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Abu Bakar N, Chung BLY, Smykla J, Karsani SA, Alias SA. Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions. Mycologia 2024; 116:449-463. [PMID: 38484286 DOI: 10.1080/00275514.2024.2313429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/30/2024] [Indexed: 05/01/2024]
Abstract
Proteomics has been used extensively in the field of mycology, mainly in trying to understand the complex network of protein-protein interactions that has been implicated in the molecular functions of fungi. It is also a useful tool to compare metabolic differences within a genus. Species of Pseudogymnoascus, a genus under the phyla Ascomycota, have been shown to play an important role in the soil environment. They have been found in both polar and temperate regions and are a known producer of many extracellular hydrolases that contribute to soil decomposition. Despite the apparent importance of Pseudogymnoascus spp. in the soil ecosystem, investigations into their molecular functions are still very limited. In the present study, proteomic characterization of six Pseudogymnoascus spp. isolated from three biogeographic regions (the Arctic, Antarctic, and temperate regions) was carried out using tandem mass spectrometry. Prior to proteomic analysis, the optimization for protein extraction was carried out. Trichloroacetic acid‑acetone‑phenol was found to be the best extraction method to be used for proteomic profiling of Pseudogymnoascus spp. The proteomic analysis identified 2003 proteins that were successfully mapped to the UniProtKB database. The identified proteins were clustered according to their biological processes and molecular functions. The shared proteins found in all Pseudogymnoascus spp. (1201 proteins) showed a significantly close relationship in their basic cellular functions, despite differences in morphological structures. Analysis of Pseudogymnoascus spp. proteome also identified proteins that were unique to each region. However, a high number of these proteins belonged to protein families of similar molecular functions, namely, transferases and hydrolases. Our proteomic data can be used as a reference for Pseudogymnoascus spp. across different global regions and a foundation for future soil ecosystem function research.
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Affiliation(s)
- Nurlizah Abu Bakar
- Institute of Ocean and Earth Sciences, Universiti Malaya, C308, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
- National Antarctic Research Centre, Universiti Malaya, B303, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
| | - Benjamin Lau Yii Chung
- Advanced Biotechnology and Breeding Centre, Persiaran Institusi, Malaysian Palm Oil Board, No. 6, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Jerzy Smykla
- Department of Biodiversity, Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, Krakow 31-120, Poland
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, Universiti Malaya, C308, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
- National Antarctic Research Centre, Universiti Malaya, B303, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
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Palma D, Oliva V, Montanares M, Gil-Durán C, Travisany D, Chávez R, Vaca I. Expanding the Toolbox for Genetic Manipulation in Pseudogymnoascus: RNAi-Mediated Silencing and CRISPR/Cas9-Mediated Disruption of a Polyketide Synthase Gene Involved in Red Pigment Production in P. verrucosus. J Fungi (Basel) 2024; 10:157. [PMID: 38392828 PMCID: PMC10889956 DOI: 10.3390/jof10020157] [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: 11/03/2023] [Revised: 01/25/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Fungi belonging to the genus Pseudogymnoascus have garnered increasing attention in recent years. One of the members of the genus, P. destructans, has been identified as the causal agent of a severe bat disease. Simultaneously, the knowledge of Pseudogymnoascus species has expanded, in parallel with the increased availability of genome sequences. Moreover, Pseudogymnoascus exhibits great potential as a producer of specialized metabolites, displaying a diverse array of biological activities. Despite these significant advancements, the genetic landscape of Pseudogymnoascus remains largely unexplored due to the scarcity of suitable molecular tools for genetic manipulation. In this study, we successfully implemented RNAi-mediated gene silencing and CRISPR/Cas9-mediated disruption in Pseudogymnoascus, using an Antarctic strain of Pseudogymnoascus verrucosus as a model. Both methods were applied to target azpA, a gene involved in red pigment biosynthesis. Silencing of the azpA gene to levels of 90% or higher eliminated red pigment production, resulting in transformants exhibiting a white phenotype. On the other hand, the CRISPR/Cas9 system led to a high percentage (73%) of transformants with a one-nucleotide insertion, thereby inactivating azpA and abolishing red pigment production, resulting in a white phenotype. The successful application of RNAi-mediated gene silencing and CRISPR/Cas9-mediated disruption represents a significant advancement in Pseudogymnoascus research, opening avenues for comprehensive functional genetic investigations within this underexplored fungal genus.
