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Kuo CY, Tay RJ, Lin HC, Juan SC, Vidal-Diez de Ulzurrun G, Chang YC, Hoki J, Schroeder FC, Hsueh YP. The nematode-trapping fungus Arthrobotrys oligospora detects prey pheromones via G protein-coupled receptors. Nat Microbiol 2024; 9:1738-1751. [PMID: 38649409 DOI: 10.1038/s41564-024-01679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
The ability to sense prey-derived cues is essential for predatory lifestyles. Under low-nutrient conditions, Arthrobotrys oligospora and other nematode-trapping fungi develop dedicated structures for nematode capture when exposed to nematode-derived cues, including a conserved family of pheromones, the ascarosides. A. oligospora senses ascarosides via conserved MAPK and cAMP-PKA pathways; however, the upstream receptors remain unknown. Here, using genomic, transcriptomic and functional analyses, we identified two families of G protein-coupled receptors (GPCRs) involved in sensing distinct nematode-derived cues. GPCRs homologous to yeast glucose receptors are required for ascaroside sensing, whereas Pth11-like GPCRs contribute to ascaroside-independent nematode sensing. Both GPCR classes activate conserved cAMP-PKA signalling to trigger trap development. This work demonstrates that predatory fungi use multiple GPCRs to sense several distinct nematode-derived cues for prey recognition and to enable a switch to a predatory lifestyle. Identification of these receptors reveals the molecular mechanisms of cross-kingdom communication via conserved pheromones also sensed by plants and animals.
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Affiliation(s)
- Chih-Yen Kuo
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Rebecca J Tay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Chian Juan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason Hoki
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yen-Ping Hsueh
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
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2
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Shi J, Liu J, Li H, Tang Y, Liu S, Sun Z, Yu Z, Ji X. DNA methylation plays important roles in lifestyle transition of Arthrobotrys oligospora. IET Syst Biol 2024; 18:92-102. [PMID: 38760669 PMCID: PMC11179157 DOI: 10.1049/syb2.12094] [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: 01/27/2024] [Revised: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
Trap formation is the key indicator of carnivorous lifestyle transition of nematode-trapping fungi (NTF). Here, the DNA methylation profile was explored during trap induction of Arthrobotrys oligospora, a typical NTF that captures nematodes by developing adhesive networks. Whole-genome bisulfite sequencing identified 871 methylation sites and 1979 differentially methylated regions (DMRs). This first-of-its-kind investigation unveiled the widespread presence of methylation systems in NTF, and suggested potential regulation of ribosomal RNAs through DNA methylation. Functional analysis indicated DNA methylation's involvement in complex gene regulations during trap induction, impacting multiple biological processes like response to stimulus, transporter activity, cell reproduction and molecular function regulator. These findings provide a glimpse into the important roles of DNA methylation in trap induction and offer new insights for understanding the molecular mechanisms driving carnivorous lifestyle transition of NTF.
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Affiliation(s)
- Jiajia Shi
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Jiaxin Liu
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Heng Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yao Tang
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Shuqun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhirong Sun
- Institute of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xinglai Ji
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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3
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Jia H, Xia R, Zhang R, Liang G, Zhuang Y, Zhou Y, Li D, Wang F. Transcriptome analysis highlights the influence of temperature on hydrolase and traps in nematode-trapping fungi. Front Microbiol 2024; 15:1384459. [PMID: 38774504 PMCID: PMC11106486 DOI: 10.3389/fmicb.2024.1384459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/01/2024] [Indexed: 05/24/2024] Open
Abstract
Pine wilt disease caused by Bursaphelenchus xylophilus poses a serious threat to the economic and ecological value of forestry. Nematode trapping fungi trap and kill nematodes using specialized trapping devices, which are highly efficient and non-toxic to the environment, and are very promising for use as biological control agents. In this study, we isolated several nematode-trapping fungi from various regions and screened three for their high nematocidal efficiency. However, the effectiveness of these fungi as nematicides is notably influenced by temperature and exhibits different morphologies in response to temperature fluctuations, which are categorized as "NA," "thin," "dense," and "sparse." The trend of trap formation with temperature was consistent with the trend of nematocidal efficiency with temperature. Both of which initially increased and then decreased with increasing temperature. Among them, Arthrobotrys cladodes exhibited the highest level of nematocidal activity and trap formation among the tested species. Transcriptome data were collected from A. cladodes with various trap morphologies. Hydrolase activity was significantly enriched according to GO and KEGG enrichment analyses. Eight genes related to hydrolases were found to be consistent with the trend of trap morphology with temperature. Weighted gene co-expression analysis and the Cytoscape network revealed that these 8 genes are associated with either mitosis or autophagy. This suggests that they contribute to the formation of "dense" structures in nematode-trapping fungi. One of these genes is the serine protein hydrolase gene involved in autophagy. This study reveals a potentially critical role for hydrolases in trap formation and nematocidal efficiency. And presents a model where temperature affects trap formation and nematocidal efficiency by influencing the serine protease prb1 involved in the autophagy process.
