Poly(butylene adipate-co-terephthalate) biodegradation by Purpureocillium lilacinum strain BA1S. Appl Microbiol Biotechnol 2023; 107:6057-6070. [PMID: 37526695 DOI: 10.1007/s00253-023-12704-z] [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: 05/15/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023]
Abstract
Poly(butylene adipate-co-terephthalate) (PBAT), a promising biodegradable aliphatic-aromatic copolyester material, can be applied as an alternative material to reduce the adverse effects of conventional plastics. However, the degradation of PBAT plastics in soil is time-consuming, and effective PBAT-degrading microorganisms have rarely been reported. In this study, the biodegradation properties of PBAT by an elite fungal strain and related mechanisms were elucidated. Four PBAT-degrading fungal strains were isolated from farmland soils, and Purpureocillium lilacinum strain BA1S showed a prominent degradation rate. It decomposed approximately 15 wt.% of the PBAT films 30 days after inoculation. Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and Liquid chromatography mass spectrometry (LC‒MS) were conducted to analyze the physicochemical properties and composition of the byproducts after biodegradation. In the presence of PBAT, the lipolytic enzyme activities of BA1S were remarkably induced, and its cutinase gene was also significantly upregulated. Of note, the utilization of PBAT in BA1S cells was closely correlated with intracellular cytochrome P450 (CYP) monooxygenase. Furthermore, CreA-mediated carbon catabolite repression was confirmed to be involved in regulating PBAT-degrading hydrolases and affected the degradation efficiency. This study provides new insight into the degradation of PBAT by elite fungal strains and increases knowledge on the mechanism, which can be applied to control the biodegradability of PBAT films in the future. KEY POINTS: • Purpureocillium lilacinum strain BA1S was isolated from farmland soils and degraded PBAT plastic films at a prominent rate. • The lipolytic enzyme activities of strain BA1S were induced during coculture with PBAT, and the cutinase gene was significantly upregulated during PBAT degradation. • CreA-mediated carbon catabolite repression of BA1S plays an essential role in regulating the expression of PBAT-degrading hydrolases.
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Affiliation(s)
- Wei-Sung Tseng
- Institute of Biotechnology, National Taiwan University, R412, No. 81, Chang-Xing St, Taipei, 106, Taiwan
| | - Min-Jia Lee
- Institute of Biotechnology, National Taiwan University, R412, No. 81, Chang-Xing St, Taipei, 106, Taiwan
| | - Jin-An Wu
- Material and Chemical Research Laboratories, Industrial Technology Research Institute, 321 Kuang Fu Rd., Section 2, Hsinchu, Taiwan
| | - Shin-Liang Kuo
- Material and Chemical Research Laboratories, Industrial Technology Research Institute, 321 Kuang Fu Rd., Section 2, Hsinchu, Taiwan
| | - Sheng-Lung Chang
- Material and Chemical Research Laboratories, Industrial Technology Research Institute, 321 Kuang Fu Rd., Section 2, Hsinchu, Taiwan
| | - Shu-Jiuan Huang
- Material and Chemical Research Laboratories, Industrial Technology Research Institute, 321 Kuang Fu Rd., Section 2, Hsinchu, Taiwan
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, R412, No. 81, Chang-Xing St, Taipei, 106, Taiwan.
- Department of Agricultural Chemistry, National Taiwan University No, 1, Sec. Roosevelt Road, Taipei, 106, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, No.128, Sec.2, Academia Rd., Nankang, Taipei, 115, Taiwan.
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15
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Kong L, Chen J, Dong K, Shafik K, Xu W. Genomic analysis of Colletotrichum camelliae responsible for tea brown blight disease. BMC Genomics 2023; 24:528. [PMID: 37674131 PMCID: PMC10483846 DOI: 10.1186/s12864-023-09598-6] [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: 11/22/2022] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Colletotrichum camelliae, one of the most important phytopathogenic fungi infecting tea plants (Camellia sinensis), causes brown blight disease resulting in significant economic losses in yield of some sensitive cultivated tea varieties. To better understand its phytopathogenic mechanism, the genetic information is worth being resolved. RESULTS Here, a high-quality genomic sequence of C. camelliae (strain LT-3-1) was sequenced using PacBio RSII sequencing platform, one of the most advanced Three-generation sequencing platforms and assembled. The result showed that the fungal genomic sequence is 67.74 Mb in size (with the N50 contig 5.6 Mb in size) containing 14,849 putative genes, of which about 95.27% were annotated. The data revealed a large class of genomic clusters potentially related to fungal pathogenicity. Based on the Pathogen Host Interactions database, a total of 1698 genes (11.44% of the total ones) were annotated, containing 541 genes related to plant cell wall hydrolases which is remarkably higher than those of most species of Colletotrichum and others considered to be hemibiotrophic and necrotrophic fungi. It's likely that the increase in cell wall-degrading enzymes reflects a crucial adaptive characteristic for infecting tea plants. CONCLUSION Considering that C. camelliae has a specific host range and unique morphological and biological traits that distinguish it from other species of the genus Colletotrichum, characterization of the fungal genome will improve our understanding of the fungus and its phytopathogenic mechanism as well.
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Affiliation(s)
- Linghong Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Jiao Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Kaili Dong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Karim Shafik
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
- Department of plant pathology, Faculty of Agriculture, Alexandria University, Alexandria, 21526, Egypt
| | - Wenxing Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China.
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China.
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16
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Khan MF, Hof C, Niemcová P, Murphy CD. Recent advances in fungal xenobiotic metabolism: enzymes and applications. World J Microbiol Biotechnol 2023; 39:296. [PMID: 37658215 PMCID: PMC10474215 DOI: 10.1007/s11274-023-03737-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
Fungi have been extensively studied for their capacity to biotransform a wide range of natural and xenobiotic compounds. This versatility is a reflection of the broad substrate specificity of fungal enzymes such as laccases, peroxidases and cytochromes P450, which are involved in these reactions. This review gives an account of recent advances in the understanding of fungal metabolism of drugs and pollutants such as dyes, agrochemicals and per- and poly-fluorinated alkyl substances (PFAS), and describes the key enzymes involved in xenobiotic biotransformation. The potential of fungi and their enzymes in the bioremediation of polluted environments and in the biocatalytic production of important compounds is also discussed.
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Affiliation(s)
- Mohd Faheem Khan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Carina Hof
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Patricie Niemcová
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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17
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Zheng Y, Zhang W, Xiong Y, Wang J, Jin S, Qiao H, Jiang S, Fu H. Dual roles of CYP302A1 in regulating ovarian maturation and molting in Macrobrachium nipponense. J Steroid Biochem Mol Biol 2023; 232:106336. [PMID: 37247747 DOI: 10.1016/j.jsbmb.2023.106336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
CYP302A1 is a member of the Halloween genes in the cytochrome P450 supergene family, which play an important regulatory role in the synthesis of 20-hydroxyecdysone (20E) in crustaceans and insects. In this study, we found that the Mn-CYP302A1sequence included typical CYP450 conserved domains. Phylogenic showed that it is closely related to crustaceans and insects. q-PCR analysis indicated that Mn-CYP302A1 was highly expressed in the ovaries and peaked before ovarian maturation. Mn-CYP302A1 expression was higher at the post-larval stage of day 15 than at other stages of embryogenesis. In situ hybridization indicated that Mn-CYP302A1 was mainly distributed in the nucleus, yolk granules, cell membrane and cytoplasm To further establish the function of CYP302A1, a 21-day RNA interference experiment was conducted. On day 16, the Gonad Somatic Index of the control group and the experimental group showed significant differences, with GSI of 11.72% in the control group and 3.21% in the experimental group. The cumulative proportion of the second entry into stage O-Ⅲ was 100% in the control group, while it was 41.67% in the experimental group on day 21. The ecdysone content was 8.91nmol/L in the control group and 6.11nmol/L in the experimental group on day 9. A significant difference in the molting proportion between the control group and the experimental group was also observed (49% in the control group and 34% in the experimental group) on day 16. Statistical results showed that the average molting cycle of the control group was 14.5 days, while that of the experimental group was 16.5 days. However, the morphological structure of ovarian tissue did not abnormal change. Therefore, the results of this study suggest that Mn-CYP302A1 can promote ovarian maturation and molting in female M. nipponense.