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Affiliation(s)
- Diego Palma
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Vicente Oliva
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Mariana Montanares
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago 9170022, Chile
| | - Dante Travisany
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de Las Américas, Santiago 7500975, Chile
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago 9170022, Chile
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
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Dalakouras A, Katsaouni A, Avramidou M, Dadami E, Tsiouri O, Vasileiadis S, Makris A, Georgopoulou ME, Papadopoulou KK. A beneficial fungal root endophyte triggers systemic RNA silencing and DNA methylation of a host reporter gene. RNA Biol 2023; 20:20-30. [PMID: 36573793 PMCID: PMC9809956 DOI: 10.1080/15476286.2022.2159158] [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] [Indexed: 12/28/2022] Open
Abstract
A growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and pathogenic fungi, where a bi-directional trans-kingdom RNAi is established to the advantage of either the host or the pathogen. Similar mechanisms acting during plant association with non-pathogenic symbiotic microorganisms have been elusive to this date. To determine whether root endophytes can induce systemic RNAi responses to their host plants, we designed an experimental reporter-based system consisting of the root-restricted, beneficial fungal endophyte, Fusarium solani strain K (FsK) and its host Nicotiana benthamiana. Since not all fungi encode the RNAi machinery, we first needed to validate that FsK does so, by identifying its core RNAi enzymes (2 Dicer-like genes, 2 Argonautes and 4 RNA-dependent RNA polymerases) and by showing its susceptibility to in vitro RNAi upon exogenous application of double stranded RNAs (dsRNAs). Upon establishing this, we transformed FsK with a hairpin RNA (hpRNA) construct designed to target a reporter gene in its host N. benthamiana. The hpRNA was processed by FsK RNAi machinery predominantly into 21-24-nt small RNAs that triggered RNA silencing but not DNA methylation in the fungal hyphae. Importantly, when the hpRNA-expressing FsK was used to inoculate N. benthamiana, systemic RNA silencing and DNA methylation of the host reporter gene was recorded. Our data suggest that RNAi signals can be translocated by root endophytes to their hosts and can modulate gene expression during mutualism, which may be translated to beneficial phenotypes.
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Affiliation(s)
- Athanasios Dalakouras
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece,Hellenic Agricultural Organization Demeter, Institute of Industrial and Forage Crops, Larissa, Greece,CONTACT Athanasios Dalakouras University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece; Hellenic Agricultural Organization Demeter, Institute of Industrial and Forage Crops, Larissa, Greece
| | - Afrodite Katsaouni
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Marianna Avramidou
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Elena Dadami
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Olga Tsiouri
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Athanasios Makris
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
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Zhang T, Gu G, Liu G, Su J, Zhan Z, Zhao J, Qian J, Cai G, Cen S, Zhang D, Yu L. Late-stage cascade of oxidation reactions during the biosynthesis of oxalicine B in Penicillium oxalicum. Acta Pharm Sin B 2023; 13:256-270. [PMID: 36815048 PMCID: PMC9939320 DOI: 10.1016/j.apsb.2022.09.008] [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: 08/03/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
Oxalicine B (1) is an α-pyrone meroterpenoid with a unique bispirocyclic ring system derived from Penicillium oxalicum. The biosynthetic pathway of 15-deoxyoxalicine B (4) was preliminarily reported in Penicillium canescens, however, the genetic base and biochemical characterization of tailoring reactions for oxalicine B (1) has remained enigmatic. In this study, we characterized three oxygenases from the metabolic pathway of oxalicine B (1), including a cytochrome P450 hydroxylase OxaL, a hydroxylating Fe(II)/α-KG-dependent dioxygenase OxaK, and a multifunctional cytochrome P450 OxaB. Intriguingly, OxaK can catalyze various multicyclic intermediates or shunt products of oxalicines with impressive substrate promiscuity. OxaB was further proven via biochemical assays to have the ability to convert 15-hydroxdecaturin A (3) to 1 with a spiro-lactone core skeleton through oxidative rearrangement. We also solved the mystery of OxaL that controls C-15 hydroxylation. Chemical investigation of the wild-type strain and deletants enabled us to identify 10 metabolites including three new compounds, and the isolated compounds displayed potent anti-influenza A virus bioactivities exhibiting IC50 values in the range of 4.0-19.9 μmol/L. Our studies have allowed us to propose a late-stage biosynthetic pathway for oxalicine B (1) and create downstream derivatizations of oxalicines by employing enzymatic strategies.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guowei Gu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Jinhua Su
- The Third Medical Center, The General Hospital of People's Liberation Army, Beijing 100039, China
| | - Zhilai Zhan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinxiu Qian
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Dewu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China,Corresponding authors. Tel./fax: +86 10 63187118.
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China,Corresponding authors. Tel./fax: +86 10 63187118.