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Affiliation(s)
- Hanqi Jia
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Rui Xia
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Ruizhi Zhang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Guanjun Liang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Yuting Zhuang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Yantao Zhou
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Danlei Li
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Feng Wang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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4
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Zheng H, Chen T, Li W, Hong J, Xu J, Yu Z. Endosymbiotic bacteria within the nematode-trapping fungus Arthrobotrys musiformis and their potential roles in nitrogen cycling. Front Microbiol 2024; 15:1349447. [PMID: 38348183 PMCID: PMC10860758 DOI: 10.3389/fmicb.2024.1349447] [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: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024] Open
Abstract
Endosymbiotic bacteria (ESB) have important effects on their hosts, contributing to its growth, reproduction and biological functions. Although the effects of exogenous bacteria on the trap formation of nematode-trapping fungi (NTF) have been revealed, the effects of ESB on NTF remain unknown. In this study, we investigated the species diversity of ESB in the NTF Arthrobotrys musiformis using high-throughput sequencing and culture-dependent approaches, and compared bacterial profiles to assess the effects of strain source and culture media on A. musiformis. PICRUSt2 and FAPROTAX were used to predict bacterial function. Our study revealed that bacterial communities in A. musiformis displayed high diversity and heterogeneity, with Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the dominant phyla. The ESB between A. musiformis groups isolated from different habitats and cultured in the same medium were more similar to each other than the other groups isolated from the same habitat but cultured in different media. Function analysis predicted a broad and diverse functional repertoire of ESB in A. musiformis, and unveiled that ESB have the potential to function in five modules of the nitrogen metabolism. We isolated nitrogen-fixing and denitrifying bacteria from the ESB and demonstrated their effects on trap formation of A. musiformis. Among seven bacteria that we tested, three bacterial species Bacillus licheniformis, Achromobacter xylosoxidans and Stenotrophomonas maltophilia were found to be efficient in inducing trap formation. In conclusion, this study revealed extensive ESB diversity within NTF and demonstrated that these bacteria likely play important roles in nitrogen cycling, including nematode trap formation.
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Affiliation(s)
- Hua Zheng
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Tong Chen
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Wenjie Li
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianan Hong
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Zefen Yu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
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5
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Fu R, Sun W, Liu B, Sun J, Wu Q, Liu X, Xiang M. Genome and transcriptome reveal lithophilic adaptation of Cladophialophora brunneola, a new rock-inhabiting fungus. Mycology 2024; 14:326-343. [PMID: 38187882 PMCID: PMC10769131 DOI: 10.1080/21501203.2023.2256764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/04/2023] [Indexed: 01/09/2024] Open
Abstract
Rock-inhabiting fungi (RIF) are slow-growing microorganisms that inhabit rocks and exhibit exceptional stress tolerance owing to their thick melanised cell walls. This study reports the identification of a novel rock-inhabiting fungus, Cladophialophora brunneola sp. nov. which was isolated from a karst landform in Guizhou, China, using a combination of morphological and phylogenetic analyses. The genome of C. brunneola was sequenced and assembled, with a total size of approximately 33.8 Mb, encoding 14,168 proteins and yielding an N50 length of 1.88 Mb. C. brunneola possessed a larger proportion of species-specific genes, and phylogenomic analysis positioned it in an early diverged lineage within Chaetothyriales. In comparison to non-RIF, C. brunneola displayed reduction in carbohydrate-active enzyme families (CAZymes) and secondary metabolite biosynthetic gene clusters (BGCs). Transcriptome analysis conducted under PEG-induced drought stress revealed elevated expression levels of genes associated with melanin synthesis pathways, cell wall biosynthesis, and lipid metabolism. This study contributes to our understanding of the genomic evolution and polyextremotolerance exhibited by rock-inhabiting fungi.