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Affiliation(s)
- Yalu Zheng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jisheng Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hui Qiao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Sufei Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Hongtuo Fu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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Li Z, Hu JR, Li WH, Wang HC, Guo ZN, Cheng X, Cai LT, Shi CH. Characteristics of Epicoccum latusicollum as revealed by genomic and metabolic phenomic analysis, the causal agent of tobacco Epicoccus leaf spot. FRONTIERS IN PLANT SCIENCE 2023; 14:1199956. [PMID: 37828924 PMCID: PMC10565823 DOI: 10.3389/fpls.2023.1199956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/03/2023] [Indexed: 10/14/2023]
Abstract
Epicoccum latusicollum is a fungus that causes a severe foliar disease on flue-cured tobacco in southwest China, resulting in significant losses in tobacco yield and quality. To better understand the organism, researchers investigated its optimal growth conditions and metabolic versatility using a combination of traditional methods and the Biolog Phenotype MicroArray technique. The study found that E. latusicollum exhibited impressive metabolic versatility, being able to metabolize a majority of carbon, nitrogen, sulfur, and phosphorus sources tested, as well as adapt to different environmental conditions, including broad pH ranges and various osmolytes. The optimal medium for mycelial growth was alkyl ester agar medium, while oatmeal agar medium was optimal for sporulation, and the optimum temperature for mycelial growth was 25°C. The lethal temperature was 40°C. The study also identified arbutin and amygdalin as optimal carbon sources and Ala-Asp and Ala-Glu as optimal nitrogen sources for E. latusicollum. Furthermore, the genome of E. latusicollum strain T41 was sequenced using Illumina HiSeq and Pacific Biosciences technologies, with 10,821 genes predicted using Nonredundant, Gene Ontology, Clusters of Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and SWISS-PROT databases. Analysis of the metabolic functions of phyllosphere microorganisms on diseased tobacco leaves affected by E. latusicollum using the Biolog Eco microplate revealed an inability to efficiently metabolize a total of 29 carbon sources, with only tween 40 showing some metabolizing ability. The study provides new insights into the structure and function of phyllosphere microbiota and highlights important challenges for future research, as well as a theoretical basis for the integrated control and breeding for disease resistance of tobacco Epicoccus leaf spot. This information can be useful in developing new strategies for disease control and management, as well as enhancing crop productivity and quality.
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Affiliation(s)
- Zhen Li
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Jing-rong Hu
- Institute of Advanced Agricultural Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Zhen-ni Guo
- MGI Tech Co., Ltd Research and Development Centre for Laboratory Automation, Shenzhen, Guangzhou, China
| | - Xing Cheng
- College of Ecology and Environment, Hainan University, Haikou, Hainan, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Cai-hua Shi
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- School of Food Science and Technology & School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, Hubei, China
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Liang L, Zhang W, Hao J, Wang Y, Wei S, Zhang S, Hu Y, Lv Y. Estragole Inhibits Growth and Aflatoxin Biosynthesis of Aspergillus flavus by Affecting Reactive Oxygen Species Homeostasis. Microbiol Spectr 2023; 11:e0134823. [PMID: 37289093 PMCID: PMC10434025 DOI: 10.1128/spectrum.01348-23] [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: 03/28/2023] [Accepted: 05/21/2023] [Indexed: 06/09/2023] Open
Abstract
A variety of essential oils and edible compounds have been widely recognized for their antifungal activity in recent years. In this study, we explored the antifungal activity of estragole from Pimenta racemosa against Aspergillus flavus and investigated the underlying mechanism of action. The results showed that estragole had significant antifungal activity against A. flavus, with a minimum inhibitory concentration of 0.5 μL/mL against spore germination. Additionally, estragole inhibited the biosynthesis of aflatoxin in a dose-dependent manner, and aflatoxin biosynthesis was significantly inhibited at 0.125 μL/mL. Pathogenicity assays showed that estragole had potential antifungal activity against A. flavus in peanut and corn grains by inhibiting conidia and aflatoxin production. Transcriptomic analysis showed that the differentially expressed genes (DEGs) were mainly related to oxidative stress, energy metabolism, and secondary metabolite synthesis following estragole treatment. Importantly, we experimentally verified reactive oxidative species accumulation following downregulation of antioxidant enzymes, including catalase, superoxide dismutase, and peroxidase. These results suggest that estragole inhibits the growth and aflatoxin biosynthesis of A. flavus by modulating intracellular redox homeostasis. These findings expand our knowledge on the antifungal activity and molecular mechanisms of estragole, and provide a basis for estragole as a potential agent against A. flavus contamination. IMPORTANCE Aspergillus flavus contaminates crops and produces aflatoxins, carcinogenic secondary metabolites which pose a serious threat to agricultural production and animal and human health. Currently, control of A. flavus growth and mycotoxin contamination mainly relies on antimicrobial chemicals, agents with side effects such as toxic residues and the emergence of resistance. With their safety, environmental friendliness, and high efficiency, essential oils and edible compounds have become promising antifungal agents to control growth and mycotoxin biosynthesis in hazardous filamentous fungi. In this study, we explored the antifungal activity of estragole from Pimenta racemosa against A. flavus and investigated its underlying mechanism. The results demonstrated that estragole inhibits the growth and aflatoxin biosynthesis of A. flavus by modulating intracellular redox homeostasis.
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Affiliation(s)
- Liuke Liang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Wei Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Jing Hao
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yanyu Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yuansen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
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Nsele NN, Padayachee T, Nelson DR, Syed K. Pezizomycetes Genomes Reveal Diverse P450 Complements Characteristic of Saprotrophic and Ectomycorrhizal Lifestyles. J Fungi (Basel) 2023; 9:830. [PMID: 37623601 PMCID: PMC10455484 DOI: 10.3390/jof9080830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are heme proteins that play a role in organisms' primary and secondary metabolism. P450s play an important role in organism adaptation since lifestyle influences P450 composition in their genome. This phenomenon is well-documented in bacteria but less so in fungi. This study observed this phenomenon where diverse P450 complements were identified in saprophytic and ectomycorrhizal Pezizomycetes. Genome-wide data mining, annotation, and phylogenetic analysis of P450s in 19 Pezizomycetes revealed 668 P450s that can be grouped into 153 P450 families and 245 P450 subfamilies. Only four P450 families, namely, CYP51, CYP61, CYP5093, and CYP6001, are conserved across 19 Pezizomycetes, indicating their important role in these species. A total of 5 saprophyte Pezizomycetes have 103 P450 families, whereas 14 ectomycorrhizal Pezizomycetes have 89 P450 families. Only 39 P450 families were common, and 50 and 64 P450 families, respectively, were unique to ectomycorrhizal and saprophytic Pezizomycetes. These findings suggest that the switch from a saprophytic to an ectomycorrhizal lifestyle led to both the development of diverse P450 families as well as the loss of P450s, which led to the lowest P450 family diversity, despite the emergence of novel P450 families in ectomycorrhizal Pezizomycetes.
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Affiliation(s)
- Nomfundo Ntombizinhle Nsele
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.N.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.N.); (T.P.)
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.N.); (T.P.)
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Gao H, Ye S, Liu Y, Fan X, Yin C, Liu Y, Liu J, Qiao Y, Chen X, Yao F, Shi D. Transcriptome analysis provides insight into gamma irradiation delaying quality deterioration of postharvest Lentinula edodes during cold storage. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 6:100172. [PMID: 37213208 PMCID: PMC10199187 DOI: 10.1016/j.fochms.2023.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/27/2023] [Accepted: 05/06/2023] [Indexed: 05/23/2023]
Abstract
To better determine how gamma irradiation (GI) improves abiotic stress resistance, a transcriptome analysis of postharvest L. edodes in response to 1.0 kGy GI was conducted, and further the underlying mechanism of GI in delaying quality deterioration over 20 d of cold storage was explored. The results suggested that GI was involved in multiple metabolic processes in irradiated postharvest L. edodes. In comparison with the control group, the GI group contained 430 differentially expressed genes, including 151 upregulated genes and 279 downregulated genes, which unveiled characteristic expression profiles and pathways. The genes involved in the pentose phosphate pathway were mainly upregulated and the expression level of the gene encoding deoxy-D-gluconate 3-dehydrogenase was 9.151-fold higher. In contrast, the genes related to other energy metabolism pathways were downregulated. Concurrently, GI inhibited the expression of genes associated with delta 9-fatty acid desaturase, ribosomes, and HSP20; thus, GI helped postpone the degradation of lipid components, suppress transcriptional metabolism and regulate the stress response. Additionally, the metabolic behavior of DNA repair induced by GI intensified by noticeable upregulation. These regulatory effects could play a potential and nonnegligible role in delaying the deterioration of L. edodes quality. The results provide new information on the regulatory mechanism of postharvest L. edodes when subjected to 1.0 kGy GI during cold storage.