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Zhang T, Cai G, Rong X, Xu J, Jiang B, Wang H, Li X, Wang L, Zhang R, He W, Yu L. Mining and characterization of the PKS-NRPS hybrid for epicoccamide A: a mannosylated tetramate derivative from Epicoccum sp. CPCC 400996. Microb Cell Fact 2022; 21:249. [PMID: 36419162 PMCID: PMC9685919 DOI: 10.1186/s12934-022-01975-2] [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: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Genomic analysis indicated that the genomes of ascomycetes might carry dozens of biosynthetic gene clusters (BGCs), yet many clusters have remained enigmatic. The ascomycete genus Epicoccum, belonging to the family Didymellaceae, is ubiquitous that colonizes different types of substrates and is associated with phyllosphere or decaying vegetation. Species of this genus are prolific producers of bioactive substances. The epicoccamides, as biosynthetically distinct mannosylated tetramate, were first isolated in 2003 from Epicoccum sp. In this study, using a combination of genome mining, chemical identification, genetic deletion, and bioinformatic analysis, we identified the required BGC epi responsible for epicoccamide A biosynthesis in Epicoccum sp. CPCC 400996. RESULTS The unconventional biosynthetic gene cluster epi was obtained from an endophyte Epicoccum sp. CPCC 400996 through AntiSMASH-based genome mining. The cluster epi includes six putative open reading frames (epiA-epiF) altogether, in which the epiA encodes a tetramate-forming polyketide synthase and nonribosomal peptide synthetases (PKS-NRPS hybrid). Sequence alignments and bioinformatic analysis to other metabolic pathways of fungal tetramates, we proposed that the gene cluster epi could be involved in generating epicoccamides. Genetic knockout of epiA completely abolished the biosynthesis of epicoccamide A (1), thereby establishing the correlation between the BGC epi and biosynthesis of epicoccamide A. Bioinformatic adenylation domain signature analysis of EpiA and other fungal PKS-NRPSs (NRPs) indicated that the EpiA is L-alanine incorporating tetramates megasynthase. Furthermore, based on the molecular structures of epicoccamide A and deduced gene functions of the cluster epi, a hypothetic metabolic pathway for biosynthesizing compound 1 was proposed. The corresponding tetramates releasing during epicoccamide A biosynthesis was catalyzed through Dieckmann-type cyclization, in which the reductive (R) domain residing in terminal module of EpiA accomplished the conversion. These results unveiled the underlying mechanism of epicoccamides biosynthesis and these findings might provide opportunities for derivatization of epicoccamides or generation of new chemical entities. CONCLUSION Genome mining and genetic inactivation experiments unveiled a previously uncharacterized PKS - NRPS hybrid-based BGC epi responsible for the generation of epicoccamide A (1) in endophyte Epicoccum sp. CPCC 400996. In addition, based on the gene cluster data, a hypothetical biosynthetic pathway of epicoccamide A was proposed.
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Affiliation(s)
- Tao Zhang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Guowei Cai
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China ,grid.452240.50000 0004 8342 6962Medical Research Center, Binzhou Medical University Hospital, Binzhou, 256603 Shandong China
| | - Xiaoting Rong
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China ,grid.510447.30000 0000 9970 6820College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212003 Jiangsu China
| | - Jingwen Xu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Bingya Jiang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Hao Wang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Xinxin Li
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Lu Wang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Ran Zhang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Wenni He
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Liyan Yu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
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Zhang T, Cai G, Rong X, Wang Y, Gong K, Liu W, Wang L, Pang X, Yu L. A Combination of Genome Mining with an OSMAC Approach Facilitates the Discovery of and Contributions to the Biosynthesis of Melleolides from the Basidiomycete Armillaria tabescens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12430-12441. [PMID: 36134616 DOI: 10.1021/acs.jafc.2c04079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genome mining revealed that the genomes of basidiomycetes may include a considerable number of biosynthetic gene clusters (BGCs), yet numerous clusters remain unidentified. Herein, we report a combination of genome mining with an OSMAC (one strain, many compounds) approach to characterize the spectrum of melleolides produced by Armillaria tabescens CPCC 401429. Using F1 fermentation medium, the metabolic pathway of the gene cluster mel was successfully upregulated. From the extracts of the wild-type strain, two new melleolides (1 and 2), along with five new orsellinic acid-derived lactams (10-14), were isolated, and their structures were elucidated by LC-HR-ESIMS/MS and 2D-NMR. Several melleolides exhibited moderate anti-carcinoma (A549, NCI-H520, and H1299) effects with IC50 values of 4.0-48.8 μM. RNA-sequencing based transcriptomic profiling broadened our knowledge of the genetic background, regulation, and mechanisms of melleolide biosynthesis. These results may promote downstream metabolic engineering studies of melleolides. Our study demonstrates the approach is effective for discovering new secondary metabolites from Armillaria sp. and will facilitate the mining of the unexploited biosynthetic potential in other basidiomycetes.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256603, China
| | - Xiaoting Rong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212003, China
| | - Yuquan Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - KaiKai Gong
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256603, China
| | - Wancang Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lu Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xu Pang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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7
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Zhang T, Pang X, Zhao J, Guo Z, He W, Cai G, Su J, Cen S, Yu L. Discovery and Activation of the Cryptic Cluster from Aspergillus sp. CPCC 400735 for Asperphenalenone Biosynthesis. ACS Chem Biol 2022; 17:1524-1533. [PMID: 35616995 DOI: 10.1021/acschembio.2c00204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Postgenomic analysis manifested that filamentous fungi contain numerous natural product biosynthetic gene clusters in their genome, yet most clusters remain cryptic or down-regulated. Herein, we report the successful manipulation of strain Aspergillus sp. CPCC 400735 that enables its genetic engineering via targeted overexpression of pathway-specific transcriptional regulator AspE. The down-regulated metabolic pathway encoded by the biosynthetic gene cluster asp was successfully up-activated. Analyses of mutant Ai-OE::aspE extracts led to isolation and characterization of 13 asperphenalenone derivatives, of which 11 of them are new compounds. All of the asperphenalenones exhibited conspicuous anti-influenza A virus effects with IC50 values of 0.45-2.22 μM. Additionally, their identification provided insight into biosynthesis of asperphenalenones and might benefit studies of downstream combinatorial biosynthesis. Our study further demonstrates the effective application of targeted overexpressing pathway-specific activator and novel metabolite discovery in microorganisms. These will accelerate the exploitation of the untapped resources and biosynthetic capability in filamentous fungi.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xu Pang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhe Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenni He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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Blehert DS, Lorch JM. Laboratory Maintenance and Culture of Pseudogymnoascus destructans, the Fungus That Causes Bat White-Nose Syndrome. Curr Protoc 2021; 1:e23. [PMID: 33497534 DOI: 10.1002/cpz1.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pseudogymnoascus destructans is a fungal pathogen that causes white-nose syndrome, an emerging and fatal disease of North American bats that has led to unprecedented population declines. As a psychrophile, P. destructans is adapted to infect bats during winter hibernation, when host metabolic activity and core body temperature are greatly reduced. The ability to maintain and cultivate isolates of P. destructans in the laboratory is necessary for conducting research with this fungus. This article describes protocols for culturing P. destructans from bat wing skin and soil, for cryopreserving the fungus, and for preparing liquid suspensions for laboratory experimentation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Isolating Pseudogymnoascus destructans from bat wing skin Basic Protocol 2: Isolating Pseudogymnoascus destructans from soil Basic Protocol 3: Cryopreservation of Pseudogymnoascus destructans Basic Protocol 4: Preparing liquid conidial suspension of Pseudogymnoascus destructans.
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Affiliation(s)
- David S Blehert
- U.S. Geological Survey National Wildlife Health Center, Madison, Wisconsin
| | - Jeffrey M Lorch
- U.S. Geological Survey National Wildlife Health Center, Madison, Wisconsin
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9
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Ren P, Rajkumar SS, Zhang T, Sui H, Masters PS, Martinkova N, Kubátová A, Pikula J, Chaturvedi S, Chaturvedi V. A common partitivirus infection in United States and Czech Republic isolates of bat white-nose syndrome fungal pathogen Pseudogymnoascus destructans. Sci Rep 2020; 10:13893. [PMID: 32807800 PMCID: PMC7431587 DOI: 10.1038/s41598-020-70375-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/24/2020] [Indexed: 12/15/2022] Open
Abstract
The psychrophilic (cold-loving) fungus Pseudogymnoascus destructans was discovered more than a decade ago to be the pathogen responsible for white-nose syndrome, an emerging disease of North American bats causing unprecedented population declines. The same species of fungus is found in Europe but without associated mortality in bats. We found P. destructans was infected with a mycovirus [named Pseudogymnoascus destructans partitivirus 1 (PdPV-1)]. The virus is bipartite, containing two double-stranded RNA (dsRNA) segments designated as dsRNA1 and dsRNA2. The cDNA sequences revealed that dsRNA1 dsRNA is 1,683 bp in length with an open reading frame (ORF) that encodes 539 amino acids (molecular mass of 62.7 kDa); dsRNA2 dsRNA is 1,524 bp in length with an ORF that encodes 434 amino acids (molecular mass of 46.9 kDa). The dsRNA1 ORF contains motifs representative of RNA-dependent RNA polymerase (RdRp), whereas the dsRNA2 ORF sequence showed homology with the putative capsid proteins (CPs) of mycoviruses. Phylogenetic analyses with PdPV-1 RdRp and CP sequences indicated that both segments constitute the genome of a novel virus in the family Partitiviridae. The purified virions were isometric with an estimated diameter of 33 nm. Reverse transcription PCR (RT-PCR) and sequencing revealed that all US isolates and a subset of Czech Republic isolates of P. destructans were infected with PdPV-1. However, PdPV-1 appears to be not widely dispersed in the fungal genus Pseudogymnoascus, as non-pathogenic fungi P. appendiculatus (1 isolate) and P. roseus (6 isolates) tested negative. P. destructans PdPV-1 could be a valuable tool to investigate fungal biogeography and the host-pathogen interactions in bat WNS.