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Affiliation(s)
- Hong Gao
- Key Laboratory of Cold Chain Logistics Technology for Agro-product, Ministry of Agriculture and Rural Affairs, Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Shuang Ye
- School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Yani Liu
- School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Xiuzhi Fan
- Key Laboratory of Cold Chain Logistics Technology for Agro-product, Ministry of Agriculture and Rural Affairs, Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Chaomin Yin
- Key Laboratory of Cold Chain Logistics Technology for Agro-product, Ministry of Agriculture and Rural Affairs, Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Ying Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingyu Liu
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Yu Qiao
- Key Laboratory of Cold Chain Logistics Technology for Agro-product, Ministry of Agriculture and Rural Affairs, Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xueling Chen
- Key Laboratory of Cold Chain Logistics Technology for Agro-product, Ministry of Agriculture and Rural Affairs, Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Fen Yao
- Key Laboratory of Cold Chain Logistics Technology for Agro-product, Ministry of Agriculture and Rural Affairs, Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Defang Shi
- Key Laboratory of Cold Chain Logistics Technology for Agro-product, Ministry of Agriculture and Rural Affairs, Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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22
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Jiang JP, Liu X, Liao YF, Shan J, Zhu YP, Liu CH. Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments. Front Microbiol 2023; 14:1216714. [PMID: 37455735 PMCID: PMC10339353 DOI: 10.3389/fmicb.2023.1216714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Aspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited. Methods Here, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform. Results and Discussion The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years.
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Affiliation(s)
- Jun-Peng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yi-Fan Liao
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yu-Ping Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
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Prasher IB, Ahmad N, Ahmed M, Raghuwanshi S, Kumar V, Siddiqui SI, Oh S. Live Biomass of Rigidoporus vinctus: A Sustainable Method for Decoloration and Detoxification of Dyes in Water. Microorganisms 2023; 11:1435. [PMID: 37374937 DOI: 10.3390/microorganisms11061435] [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: 04/16/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
In this study, white-rot fungus, Rigidoporus vinctus, collected from an unidentified fallen twig from Pathankot, Punjab, India, was used for biosorption of anionic Congo red and cationic Methylene blue dyes from an aqueous medium. The biosorption efficiency of the live biomass of Rigidoporus vinctus was investigated to optimize biosorbent dosage, process time, concentrations of dyes, and pH of solutions. The results indicated that Rigidoporus vinctus is more efficient than other reported bio-adsorbents for Congo red and Methylene blue dyes. The maximum biosorption activity of Rigidoporus vinctus for Congo red was found at pH 2, and that for Methylene blue was at pH 10, after 24 h of the reaction period. The process followed pseudo-second-order kinetics, which indicated that the interaction of both dyes to the adsorption sites on the surface of Rigidoporus vinctus was responsive to biosorption. The biosorption process could be well explained by the Langmuir isotherm for both dyes. The maximum monolayer biosorption capacity of Rigidoporus vinctus for Congo red and Methylene blue was observed to be 54.0 mg/g and 80.6 mg/g, respectively. The seed germination test was carried out, and it was assessed that the toxicity of dyes was reduced up to significant levels. Based on the present experimental findings, it can be concluded that biosorption using the live biomass of Rigidoporus vinctus can effectively decolorize dye-containing wastewater, thus reducing the hazardous effects of dyes on human beings.
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Affiliation(s)
- I B Prasher
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Naushad Ahmad
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mukhtar Ahmed
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Vijay Kumar
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Sharf Ilahi Siddiqui
- Department of Chemistry, Ramjas College, University of Delhi, Delhi 110007, India
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea
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Gong Z, Jin L, Yu X, Wang B, Hu S, Ruan H, Sung YJ, Lee HG, Jin F. Biodegradation of Low Density Polyethylene by the Fungus Cladosporium sp. Recovered from a Landfill Site. J Fungi (Basel) 2023; 9:605. [PMID: 37367541 DOI: 10.3390/jof9060605] [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: 04/23/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Low density polyethylene (LDPE) has been widely used commercially for decades; however, as a non-degradable material, its continuous accumulation has contributed to serious environmental issues. A fungal strain, Cladosporium sp. CPEF-6 exhibiting a significant growth advantage on MSM-LDPE (minimal salt medium), was isolated and selected for biodegradation analysis. LDPE biodegradation was analyzed by weight loss percent, change in pH during fungal growth, environmental scanning electron microscopy (ESEM), and Fourier transformed infrared spectroscopy (FTIR). Inoculation with the strain Cladosporium sp. CPEF-6 resulted in a 0.30 ± 0.06% decrease in the weight of untreated LDPE (U-LDPE). After heat treatment (T-LDPE), the weight loss of LDPE increased significantly and reached 0.43 ± 0.01% after 30 days of culture. The pH of the medium was measured during LDPE degradation to assess the environmental changes caused by enzymes and organic acids secreted by the fungus. The fungal degradation of LDPE sheets was characterized by ESEM analysis of topographical alterations, such as cracks, pits, voids, and roughness. FTIR analysis of U-LDPE and T-LDPE revealed the appearance of novel functional groups associated with hydrocarbon biodegradation as well as changes in the polymer carbon chain, confirming the depolymerization of LDPE. This is the first report demonstrating the capacity of Cladosporium sp. to degrade LDPE, with the expectation that this finding can be used to ameliorate the negative impact of plastics on the environment.
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Affiliation(s)
- Zhu Gong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Long Jin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Xingye Yu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Baoteng Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Shuang Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Yun-Ju Sung
- Technology Transfer Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Fengjie Jin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
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25
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Yang J, Wang S, Zhang Y, Chen Y, Zhou H, Zhang G. Identification, Culture Characteristics and Whole-Genome Analysis of Pestalotiopsis neglecta Causing Black Spot Blight of Pinus sylvestris var. mongolica. J Fungi (Basel) 2023; 9:jof9050564. [PMID: 37233276 DOI: 10.3390/jof9050564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Black spot needle blight is a serious conifer disease of Pinus sylvestris var. mongolica occurring in Northeast China, which is usually caused by the plant pathogenic fungus Pestalotiopsis neglecta. From the diseased pine needles collected in Honghuaerji, the P. neglecta strain YJ-3 was isolated and identified as the phytopathogen, and its culture characteristics were studied. Then, we generated a highly contiguous 48.36-Mbp genome assembly (N50 = 6.62 Mbp) of the P. neglecta strain YJ-3 by combining the PacBio RS II Single Molecule Real Time (SMRT) and Illumina HiSeq X Ten sequencing platforms. The results showed that a total of 13,667 protein-coding genes were predicted and annotated using multiple bioinformatics databases. The genome assembly and annotation resource reported here will be useful for the study of fungal infection mechanisms and pathogen-host interaction.
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Affiliation(s)
- Jing Yang
- College of Forestry, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Shuren Wang
- Heilongjiang Province Key Laboratory of Forest Protection, School of Forest, Northeast Forestry University, Hexing Road 26, Xiangfang District, Harbin 150040, China
| | - Yundi Zhang
- Heilongjiang Province Key Laboratory of Forest Protection, School of Forest, Northeast Forestry University, Hexing Road 26, Xiangfang District, Harbin 150040, China
| | - Yunze Chen
- School of Biological Sciences, Guizhou Education University, Wudang District, Guiyang 550018, China
| | - Heying Zhou
- College of Forestry, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Guocai Zhang
- Heilongjiang Province Key Laboratory of Forest Protection, School of Forest, Northeast Forestry University, Hexing Road 26, Xiangfang District, Harbin 150040, China
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26
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González-Rodríguez S, Trueba-Santiso A, Lu-Chau TA, Moreira MT, Eibes G. Valorization of bioethanol by-products to produce unspecific peroxygenase with Agrocybe aegerita: technological and proteomic perspectives. N Biotechnol 2023; 76:63-71. [PMID: 37169331 DOI: 10.1016/j.nbt.2023.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/22/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
Unspecific peroxygenase (UPO) presents a wide range of biotechnological applications. This study targets the use of by-products from bioethanol synthesis to produce UPO by Agrocybe aegerita. Solid-state and submerged fermentations (SSF and SmF) were evaluated, achieving the highest titers of UPO and laccase in SmF using vinasse as nutrients source. Optimized UPO production of 331U/L was achieved in 50% (v:v) vinasse with an inoculum grown for 14 days. These conditions were scaled-up to a 4L reactor, achieving a UPO activity of 265U/L. Fungal proteome expression was analyzed before and after UPO activity appeared by shotgun mass spectrometry proteomics. Laccase, dye-decolorizing peroxidases (DyP), lectins and proteins involved in reactive oxygen species (ROS) production and control were detected (in addition to UPO). Interestingly, the metabolism of complex sugars and nitrogen sources had a different activity at the beginning and end of the submerged fermentation. DATA AVAILABILITY: The data used to support the findings of this study are available from the corresponding author upon reasonable request.