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Affiliation(s)
- Ping Ren
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA. .,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Sunanda S Rajkumar
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,ICMR Medical Research Institute, Puducherry, India
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Haixin Sui
- Cellular and Molecular Basis of Diseases Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University of Albany School of Public Health, Albany, NY, USA
| | - Paul S Masters
- Department of Biomedical Sciences, University of Albany School of Public Health, Albany, NY, USA.,Viral Replication and Vector Biology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Natalia Martinkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alena Kubátová
- Department of Botany, Faculty of Science, Charles University in Prague, Praha, Czech Republic
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University of Albany School of Public Health, Albany, NY, USA
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA. .,Department of Biomedical Sciences, University of Albany School of Public Health, Albany, NY, USA.
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Díaz A, Villanueva P, Oliva V, Gil-Durán C, Fierro F, Chávez R, Vaca I. Genetic Transformation of the Filamentous Fungus Pseudogymnoascus verrucosus of Antarctic Origin. Front Microbiol 2019; 10:2675. [PMID: 31824460 PMCID: PMC6883257 DOI: 10.3389/fmicb.2019.02675] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/04/2019] [Indexed: 11/24/2022] Open
Abstract
Cold-adapted fungi isolated from Antarctica, in particular those belonging to the genus Pseudogymnoascus, are producers of secondary metabolites with interesting bioactive properties as well as enzymes with potential biotechnological applications. However, at genetic level, the study of these fungi has been hindered by the lack of suitable genetic tools such as transformation systems. In fungi, the availability of transformation systems is a key to address the functional analysis of genes related with the production of a particular metabolite or enzyme. To the best of our knowledge, the transformation of Pseudogymnoascus strains of Antarctic origin has not been achieved yet. In this work, we describe for the first time the successful transformation of a Pseudogymnoascus verrucosus strain of Antarctic origin, using two methodologies: the polyethylene glycol (PEG)-mediated transformation, and the electroporation of germinated conidia. We achieved transformation efficiencies of 15.87 ± 5.16 transformants per μg of DNA and 2.67 ± 1.15 transformants per μg of DNA for PEG-mediated transformation and electroporation of germinated conidia, respectively. These results indicate that PEG-mediated transformation is a very efficient method for the transformation of this Antarctic fungus. The genetic transformation of Pseudogymnoascus verrucosus described in this work represents the first example of transformation of a filamentous fungus of Antarctic origin.
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Affiliation(s)
- Anaí Díaz
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Villanueva
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Vicente Oliva
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Francisco Fierro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Mexico City, Mexico
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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11
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Fuchs BB, Chaturvedi S, Rossoni RD, de Barros PP, Torres-Velez F, Mylonakis E, Chaturvedi V. Galleria mellonella experimental model for bat fungal pathogen Pseudogymnoascus destructans and human fungal pathogen Pseudogymnoascus pannorum. Virulence 2019; 9:1539-1547. [PMID: 30289352 PMCID: PMC6177250 DOI: 10.1080/21505594.2018.1518087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Laboratory investigations of the pathogenesis of Pseudogymnoascus destructans, the fungal causal agent of bat White Nose Syndrome (WNS), presents unique challenges due to its growth requirements (4°-15°C) and a lack of infectivity in the current disease models. Pseudogymnoascus pannorum is the nearest fungal relative of P. destructans with wider psychrophilic - physiological growth range, and ability to cause rare skin infections in humans. Our broad objectives are to create the molecular toolkit for comparative study of P. destructans and P. pannorum pathogenesis. Towards these goals, we report the successful development of an invertebrate model in the greater wax moth Galleria mellonella. Both P. destructans and P. pannorum caused fatal disease in G. mellonella and elicited immune responses and histopathological changes consistent with the experimental disease.
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Affiliation(s)
- Beth Burgwyn Fuchs
- a Division of Infectious Diseases, Rhode Island Hospital , Warren Alpert Medical School at Brown University , Providence , RI , USA
| | - Sudha Chaturvedi
- b Mycology Laboratory, Division of Infectious Diseases , Wadsworth Center, New York State Department of Health , Albany , NY , USA.,c Department of Biomedical Sciences, School of Public Health , University of Albany , Albany , NY , USA
| | - Rodnei Dennis Rossoni
- d Department of Biosciences and Oral Diagnosis, Institute of Science and Technology , UNESP - Univ Estadual Paulista , Sao Jose dos Campos , Brazil
| | - Patricia P de Barros
- d Department of Biosciences and Oral Diagnosis, Institute of Science and Technology , UNESP - Univ Estadual Paulista , Sao Jose dos Campos , Brazil
| | - Fernando Torres-Velez
- e Division of Infectious Diseases , Wadsworth Center, New York State Department of Health , Albany , NY , USA
| | - Eleftherios Mylonakis
- a Division of Infectious Diseases, Rhode Island Hospital , Warren Alpert Medical School at Brown University , Providence , RI , USA
| | - Vishnu Chaturvedi
- b Mycology Laboratory, Division of Infectious Diseases , Wadsworth Center, New York State Department of Health , Albany , NY , USA.,c Department of Biomedical Sciences, School of Public Health , University of Albany , Albany , NY , USA
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12
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Wang Y, Li G, Jiao X, Cheng X, Abdullah M, Li D, Lin Y, Cai Y, Nie F. Molecular characterization and overexpression of mnp6 and vp3 from Pleurotus ostreatus revealed their involvement in biodegradation of cotton stalk lignin. Biol Open 2019; 8:bio036483. [PMID: 30584069 PMCID: PMC6398461 DOI: 10.1242/bio.036483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 11/22/2018] [Indexed: 01/18/2023] Open
Abstract
Fungal secretory heme peroxidase (Class II POD) plays a significant role in biomass conversion due to its lignin-degrading activity. In this study, genome-wide identification and bioinformatics were performed to analyze P leurotus ostreatus peroxidases (PoPODs). A total of six manganese peroxidases (MnPs) and three versatile peroxidases (VPs) were obtained. Bioinformatics analysis and qRT-PCR showed that P. ostreatus mnp6 (Pomnp6) and P. ostreatus vp3 (Povp3) could be involved in lignin degradation. Both Pomnp6 and Povp3 transgenetic fungi showed significantly increased lignin degradation of cotton stalks. 1H-NMR revealed that Pomnp6 and Povp3 may preferentially degrade S-lignin in cotton stalks and mainly break β-O-4' bond linkages and hydroxyl. These results support the possible utility of Pomnp6 and Povp3 in natural straw resources and development of sustainable energy.
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Affiliation(s)
- Yan Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Guoqing Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaoyu Jiao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Xi Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Dahui Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Fan Nie
- Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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13
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Zhang T, Ren P, De Jesus M, Chaturvedi V, Chaturvedi S. Green Fluorescent Protein Expression in Pseudogymnoascus destructans to Study Its Abiotic and Biotic Lifestyles. Mycopathologia 2018; 183:805-814. [PMID: 29987576 DOI: 10.1007/s11046-018-0285-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/28/2018] [Indexed: 12/11/2022]
Abstract
Pseudogymnoascus destructans (Pd) is the etiologic agent of bat White-nose syndrome, a disease that has caused the unprecedented reduction in the hibernating bat populations across eastern North America. The Pd pathogenesis appears to be a complex adaptation of fungus in its abiotic (caves and mines) and biotic (bats) environments. There is a general lack of experimental tools for the study of Pd biology. We described the successful expression of codon-optimized synthetic green fluorescent protein sGFP in Pd. The sGFP(S65T) gene was first fused in frame with the Aspergillus nidulans promoter in the tumor-inducing plasmid pRF-HUE, and the resulting plasmid pHUE-sGFP(S65T) was transformed into Pd by Agrobacterium tumefaciens-mediated transformation system. The integration of sGFP(S65T) in Pd genome was analyzed by PCR, and single integration frequency of approximately 66% was confirmed by Southern hybridization. Fluorescent microscopy and flow cytometric analyses of two randomly selected transformants with single integration revealed high expression of sGFP in both spores and hyphal structures. The biology of mutants as judged by sporulation, growth rate, and urease production was not altered indicating sGFP is not toxic to Pd. Thus, we have generated a valuable tool that will facilitate the elucidation of Pd biology, ecology, and pathogenicity in real time.
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Affiliation(s)
- Tao Zhang
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Ping Ren
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Magdia De Jesus
- Immunology and Infectious Disease Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA.
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA.
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14
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Donaldson ME, Davy CM, Vanderwolf KJ, Willis CKR, Saville BJ, Kyle CJ. Growth medium and incubation temperature alter the Pseudogymnoascus destructans transcriptome: implications in identifying virulence factors. Mycologia 2018; 110:300-315. [PMID: 29737946 DOI: 10.1080/00275514.2018.1438223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pseudogymnoascus destructans is the causal agent of bat white-nose syndrome (WNS), which is devastating some North American bat populations. Previous transcriptome studies provided insight regarding the molecular mechanisms involved in WNS; however, it is unclear how different environmental parameters could influence pathogenicity. This information could be useful in developing management strategies to mitigate the negative impacts of P. destructans on bats. We cultured three P. destructans isolates from Atlantic Canada on two growth media (potato dextrose agar and Sabouraud dextrose agar) that differ in their nitrogen source, and at two separate incubation temperatures (4 C and 15 C) that approximate the temperature range of bat hibernacula during the winter and a temperature within its optimal mycelial growth range. We conducted RNA sequencing to determine transcript levels in each sample and performed differential gene expression (DGE) analyses to test the influence of growth medium and incubation temperature on gene expression. We also compared our in vitro results with previous RNA-sequencing data sets generated from P. destructans growing on the wings of a susceptible host, Myotis lucifugus. Our findings point to a critical role for substrate and incubation temperature in influencing the P. destructans transcriptome. DGE analyses suggested that growth medium plays a larger role than temperature in determining P. destructans gene expression and that although the psychrophilic fungus responds to different nitrogen sources, it may have evolved for continued growth at a broad range of low temperatures. Further, our data suggest that down-regulation of the RNA-interference pathway and increased fatty acid metabolism are involved in the P. destructans-bat interaction. Finally, we speculate that to reduce the activation of host defense responses, P. destructans minimizes changes in the expression of genes encoding secreted proteins during bat colonization.