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Affiliation(s)
- Sandra González-Rodríguez
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain.
| | - Alba Trueba-Santiso
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - Thelmo A Lu-Chau
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - María Teresa Moreira
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - Gemma Eibes
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
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Haduch A, Bromek E, Kuban W, Daniel WA. The Engagement of Cytochrome P450 Enzymes in Tryptophan Metabolism. Metabolites 2023; 13:metabo13050629. [PMID: 37233670 DOI: 10.3390/metabo13050629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Tryptophan is metabolized along three main metabolic pathways, namely the kynurenine, serotonin and indole pathways. The majority of tryptophan is transformed via the kynurenine pathway, catalyzed by tryptophan-2,3-dioxygenase or indoleamine-2,3-dioxygenase, leading to neuroprotective kynurenic acid or neurotoxic quinolinic acid. Serotonin synthesized by tryptophan hydroxylase, and aromatic L-amino acid decarboxylase enters the metabolic cycle: serotonin → N-acetylserotonin → melatonin → 5-methoxytryptamine→serotonin. Recent studies indicate that serotonin can also be synthesized by cytochrome P450 (CYP), via the CYP2D6-mediated 5-methoxytryptamine O-demethylation, while melatonin is catabolized by CYP1A2, CYP1A1 and CYP1B1 via aromatic 6-hydroxylation and by CYP2C19 and CYP1A2 via O-demethylation. In gut microbes, tryptophan is metabolized to indole and indole derivatives. Some of those metabolites act as activators or inhibitors of the aryl hydrocarbon receptor, thus regulating the expression of CYP1 family enzymes, xenobiotic metabolism and tumorigenesis. The indole formed in this way is further oxidized to indoxyl and indigoid pigments by CYP2A6, CYP2C19 and CYP2E1. The products of gut-microbial tryptophan metabolism can also inhibit the steroid-hormone-synthesizing CYP11A1. In plants, CYP79B2 and CYP79B3 were found to catalyze N-hydroxylation of tryptophan to form indole-3-acetaldoxime while CYP83B1 was reported to form indole-3-acetaldoxime N-oxide in the biosynthetic pathway of indole glucosinolates, considered to be defense compounds and intermediates in the biosynthesis of phytohormones. Thus, cytochrome P450 is engaged in the metabolism of tryptophan and its indole derivatives in humans, animals, plants and microbes, producing biologically active metabolites which exert positive or negative actions on living organisms. Some tryptophan-derived metabolites may influence cytochrome P450 expression, affecting cellular homeostasis and xenobiotic metabolism.
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Affiliation(s)
- Anna Haduch
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Ewa Bromek
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Wojciech Kuban
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Władysława Anna Daniel
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Kraków, Poland
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28
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Permana D, Kitaoka T, Ichinose H. Conversion and synthesis of chemicals catalyzed by fungal cytochrome P450 monooxygenases: A review. Biotechnol Bioeng 2023. [PMID: 37139574 DOI: 10.1002/bit.28411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
Cytochrome P450s (also called CYPs or P450s) are a superfamily of heme-containing monooxygenases. They are distributed in all biological kingdoms. Most fungi have at least two P450-encoding genes, CYP51 and CYP61, which are housekeeping genes that play important roles in the synthesis of sterols. However, the kingdom fungi is an interesting source of numerous P450s. Here, we review reports on fungal P450s and their applications in the bioconversion and biosynthesis of chemicals. We highlight their history, availability, and versatility. We describe their involvement in hydroxylation, dealkylation, oxygenation, C═C epoxidation, C-C cleavage, C-C ring formation and expansion, C-C ring contraction, and uncommon reactions in bioconversion and/or biosynthesis pathways. The ability of P450s to catalyze these reactions makes them promising enzymes for many applications. Thus, we also discuss future prospects in this field. We hope that this review will stimulate further study and exploitation of fungal P450s for specific reactions and applications.
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Affiliation(s)
- Dani Permana
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Research Center for Environmental and Clean Technology, The National Research and Innovation Agency of the Republic of Indonesia (Badan Riset dan Inovasi Nasional (BRIN)), Bandung Advanced Science and Creative Engineering Space (BASICS), Kawasan Sains dan Teknologi (KST) Prof. Dr. Samaun Samadikun, Bandung, Indonesia
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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29
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Nehela Y, Mazrou YSA, Taha NA, Elzaawely AA, Xuan TD, Makhlouf AH, El-Nagar A. Hydroxylated Cinnamates Enhance Tomato Resilience to Alternaria alternata, the Causal Agent of Early Blight Disease, and Stimulate Growth and Yield Traits. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091775. [PMID: 37176833 PMCID: PMC10181299 DOI: 10.3390/plants12091775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
The important vegetable crop, tomato, is challenged with numerous abiotic and biotic stressors, particularly the newly emerged fungicide-resistant strains of phytopathogenic fungi such as Alternaria alternata, the causal agent of early blight disease. The current study investigated the potential antifungal activity of four cinnamate derivatives including cinnamic acid, ρ-coumaric acid, caffeic acid, and ferulic acid against A. alternata. Our in vitro findings showed that all tested compounds exhibited dose-dependent fungistatic action against A. alternata when their concentrations were increased from 0.1, 0.3, 0.5, and 0.7, to 0.9 mM, respectively. The high concentration of ferulic acid (0.9 mM) completely inhibited the radial mycelial growth of A. alternata and it was comparable to the positive control (difenoconazole fungicide). Additionally, under greenhouse conditions, foliar application of the four tested cinnamates significantly reduced the severity of early blight disease without any phytotoxicity on treated tomato plants. Moreover, it significantly improved the growth traits (plant height, total leaf area, number of leaves per plant, and shoot fresh weight), total chlorophyll, and yield components (number of flowers per plant, number of fruits per plant, and fruit yield) of treated A. alternata-infected plants. Collectively, our findings suggest that cinnamate derivatives could be good candidates as eco-friendly alternatives to reduce the use of chemical fungicides against A. alternata.
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Affiliation(s)
- Yasser Nehela
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
| | - Yasser S A Mazrou
- Business Administration Department, Community College, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
- Department of Agriculture Economic, Faculty of Agriculture, Tanta University, Tanta 31511, Egypt
| | - Naglaa A Taha
- Vegetable Diseases Research Department, Agricultural Research Center, Plant Pathology Research Institute, Giza 12619, Egypt
| | - Abdelnaser A Elzaawely
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
| | - Tran Dang Xuan
- Transdisciplinary Science and Engineering Program, Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi-Hiroshima 739-8529, Japan
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima 739-8529, Japan
| | - Abeer H Makhlouf
- Department of Agricultural Botany, Faculty of Agriculture, Minufiya University, Shibin El-Kom 32511, Egypt
| | - Asmaa El-Nagar
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
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Gudeta K, Kumar V, Bhagat A, Julka JM, Bhat SA, Ameen F, Qadri H, Singh S, Amarowicz R. Ecological adaptation of earthworms for coping with plant polyphenols, heavy metals, and microplastics in the soil: A review. Heliyon 2023; 9:e14572. [PMID: 36994405 PMCID: PMC10040515 DOI: 10.1016/j.heliyon.2023.e14572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
In recent years, soil pollution by massive accumulation of heavy metals (HMs), microplastics, and refractory hydrocarbon chemicals has become an emerging and global concern, drawing worldwide attention. These pollutants influence soil diversity by hindering the reproduction, abundance, thereby affecting aboveground productivity. The scientific community has recently emphasized the contribution of earthworms to heavy metal accumulation, microplastic degradation, and the decomposition of organic matter in the soil, which helps maintain the soil structure. This review paper aimed to compile scientific facts on how earthworms cope with the effect of HMs, microplastics, and plant polyphenols so that vermiremediation could be widely applied for well-being of the soil ecosystem by environmentalists. Earthworms have special surface-active metabolites in their guts called drilodefensins that help them defend themselves against the oxidative action of plant polyphenols. They also combat the effects of toxic microplastics, and other oxidative compounds by elevating the antioxidant activities of their enzymes and converting them into harmless compounds or useful nutrients. Moreover, earthworms also act as biofilters, bioindicators, bioaccumulators, and transformers of oxidative polyphenols, microplastics, toxic HMs, and other pollutant hydrocarbons. Microorganisms (fungi and bacteria) in earthworms' gut of also assist in the fixation, accumulation, and transformation of these toxicants to prevent their effects. As a potential organism for application in ecotoxicology, it is recommended to propagate earthworms in agricultural fields; isolate, and culture enormously in industry, and inoculate earthworms in the polluted soil, thereby abate toxicity and minimizing the health effect caused by these pollutants as well enhance the productivity of crops.
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Affiliation(s)
- Kasahun Gudeta
- Shoolini University of Biotechnology and Management Sciences, School of Biological and Environmental Sciences, Solan, 173229, Himachal Pradesh, India
- Adama Science and Technology University, Department of Applied Biology, P.O. Box 1888, Adama, Ethiopia
| | - Vineet Kumar
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Ankeet Bhagat
- Department of Zoology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Jatinder Mohan Julka
- Shoolini University of Biotechnology and Management Sciences, School of Biological and Environmental Sciences, Solan, 173229, Himachal Pradesh, India
| | - Sartaj Ahmad Bhat
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- Corresponding author.