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Affiliation(s)
- Michael E Donaldson
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada
| | - Christina M Davy
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,b Wildlife Research and Monitoring Section , Ontario Ministry of Natural Resources and Forestry , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada
| | - Karen J Vanderwolf
- c New Brunswick Museum , 277 Douglas Avenue, Saint John , New Brunswick , E2K 1E5, Canada.,d Department of Pathobiological Sciences , University of Wisconsin-Madison , 2015 Linden Drive, Madison , Wisconsin 53706
| | - Craig K R Willis
- e Department of Biology , University of Winnipeg , 515 Portage Avenue, Winnipeg , Manitoba , R3B 2E9, Canada
| | - Barry J Saville
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,f Forensic Science Department , Trent University , 2140 East Bank Drive, Peterborough , Ontario, K9L 1Z8 , Canada
| | - Christopher J Kyle
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,f Forensic Science Department , Trent University , 2140 East Bank Drive, Peterborough , Ontario, K9L 1Z8 , Canada
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15
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Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. eLife 2018. [PMID: 29521624 PMCID: PMC5922974 DOI: 10.7554/elife.32110] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi. The fungus Rhodosporidium toruloides can grow on substances extracted from plant matter that is inedible to humans such as corn stalks, wood pulp, and grasses. Under some growth conditions, the fungus can accumulate massive stores of hydrocarbon-rich fats and pigments. A community of scientists and engineers has begun genetically modifying R. toruloides to convert these naturally produced fats and pigments into fuels, chemicals and medicines. These could form sustainable replacements for products made from petroleum or harvested from threatened animal and plant species. Fungi, plants, animals and other eukaryotes store fat in specialized compartments called lipid droplets. The genes that control the metabolism – the production, use and storage – of fat in lipid bodies have been studied in certain eukaryotes, including species of yeast. However, R. toruloides is only distantly related to the most well-studied of these species. This means that we cannot be certain that a gene will play the same role in R. toruloides as in those species. To assemble the most comprehensive list possible of the genes in R. toruloides that affect the production, use, or storage of fat in lipid bodies, Coradetti, Pinel et al. constructed a population of hundreds of thousands of mutant fungal strains, each with its own unique DNA ‘barcode’. The effects that mutations in over 6,000 genes had on growth and fat accumulation in these fungi were measured simultaneously in several experiments. This general approach is not new, but technical limitations had, until now, restricted its use in fungi to a few species. Coradetti, Pinel et al. identified hundreds of genes that affected the ability of R. toruloides to metabolise fat. Many of these genes were related to genes with known roles in fat metabolism in other eukaryotes. Other genes are involved in different cell processes, such as the recycling of waste products in the cell. Their identification adds weight to the view that the links between these cellular processes and fat metabolism are deep and widespread amongst eukaryotes. Finally, some of the genes identified by Coradetti, Pinel et al. are not closely related to any well-studied genes. Further study of these genes could help us to understand why R. toruloides can accumulate much larger amounts of fat than most other fungi. The methods developed by Coradetti, Pinel et al. should be possible to implement in many species of fungi. As a result these techniques may eventually contribute to the development of new treatments for human fungal diseases, the protection of important food crops, and a deeper understanding of the roles various fungi play in the broader ecosystem.
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Affiliation(s)
| | - Dominic Pinel
- Energy Biosciences Institute, Berkeley, United States
| | | | - Masakazu Ito
- Energy Biosciences Institute, Berkeley, United States
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, United States.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, United States
| | - Ya-Fang Cheng
- Energy Biosciences Institute, Berkeley, United States
| | - Stefan Bauer
- Energy Biosciences Institute, Berkeley, United States
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel B Brem
- The Buck Institute for Research on Aging, Novato, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Adam P Arkin
- Energy Biosciences Institute, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Jeffrey M Skerker
- Energy Biosciences Institute, Berkeley, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
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16
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Hooykaas PJJ, van Heusden GPH, Niu X, Reza Roushan M, Soltani J, Zhang X, van der Zaal BJ. Agrobacterium-Mediated Transformation of Yeast and Fungi. Curr Top Microbiol Immunol 2018; 418:349-374. [PMID: 29770864 DOI: 10.1007/82_2018_90] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Two decades ago, it was discovered that the well-known plant vector Agrobacterium tumefaciens can also transform yeasts and fungi when these microorganisms are co-cultivated on a solid substrate in the presence of a phenolic inducer such as acetosyringone. It is important that the medium has a low pH (5-6) and that the temperature is kept at room temperature (20-25 °C) during co-cultivation. Nowadays, Agrobacterium-mediated transformation (AMT) is the method of choice for the transformation of many fungal species; as the method is simple, the transformation efficiencies are much higher than with other methods, and AMT leads to single-copy integration much more frequently than do other methods. Integration of T-DNA in fungi occurs by non-homologous end-joining (NHEJ), but also targeted integration of the T-DNA by homologous recombination (HR) is possible. In contrast to AMT of plants, which relies on the assistance of a number of translocated virulence (effector) proteins, none of these (VirE2, VirE3, VirD5, VirF) are necessary for AMT of yeast or fungi. This is in line with the idea that some of these proteins help to overcome plant defense. Importantly, it also showed that VirE2 is not necessary for the transport of the T-strand into the nucleus. The yeast Saccharomyces cerevisiae is a fast-growing organism with a relatively simple genome with reduced genetic redundancy. This yeast species has therefore been used to unravel basic molecular processes in eukaryotic cells as well as to elucidate the function of virulence factors of pathogenic microorganisms acting in plants or animals. Translocation of Agrobacterium virulence proteins into yeast was recently visualized in real time by confocal microscopy. In addition, the yeast 2-hybrid system, one of many tools that have been developed for use in this yeast, was used to identify plant and yeast proteins interacting with the translocated Agrobacterium virulence proteins. Dedicated mutant libraries, containing for each gene a mutant with a precise deletion, have been used to unravel the mode of action of some of the Agrobacterium virulence proteins. Yeast deletion mutant collections were also helpful in identifying host factors promoting or inhibiting AMT, including factors involved in T-DNA integration. Thus, the homologous recombination (HR) factor Rad52 was found to be essential for targeted integration of T-DNA by HR in yeast. Proteins mediating double-strand break (DSB) repair by end-joining (Ku70, Ku80, Lig4) turned out to be essential for non-homologous integration. Inactivation of any one of the genes encoding these end-joining factors in other yeasts and fungi was employed to reduce or totally eliminate non-homologous integration and promote efficient targeted integration at the homologous locus by HR. In plants, however, their inactivation did not prevent non-homologous integration, indicating that T-DNA is captured by different DNA repair pathways in plants and fungi.
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Affiliation(s)
- Paul J J Hooykaas
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| | - G Paul H van Heusden
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Xiaolei Niu
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - M Reza Roushan
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Jalal Soltani
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Xiaorong Zhang
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Bert J van der Zaal
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
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17
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Andargie M, Yang C, Li J. Generation of β-glucuronidase reporter-tagged strain to monitor Ustilaginoidea virens infection in rice. J Microbiol Methods 2016; 131:148-155. [DOI: 10.1016/j.mimet.2016.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/21/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
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18
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Wang Y, Yuan Y, Liu B, Zhang Z, Yue T. Biocontrol activity and patulin-removal effects of Bacillus subtilis
, Rhodobacter sphaeroides
and Agrobacterium tumefaciens
against Penicillium expansum. J Appl Microbiol 2016; 121:1384-1393. [DOI: 10.1111/jam.13208] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/15/2016] [Accepted: 06/16/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Y. Wang
- College of Food Science and Engineering; Northwest A&F University; Yangling China
| | - Y. Yuan
- College of Food Science and Engineering; Northwest A&F University; Yangling China
| | - B. Liu
- College of Food Science and Engineering; Northwest A&F University; Yangling China
| | - Z. Zhang
- College of Food Science and Engineering; Qingdao Agricultural University; Qingdao China
| | - T. Yue
- College of Food Science and Engineering; Northwest A&F University; Yangling China
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19
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Vitamin B2 as a virulence factor in Pseudogymnoascus destructans skin infection. Sci Rep 2016; 6:33200. [PMID: 27620349 PMCID: PMC5020413 DOI: 10.1038/srep33200] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 08/22/2016] [Indexed: 12/02/2022] Open
Abstract
Pathogenic and non-pathogenic related microorganisms differ in secondary metabolite production. Here we show that riboflavin overproduction by a fungal pathogen and its hyperaccumulation in affected host tissue exacerbates a skin infection to necrosis. In white-nose syndrome (WNS) skin lesions caused by Pseudogymnoascus destructans, maximum riboflavin concentrations reached up to 815 μg ml−1, indicating bioaccumulation and lack of excretion. We found that high riboflavin concentrations are cytotoxic under conditions specific for hibernation, affect bats’ primary fibroblasts and induce cell detachment, loss of mitochondrial membrane potential, polymerization of cortical actin, and cell necrosis. Our results explain molecular pathology of WNS, where a skin infection becomes fatal. Hyperaccumulation of vitamin B2 coupled with reduced metabolism and low tissue oxygen saturation during hibernation prevents removal of excess riboflavin in infected bats. Upon reperfusion, oxygen reacts with riboflavin resulting in dramatic pathology after arousal. While multiple molecules enable invasive infection, riboflavin-associated extensive necrosis likely contributes to pathophysiology and altered arousal pattern in infected bats. Bioaccumulation of a vitamin under natural infection represents a novel condition in a complex host-pathogen interplay.
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