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Humaira Qadri
- Department of Environmental Sciences, J&K Higher Education Department, Govt. Degree College, Baramulla, 193101, Kashmir, Jammu and Kashmir, India
| | - Sumit Singh
- Department of Zoology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ryszard Amarowicz
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, 10-748, Poland
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Li S, Chang Y, Liu Y, Tian W, Chang Z. A novel steroid hydroxylase from Nigrospora sphaerica with various hydroxylation capabilities to different steroid substrates. J Steroid Biochem Mol Biol 2023; 227:106236. [PMID: 36563764 DOI: 10.1016/j.jsbmb.2022.106236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/10/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022]
Abstract
Fungal hydroxylation of steroids is a key step in the industrial production of various steroid drugs. The main enzymes that enable these reactions are Cytochrome P450s (CYP), though very few industrially important CYPs have been identified and characterized. In this study, we identified a CYP enzyme (CYP-N2) and a cytochrome P450 reductase (CPRns) from Nigrospora sphaerica 722 by a combination of transcriptome sequencing and heterologous expression in Pichia pastoris. Gene CYP-N2 co-expressed with CPRns in Pichia pastoris GS115 showed 6β- and 15α-hydroxylation activities on progesterone. Different hydroxylation specificity of CYP-N2 was observed on different steroid substrates. CYP-N2 showed 1α-hydroxylation on cortisone and 1α-hydroxylation and 6β-hydroxylation activities on androstenedione (AD). With dehydroepiandrosterone (DHEA) as a substrate, the hydroxylated products of CYP-N2 included 7α-hydroxy-DHEA and 7α,15α-dihydroxy-DHEA. In order to precisely elucidate CYP-N2 biological function and find out the key amino acids influencing its hydroxylation capabilities in the binding pocket, new generation artificial intelligence technology AlphaFold 2 was used to predict the function-structure of CYP-N2 with high reliability. Through molecular docking, it was concluded that the residues almost binding all substrates were located in the same substrate binding pocket and the various hydroxylation abilities might be due to the different binding conformations of different substrates in the binding pocket. Alanine scanning mutagenesis was used to verify key amino acids identified by the molecular docking with steroid substrates. The 128 THR mutation resulted in conversion rate increase for substrates AD and cortisone by 2.6-fold and 2.1-fold respectively. The information obtained in this study is beneficial to facilitating the engineering of more efficient steroid hydroxylases for industrial applications.
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Affiliation(s)
- Shuailin Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, People's Republic of China
| | - Yaowen Chang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, People's Republic of China
| | - Yingnan Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, People's Republic of China
| | - Wei Tian
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, People's Republic of China.
| | - Zunxue Chang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, People's Republic of China.
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Tang Q, Ma Q, Xiao Z, Xiao Y, Wang Y, Liu L, Peng W, Wang B, Liu T, Song N. Identification and characterization of pathogenicity-related genes of Rhizoctonia solani AG3 during tobacco infection. FRONTIERS IN PLANT SCIENCE 2023; 13:1116506. [PMID: 36733585 PMCID: PMC9887180 DOI: 10.3389/fpls.2022.1116506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
Tobacco target spot disease is caused by a ubiquitous soil-borne phytopathogen Rhizoctonia solani; the pathogenic mechanisms underlying the effects of R. solani remain unclear. Deeper understanding of the functional responses to R. solani during host plant infection would help identify the molecular mechanisms essential for successful host invasion. In this study, we performed global transcriptional analysis of R. solani during various stages (12, 24, 48, 72, 96, and 120 h) of tobacco infection via an RNA sequencing method, while utilizing the pathosystem model R. solani AG3-tobacco (Nicotiana tabacum L.). After R. solani inoculation, the number of differentially expressed genes of R. solani differed at the various time points. Moreover, several gene ontology and Kyoto encyclopedia of genes and genomes pathways were unique in different infection stages, especially with respect to the genes involved in plant cell wall degradation and catalysis of biotransformation reactions, such as the pectin metabolic process and pectin catabolic process. The overexpressing-PD8 N. benthamiana plants enhanced the susceptibility to R. solani. In addition, we found that large amounts of reactive oxygen species (ROS) were generated in tobacco after infected by R. solani. R. solani encoding FAD/NAD binding oxidoreductase and peroxidase gene family to eliminating ROS and counteract oxidative stress. Moreover, Perox3 was validated that can enhance the ability of scavenging ROS by co-injecting. Overall, our findings show that pectin-degrading enzymes and cytochrome P450 genes are critical for plant infection. These results provide comprehensive insights into R. solani AG3 transcriptome responses during tobacco invasion.
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Affiliation(s)
- Qianjun Tang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Qianqian Ma
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhipeng Xiao
- Tobacco Research Institute of Hunan Provence, Changsha, Hunan, China
| | - Yansong Xiao
- Tobacco Research Institute of Hunan Provence, Changsha, Hunan, China
| | - Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Lei Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Weiye Peng
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Bing Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Tianbo Liu
- Tobacco Research Institute of Hunan Provence, Changsha, Hunan, China
| | - Na Song
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
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Nuclear Genome Sequence and Gene Expression of an Intracellular Fungal Endophyte Stimulating the Growth of Cranberry Plants. J Fungi (Basel) 2023; 9:jof9010126. [PMID: 36675947 PMCID: PMC9861600 DOI: 10.3390/jof9010126] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Ericaceae thrive in poor soil, which we postulate is facilitated by microbes living inside those plants. Here, we investigate the growth stimulation of the American cranberry (Vaccinium macrocarpon) by one of its fungal endosymbionts, EC4. We show that the symbiont resides inside the epidermal root cells of the host but extends into the rhizosphere via its hyphae. Morphological classification of this fungus is ambiguous, but phylogenetic inference based on 28S rRNA identifies EC4 as a Codinaeella species (Chaetosphaeriaceae, Sordariomycetes, Ascomycetes). We sequenced the genome and transcriptome of EC4, providing the first 'Omics' information of a Chaetosphaeriaceae fungus. The 55.3-Mbp nuclear genome contains 17,582 potential protein-coding genes, of which nearly 500 have the capacity to promote plant growth. For comparing gene sets involved in biofertilization, we annotated the published genome assembly of the plant-growth-promoting Trichoderma hamatum. The number of proteins involved in phosphate transport and solubilization is similar in the two fungi. In contrast, EC4 has ~50% more genes associated with ammonium, nitrate/nitrite transport, and phytohormone synthesis. The expression of 36 presumed plant-growth-promoting EC4 genes is stimulated when the fungus is in contact with the plant. Thus, Omics and in-plantae tests make EC4 a promising candidate for cranberry biofertilization on nutrient-poor soils.
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Whole genome sequence characterization of Aspergillus terreus ATCC 20541 and genome comparison of the fungi A. terreus. Sci Rep 2023; 13:194. [PMID: 36604572 PMCID: PMC9814666 DOI: 10.1038/s41598-022-27311-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Aspergillus terreus is well-known for lovastatin and itaconic acid production with biomedical and commercial importance. The mechanisms of metabolite formation have been extensively studied to improve their yield through genetic engineering. However, the combined repertoire of carbohydrate-active enzymes (CAZymes), cytochrome P450s (CYP) enzymes, and secondary metabolites (SMs) in the different A. terreus strains has not been well studied yet, especially with respect to the presence of biosynthetic gene clusters (BGCs). Here we present a 30 Mb whole genome sequence of A. terreus ATCC 20541 in which we predicted 10,410 protein-coding genes. We compared the CAZymes, CYPs enzyme, and SMs across eleven A. terreus strains, and the results indicate that all strains have rich pectin degradation enzyme and CYP52 families. The lovastatin BGC of lovI was linked with lovF in A. terreus ATCC 20541, and the phenomenon was not found in the other strains. A. terreus ATCC 20541 lacked a non-ribosomal peptide synthetase (AnaPS) participating in acetylaszonalenin production, which was a conserved protein in the ten other strains. Our results present a comprehensive analysis of CAZymes, CYPs enzyme, and SM diversities in A. terreus strains and will facilitate further research in the function of BGCs associated with valuable SMs.
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Li Z, Shi CH, Huang Y, Wang HC, Li WH, Cai LT. Phenotypic analysis and genome sequence of Rhizopus oryzae strain Y5, the causal agent of tobacco pole rot. Front Microbiol 2023; 13:1031023. [PMID: 36687611 PMCID: PMC9846616 DOI: 10.3389/fmicb.2022.1031023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Rhizopus oryzae is a destructive pathogen that frequently causes tobacco pole rot in curing chambers. Phenotypic characterization of the pathogen was conducted to provide basic biological and pathological information using Biolog Phenotype MicroArray (PM). In addition, the Y5 strain of R. oryzae was sequenced using Illumina HiSeq and Pacific Biosciences (PacBio) technologies. Using PM plates 1-8, 758 growth conditions were tested. Results indicated that R. oryzae could metabolize 54.21% of tested carbon sources, 86.84% of nitrogen sources, 100% of sulfur sources, and 98.31% of phosphorus sources. About 37 carbon compounds, including D-xylose, N-acetyl-D-glucosamine, D-sorbitol, β-methyl-D-glucoside, D-galactose, L-arabinose, and D-cellobiose, significantly supported the growth of the pathogen. PM 3 indicated the active nitrogen sources, including Gly-Asn, Ala-Asp., Ala-Gln, and uric acid. PM 6-8 showed 285 different nitrogen pathways, indicating that different combinations of different amino acids support the growth of the pathogen. Genome sequencing results showed that the R. oryzae Y5 strain had raw data assembled into 2,271 Mbp with an N50 value of 10,563 bp. A genome sequence of 50.3 Mb was polished and assembled into 53 contigs with an N50 length of 1,785,794 bp, maximum contig length of 3,223,184 bp, and a sum of contig lengths of 51,182,778 bp. A total of 12,680 protein-coding genes were predicted using the Nonredundant, Gene Ontology, Clusters of Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and SWISS-PROT databases. The genome sequence and annotation resources of R. oryzae provided a reference for studying its biological characteristics, trait-specific genes, pathogen-host interaction, pathogen evolution, and population genetic diversity. The phenomics and genome of R. oryzae will provide insights into microfungal biology, pathogen evolution, and the genetic diversity of epidemics.
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Affiliation(s)
- Zhen Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, China,Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Cai-hua Shi
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, China,School of Food Science and Technology & School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China,*Correspondence: Cai-hua Shi,
| | - Yang Huang
- China Tobacco Sichuan Industrial Corporation Technical Centre, Chengdu, China
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China,Han-cheng Wang,
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
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Nguyen LH, Nguyen BS, Le DT, Alomar TS, AlMasoud N, Ghotekar S, Oza R, Raizada P, Singh P, Nguyen VH. A concept for the biotechnological minimizing of emerging plastics, micro- and nano-plastics pollutants from the environment: A review. ENVIRONMENTAL RESEARCH 2023; 216:114342. [PMID: 36181894 DOI: 10.1016/j.envres.2022.114342] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/31/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Plastics, micro- and nano-plastics pollution are undoubtedly a severe and crucial ecological threat due to the durability of plastics and their destructive impacts on humans and wildlife. Most scientific investigations have addressed the classification, types, distribution, ingestion, fate, impacts, degradation, and various adverse effect of plastics. Heretofore, scanty reports have addressed implementing strategies for the remediation and mitigation of plastics. Therefore, in this paper, we review the current studies on the degradation of plastics, micro- and nano-plastics aided by microorganisms, and explore the relevant degradation properties and mechanisms. Diverse microorganisms are classified, such as bacteria, fungi, algae, cyanobacteria, wax worms, and enzymes that can decompose various plastics. Furthermore, bio-degradation is influenced by microbial features and environmental parameters; therefore, the ecological factors affecting plastic degradation and the resulting degradation consequences are discussed. In addition, the mechanisms underlying microbial-mediated plastic degradation are carefully studied. Finally, upcoming research directions and prospects for plastics degradation employing microorganisms are addressed. This review covers a comprehensive overview of the microorganism-assisted degradation of plastics, micro- and nano-plastics, and serves as a resource for future research into sustainable plastics pollution management methods.
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Affiliation(s)
- Lan Huong Nguyen
- Faculty of Biology and Environment, Ho Chi Minh City University of Food Industry, 140 Le Trong Tan Street, Tay Thanh Ward, Tan Phu District, Ho Chi Minh City, Viet Nam
| | - Ba-Son Nguyen
- Department of Renewable Energy, HCMC University of Technology and Education, Ho Chi Minh City, 700000, Viet Nam
| | - Duy-Tien Le
- Faculty of Pharmacy, Lac Hong University, Dong Nai Province, Viet Nam.
| | - Taghrid S Alomar
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Najla AlMasoud
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Suresh Ghotekar
- Department of Chemistry, Smt. Devkiba Mohansinhji Chauhan College of Commerce and Science, University of Mumbai, Silvassa, 396 230, Dadra and Nagar Haveli (UT), India.
| | - Rajeshwari Oza
- Department of Chemistry, S.N. Arts, D.J.M. Commerce and B.N.S. Science College, Savitribai Phule Pune University, Sangamner, 422 605, Maharashtra, India
| | - Pankaj Raizada
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Pardeep Singh
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Van-Huy Nguyen
- Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education (CARE), Chengalpattu District, Kelambakkam, Tamil Nadu, 603103, India.
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Pham HM, Le DT, Le LT, Chu PTM, Tran LH, Pham TT, Nguyen HM, Luu TT, Hoang H, Chu HH. A highly quality genome sequence of Penicillium oxalicum species isolated from the root of Ixora chinensis in Vietnam. G3 (BETHESDA, MD.) 2022; 13:6858938. [PMID: 36454044 PMCID: PMC9911084 DOI: 10.1093/g3journal/jkac300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022]
Abstract
Penicillium oxalicum has been reported as a multienzyme-producing fungus and is widely used in industry due to great potential for cellulase release. Until now, there are only 10 available genome assemblies of P. oxalicum species deposited in the GenBank database. In this study, the genome of the I1R1 strain isolated from the root of Ixora chinensis was completely sequenced by Pacbio Sequel sequencing technology, assembled into 8 chromosomes with the genome size of 30.8 Mb, as well as a mitogenome of 26 kb. The structural and functional analyses of the I1R1 genome revealed gene model annotations encoding an enzyme set involved in significant metabolic processes, along with cytochrome P450s and secondary metabolite biosynthesis. The comparative analysis of the P. oxalicum species based on orthology and gene family duplications indicated their large and closed pan-genome of 9,500 orthologous groups. This is valuable data for future phylogenetic and population genomics studies.
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Affiliation(s)
- Huong Mai Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Dung Thi Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Lam Tung Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Phuong Thi Minh Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Linh Huyen Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Tung Thanh Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Hung Mau Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Tien Thuy Luu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Ha Hoang
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Hoang Ha Chu
- Corresponding authors: Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi 10072, Vietnam.
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DhDIT2 Encodes a Debaryomyces hansenii Cytochrome P450 Involved in Benzo(a)pyrene Degradation-A Proposal for Mycoremediation. J Fungi (Basel) 2022; 8:jof8111150. [PMID: 36354917 PMCID: PMC9698926 DOI: 10.3390/jof8111150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022] Open
Abstract
Pollutants, such as polycyclic aromatic hydrocarbons (PAHs), e.g., benzo(a)pyrene (BaP), are common components of contaminating mixtures. Such compounds are ubiquitous, extremely toxic, and they pollute soils and aquatic niches. The need for new microorganism-based remediation strategies prompted researchers to identify the most suitable organisms to eliminate pollutants without interfering with the ecosystem. We analyzed the effect caused by BaP on the growth properties of Candida albicans, Debaryomyces hansenii, Rhodotorula mucilaginosa, and Saccharomyces cerevisiae. Their ability to metabolize BaP was also evaluated. The aim was to identify an optimal candidate to be used as the central component of a mycoremediation strategy. The results show that all four yeast species metabolized BaP by more than 70%, whereas their viability was not affected. The best results were observed for D. hansenii. When an incubation was performed in the presence of a cytochrome P450 (CYP) inhibitor, no BaP degradation was observed. Thus, the initial oxidation step is mediated by a CYP enzyme. Additionally, this study identified the D. hansenii DhDIT2 gene as essential to perform the initial degradation of BaP. Hence, we propose that D. hansenii and a S. cerevisiae expressing the DhDIT2 gene are suitable candidates to degrade BaP in contaminated environments.
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Chromosome-Level Genome Sequences, Comparative Genomic Analyses, and Secondary-Metabolite Biosynthesis Evaluation of the Medicinal Edible Mushroom Laetiporus sulphureus. Microbiol Spectr 2022; 10:e0243922. [PMID: 36200896 PMCID: PMC9602373 DOI: 10.1128/spectrum.02439-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Laetiporus sulphureus mushroom is a complementary and alternative medicine that has anticancer, antioxidation, and analgesic effects and immunomodulatory activity; it is used as a treatment for cough and rheumatism and is a functional food that can improve physical fitness. Even though L. sulphureus has garnered considerable biotechnological and pharmacological interest due to its excellent cellulose-degrading ability and diverse biological activities, its biosynthetic potential regarding polysaccharides and secondary metabolites has not been thoroughly examined. In this study, we sequenced and assembled the whole genome of a wild L. sulphureus isolate, NWAFU-1, from the Qinling Mountains in China. Comparative genomes analysis revealed genomic differences between subspecies, and phylogenomic analysis revealed evolutionary divergence as well as genome expansion and contraction of individual Polyporaceae family species. Bioinformatics investigation identified candidate genes associated with mating type, polysaccharide synthesis, carbohydrate-active enzymes, and secondary-metabolite biosynthesis, which included multiple terpenoids, nonribosomal peptides, and polyketides. The locations of biosynthetic core genes were mapped and displayed on chromosomes and contigs. Totals of 143 proteins from 126 coding genes were identified and divided into 14 cytochrome P450 families. Furthermore, the biosynthetic network of tetracyclic triterpenoid active components was postulated by genome mining of related genes combined with the molecular network of metabolites. The genome analysis of L. sulphureus in this study improves the understanding of the biosynthesis of active compounds, which will lay a theoretical foundation for subsequent research on active-compound biosynthesis and promote the application of Laetiporus in the field of drug research and functional-food creation. IMPORTANCE L. sulphureus is a parasitic basidiomycete fungus that causes brown rot. The fruiting bodies of L. sulphureus are used as ancient medicines in China and Europe to cure cancer, analgesia, cough, and rheumatism and are considered a functional food that regulates the body and improves health. L. sulphureus was inferred to be a tetrapolar system based on a high-quality genome, which will aid molecular breeding and artificial farming. Screening polysaccharide synthesis candidate genes and comparing carbohydrate-associated genes in brown-rot basidiomycetes help understand their growth. Identifying core genes for secondary-metabolite biosynthesis, gene cluster family analysis, and comparative cluster analysis will guide heterologous-biosynthesis investigations of these genes and help elucidate the biosynthetic pathways for L. sulphureus bioactive natural components. The biosynthesis network of tetracyclic triterpenes was mapped using metabolite profiling and genome scanning. This work explores the biosynthetic capacity of L. sulphureus-derived natural products and lays the foundation for biosynthetic studies of them.
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Tang S, Jin L, Lei P, Shao C, Wu S, Yang Y, He Y, Ren R, Xu J. Whole-genome assembly and analysis of a medicinal fungus: Inonotus hispidus. Front Microbiol 2022; 13:967135. [PMID: 36147857 PMCID: PMC9485836 DOI: 10.3389/fmicb.2022.967135] [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: 06/12/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Inonotus hispidus (I. hispidus) is a medicinal macrofungus that plays a key role in anti-tumor and antioxidant functions. To further understand and enhance the value of I. hispidus, we performed whole-genome sequencing and an analysis of its strain for the first time. I. hispidus was sequenced using the Illumina NovaSeq high-throughput sequencing platform. The genome length was 35,688,031 bp and 30 contigs, with an average length of 1,189,601.03 bp. Moreover, database alignment annotated 402 CAZyme genes and 93 functional genes involved in regulating secondary metabolites in the I. hispidus genome to find the greatest number of genes involved in terpenes in that genome, thus providing a theoretical basis for its medicinal value. Finally, the phylogenetic analysis and comparative genomic analysis of single-copy orthologous protein genes from other fungi in the same family were conducted; it was found that I. hispidus and Sanghuangporus baumii have high homology. Our results can be used to screen candidate genes for the nutritional utilization of I. hispidus and the development of high-yielding and high-quality I. hispidus via genetic means.
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Nicoletti G, White K. The Anti-Fungal Activity of Nitropropenyl Benzodioxole (NPBD), a Redox-Thiol Oxidant and Tyrosine Phosphatase Inhibitor. Antibiotics (Basel) 2022; 11:antibiotics11091188. [PMID: 36139967 PMCID: PMC9495065 DOI: 10.3390/antibiotics11091188] [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: 08/05/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Phylogenetically diverse fungal species are an increasing cause of severe disease and mortality. Identification of new targets and development of new fungicidal drugs are required to augment the effectiveness of current chemotherapy and counter increasing resistance in pathogens. Nitroalkenyl benzene derivatives are thiol oxidants and inhibitors of cysteine-based molecules, which show broad biological activity against microorganisms. Nitropropenyl benzodioxole (NPBD), one of the most active antimicrobial derivatives, shows high activity in MIC assays for phylogenetically diverse saprophytic, commensal and parasitic fungi. NPBD was fungicidal to all species except the dermatophytic fungi, with an activity profile comparable to that of Amphotericin B and Miconazole. NPBD showed differing patterns of dynamic kill rates under different growth conditions for Candida albicans and Aspergillus fumigatus and was rapidly fungicidal for non-replicating vegetative forms and microconidia. It did not induce resistant or drug tolerant strains in major pathogens on long term exposure. A literature review highlights the complexity and interactivity of fungal tyrosine phosphate and redox signaling pathways, their differing metabolic effects in fungal species and identifies some targets for inhibition. A comparison of the metabolic activities of Amphotericin B, Miconazole and NPBD highlights the multiple cellular functions of these agents and the complementarity of many mechanisms. The activity profile of NPBD illustrates the functional diversity of fungal tyrosine phosphatases and thiol-based redox active molecules and contributes to the validation of tyrosine phosphatases and redox thiol molecules as related and complementary selective targets for antimicrobial drug development. NPBD is a selective antifungal agent with low oral toxicity which would be suitable for local treatment of skin and mucosal infections.
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Lv M, Jiang B, Xing Y, Ya H, Zhang T, Wang X. Recent advances in the breakdown of microplastics: strategies and future prospectives. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:65887-65903. [PMID: 35876989 DOI: 10.1007/s11356-022-22004-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/10/2022] [Indexed: 05/26/2023]
Abstract
Microplastics pollution is becoming a major environmental issue, and exposure to microplastics has been associated with numerous adverse results to both the ecological system and humans. This work summarized the state-of-the-art developments in the breakdown of microplastics, including natural weathering, catalysts-assisted breakdown and biodegradation. Characterization techniques for microplastic breakdown involve scanning electron microscopy, Fourier infrared spectroscopy, X-ray photoelectron spectroscopy, etc. Bioavailability and adsorption capacity of microplastics may change after they are broken down, therefore leading to variety in microplastics toxicity. Further prospectives for should be focused on the determination and toxicity evaluation of microplastics breakdown products, as well as unraveling uncultivable microplastics degraders via cultivation-independent approaches. This work benefits researchers interested in environmental studies, particularly the removal of microplastics from environmental matrix.
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Affiliation(s)
- Mingjie Lv
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
| | - Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China.
- National Engineering Laboratory for Site Remediation Technologies, Beijing, 100015, People's Republic of China.
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
| | - Haobo Ya
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
- Zhejiang Development & Planning Institute, Hangzhou, 310030, China
| | - Tian Zhang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
| | - Xin Wang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, People's Republic of China
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Chen X, Luo M, Wu W, Dong Z, Zou H. Virulence-Associated Genes of Calonectria ilicola, Responsible for Cylindrocladium Black Rot. J Fungi (Basel) 2022; 8:jof8080869. [PMID: 36012857 PMCID: PMC9410443 DOI: 10.3390/jof8080869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
The Cylindrocladium black rot caused by Calonectria ilicicola is a destructive disease affecting a broad range of crops. Herein, we study virulence-associated genes of C. ilicicolaCi14017 isolated from diseased peanut roots (Arachis hypogaea L.). Ci14017 was identified via phylogenetic analysis of the internal transcribed spacer region and standard Koch’s postulate testing. Virulence-associated genes were based on genome analyses and comparative analysis of transcriptome and proteome profiles of sensitive and resistant peanut cultivars. Ci14017 identified as C. ilicicola has a 66 Mb chromosome with 18,366 predicted protein-coding genes. Overall, 46 virulence-associated genes with enhanced expression levels in the sensitive cultivars were identified. Sequence analysis indicated that the 46 gene products included two merops proteins, eight carbohydrate-active enzymes, seven cytochrome P450 enzymes, eight lipases, and 20 proteins with multi-conserved enzyme domains. The results indicate a complex infection mechanism employed by Ci14017 for causing Cylindrocladium black rot in peanuts.
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Affiliation(s)
- Xinyu Chen
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei Luo
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Wei Wu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhangyong Dong
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Correspondence: (Z.D.); (H.Z.); Tel.: +86-020-89-0031-92 (Z.D.); Tel.: +86-591-837-8469 (H.Z.)
| | - Huasong Zou
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Z.D.); (H.Z.); Tel.: +86-020-89-0031-92 (Z.D.); Tel.: +86-591-837-8469 (H.Z.)
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Zhang J, Jin X, Wang Y, Zhang B, Liu T. A Cytochrome P450 Monooxygenase in Nondefoliating Strain of Verticillium dahliae Manipulates Virulence via Scavenging Reactive Oxygen Species. PHYTOPATHOLOGY 2022; 112:1723-1729. [PMID: 35224980 DOI: 10.1094/phyto-08-21-0318-r] [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] [Indexed: 06/14/2023]
Abstract
Verticillium dahliae is a broad host-range phytopathogenic fungus that causes destructive vascular wilt on plants worldwide. Cytochrome P450 monooxygenases, also known as CYPs/P450s, are broadly distributed in organisms and are involved in a diverse array of molecular/metabolic processes. In this study, using reverse transcription quantitative PCR analysis, we observed that the expression of a P450 gene (Chr2g00380) in the E-class P450, group IV from V. dahliae isolate JR2 was highly induced during tomato infection. Targeted deletion of Chr2g00380 in JR2 did not affect hyphal growth and morphology; however, the mutants exhibited increased sensitivity to H2O2 and defects in melanized microsclerotia formation compared with the wild type. Loss of Chr2g00380 resulted in reduced virulence on tomato and tobacco plants but did not cause phenotypic changes in infection structure formation or in the penetration of cellophane membranes. These data provide evidence for an involvement of a cytochrome P450 monooxygenase in virulence in V. dahliae.
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Affiliation(s)
- Jiayi Zhang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, 100083 China
| | - Xianjiang Jin
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, 100083 China
| | - Yonglin Wang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, 100083 China
| | - Baolong Zhang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014 China
| | - Tingli Liu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014 China
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Lin S, Wei J, Yang B, Zhang M, Zhuo R. Bioremediation of organic pollutants by white rot fungal cytochrome P450: The role and mechanism of CYP450 in biodegradation. CHEMOSPHERE 2022; 301:134776. [PMID: 35500631 DOI: 10.1016/j.chemosphere.2022.134776] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Cytochrome P450 (CYP450) is a well-known protein family that is widely distributed in many organisms. Members of this family have been implicated in a broad range of reactions involved in the metabolism of various organic compounds. Recently, an increasing number of studies have shown that the CYP450 enzyme also participates in the elimination and degradation of organic pollutants, by white rot fungi (WRF), a famous group of natural degraders. This paper reviews previous investigations of white rot fungal CYP450 involved in the biodegradation of organic pollutants, with a special focus on inhibitory experiments, and the direct and indirect evidence of the role of white rot fungal CYP450 in bioremediation. The catalytic mechanisms of white rot fungal CYP450, its application potential, and future prospect for its use in bioremediation are then discussed.
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Affiliation(s)
- Shuqi Lin
- Institute of Plant and Microbiology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jinchao Wei
- Zhongye Changtian International Engineering Co., Ltd., Changsha, 410205, PR China
| | - Bentao Yang
- Zhongye Changtian International Engineering Co., Ltd., Changsha, 410205, PR China
| | - Meng Zhang
- Institute of Plant and Microbiology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Rui Zhuo
- Institute of Plant and Microbiology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China.
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Transcriptome analysis reveals putative pathogenesis genes in Alternaria panax during infecting Panax notoginseng leaves. Genes Genomics 2022; 44:855-866. [PMID: 35622230 DOI: 10.1007/s13258-022-01241-0] [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: 08/14/2021] [Accepted: 03/03/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Alternaria panax is the causative agent of black spot disease in Panax notoginseng, which causes significant yield loss. However, the molecular mechanisms underlying its pathogenicity remain mostly unknown. OBJECTIVE We sequenced the transcriptome of A. panax during infecting P. notoginseng leaves using next-generation RNA-seq to understand the molecular aspects of black spot disease. METHODS In this study, we sequenced the A. panax transcriptome during infecting P. notoginseng leaves through next-generation sequencing to explore the pathogenesis genes that may be responsible for black spot disease on P. notoginseng. RESULT The de novo transcriptome assembly of A. panax produced 23,036 unigenes, of which 18,096 genes were functionally annotated by at least one protein database. GO enrichment analysis and KEGG pathways of differentially up-regulated genes suggest that most genes are associated with metabolic processes, catalytic activity, starch, and sucrose metabolism during infection. Many pathogenesis-associated genes, including genes encoding secreted proteins, candidate secreted effectors, cell wall degrading enzymes, transcription factors, and transporters, were up-regulated in A. panax during infection. In addition, the secondary metabolite biosynthesis genes, including cytochrome P450, and nonribosomal peptide synthetases, were also identified in this study. CONCLUSIONS Differential gene expression analysis has confirmed that A. panax infection was mainly present in the middle and final stages. The findings show that these pathogenesis-associated genes in A. panax may be critical for the P. notoginseng black spots disease.
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Biotransformation of Androstenedione by Filamentous Fungi Isolated from Cultural Heritage Sites in the State Tretyakov Gallery. BIOLOGY 2022; 11:biology11060883. [PMID: 35741405 PMCID: PMC9220046 DOI: 10.3390/biology11060883] [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: 04/21/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 12/12/2022]
Abstract
Simple Summary Microorganisms are able to grow on substrates of the most diverse nature. One of the most practical habitats, in terms of cultural heritage conservation, is fine art objects such as tempera or oil paintings on canvas. Since tempera paints are produced on the basis of egg yolk, which is one of the richest sources of cholesterol in nature (up to 2% of dry weight), and in the process of aging of tempera materials, changes in cholesterol do not affect the core structure of the steroid nucleus, the group of fungi that we have isolated are tempera painting destructors is seen as a promising object for screening for their possible steroid-transforming activities. In this regard, the purpose of our work was to determine the ability to transform pharmaceutically significant steroids with dominant fungi-destructors of tempera paintings, previously isolated in the State Tretyakov Gallery. Consequently, we have demonstrated for the first time that fungi-destructors of tempera paintings have steroid-transforming activity and are promising microorganisms for screening for biotechnologically significant transformations of steroids with further industrial use. Abstract The transformation of steroids by microorganisms is widely used in medical biotechnology. A huge group of filamentous fungi is one of the most promising taxa for screening new biocatalytic reactions in order to obtain pharmaceutically significant steroids. In this work, we screened 10 filamentous fungi-destructors of egg tempera for the ability to biotransform androst-4-en-3,17-dione (AD) during cultivation in a liquid nutrient medium or in a buffer solution. These taxonomically unrelated strains, belonging to the classes Eurotiomycetes, Dothideomycetes and Sordariomycetes, are dominant representatives of the microbiome from halls where works of tempera painting are stored in the State Tretyakov Gallery (STG, Moscow, Russia). Since the binder of tempera paints, egg yolk, contains about 2% cholesterol, these degrading fungi appear to be a promising group for screening for steroid converting activity. It turned out that all the studied fungi-destructors are able to transform AD. Some strains showed transformation efficiency close to the industrial strain Curvularia lunata RNCIM F-981. In total, 33 steroids formed during the transformation of AD were characterized, for 19 of them the structure was established by gas chromatography/mass spectrometry analysis. In this work, we have shown for the first time that fungi-destructors of tempera paintings can efficiently transform steroids.
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Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
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Qian M, Zeng Y, Mao S, Jia L, Hua E, Lu F, Liu X. Engineering of a fungal steroid 11α-hydroxylase and construction of recombinant yeast for improved production of 11α-hydroxyprogesterone. J Biotechnol 2022; 353:1-8. [PMID: 35654275 DOI: 10.1016/j.jbiotec.2022.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022]
Abstract
Cytochrome P450 enzyme CYP68J5 from filamentous fungus Aspergillus ochraceus is industrially used for selective C11α-hydroxylation of canrenone and progesterone. To improve its selectivity of C11α-hydroxylation for relevant steroid substrates, a sequence-based targeted mutagenesis combined with saturation mutagenesis was conducted to search for variants with improved hydroxylation reaction specificity toward progesterone and D-ethylgonendione. Recombinant yeast expressing triple mutant V64F/E65G/N66T showed significantly increased C11α-hydroxylation selectivity (85 % VS WT 69.7 %). Saturation mutagenesis of V64, E65 and N66 resulted in the identification of single mutant V64K with greatly enhanced 11α-hydroxylation specificity toward progesterone (90.6 % VS WT 69.7 %). Furthermore, mutant N66D showed significant enhanced selectivity of C11α-hydroxylation toward D-ethylgonendione (70.8 % VS WT 58 %). Evaluation of recombinant yeast over-expressing V64K for progesterone transformation in 50 mL scale resulted in product 11α-OH progesterone concentrations of 432.5 mg/L, a 30.2 % increase compared with the CYP68J5 control. Our results also reveal that V64, E65 and N66 are key residues of CYP68J5 influencing its selectivity of C11α-hydroxylation, thus offering opportunities for further engineering of CYP68J5 for expanded industrial applications.
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Affiliation(s)
- Miao Qian
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-utilization, China, The College of Chemical Engineering and Materials Science, TUST, Tianjin 300457, China
| | - Yulong Zeng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology (TUST), Tianjin 300457, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology (TUST), Tianjin 300457, China
| | - Longgang Jia
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology (TUST), Tianjin 300457, China
| | - Erbing Hua
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology (TUST), Tianjin 300457, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology (TUST), Tianjin 300457, China.
| | - Xiaoguang Liu
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-utilization, China, The College of Chemical Engineering and Materials Science, TUST, Tianjin 300457, China.
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Dai L, Xie J, Liu Y, Chen H, Zheng J. The cytochrome P450s of Leptographium qinlingensis: Gene characteristics, phylogeny, and expression in response to terpenoids. Fungal Biol 2022; 126:395-406. [DOI: 10.1016/j.funbio.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/26/2022] [Accepted: 05/05/2022] [Indexed: 11/04/2022]
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