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Affiliation(s)
- Rong Fu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bingjie Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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6
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Lin HC, de Ulzurrun GVD, Chen SA, Yang CT, Tay RJ, Iizuka T, Huang TY, Kuo CY, Gonçalves AP, Lin SY, Chang YC, Stajich JE, Schwarz EM, Hsueh YP. Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus. PLoS Biol 2023; 21:e3002400. [PMID: 37988381 PMCID: PMC10662756 DOI: 10.1371/journal.pbio.3002400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-dwelling nematode-trapping fungi (NTF). In particular, the NTF Arthrobotrys oligospora secretes food and sex cues to lure nematodes to its mycelium and is triggered to develop specialized trapping devices. Captured nematodes are then invaded and digested by the fungus, thus serving as a food source. In this study, we examined the transcriptomic response of A. oligospora across the stages of sensing, trap development, and digestion upon exposure to the model nematode Caenorhabditis elegans. A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. Two-thirds of the predicted secretome of A. oligospora was up-regulated in the presence of C. elegans at all time points examined, and among these secreted proteins, 38.5% are predicted to be effector proteins. Furthermore, functional studies disrupting the t-SNARE protein Sso2 resulted in impaired ability to capture nematodes. Additionally, genes of the DUF3129 family, which are expanded in the genomes of several NTF, were highly up-regulated upon nematode exposure. We observed the accumulation of highly expressed DUF3129 proteins in trap cells, leading us to name members of this gene family as Trap Enriched Proteins (TEPs). Gene deletion of the most highly expressed TEP gene, TEP1, impairs the function of traps and prevents the fungus from capturing prey efficiently. In late stages of predation, we observed up-regulation of a variety of proteases, including metalloproteases. Following penetration of nematodes, these metalloproteases facilitate hyphal growth required for colonization of prey. These findings provide insights into the biology of the predatory lifestyle switch in a carnivorous fungus and provide frameworks for other fungal-nematode predator-prey systems.
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Affiliation(s)
- Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | | | - Sheng-An Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ching-Ting Yang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Rebecca J. Tay
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tomoyo Iizuka
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tsung-Yu Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Yen Kuo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - A. Pedro Gonçalves
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Siou-Ying Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Erich M. Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
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Yang X, Zhang F, Yang Y, Zhou F, Boonmee S, Xiao W, Yang X. Conidia Fusion: A Mechanism for Fungal Adaptation to Nutrient-Poor Habitats. J Fungi (Basel) 2023; 9:755. [PMID: 37504743 PMCID: PMC10381365 DOI: 10.3390/jof9070755] [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: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Conidia fusion (CF) is a commonly observed structure in fungi. However, it has not been systematically studied. This study examined 2457 strains of nematode-trapping fungi (NTF) to explore the species specificity, physiological period, and physiological significance of CF. The results demonstrated that only six species of Arthrobotrys can form CF among the sixty-five tested NTF species. The studies on the model species Arthrobotrys oligospora (DL228) showed that CF occurred in both shed and unshed plus mature and immature conidia. Additionally, the conidia fusion rate (CFR) increased significantly with the decrease of nutrient concentration in habitats. The studies on the conidia fusion body (CFB) produced by A. oligospora (DL228) revealed that the more conidia contained in the CFB, the faster and denser the mycelia of the CFB germinated in weak nutrient medium and soil plates. On the one hand, rapid mycelial extension is beneficial for the CFB to quickly find new nutrient sources in habitats with uneven nutrient distribution. On the other hand, dense mycelium increases the contact area with the environment, improving the nutrient absorption efficiency, which is conducive to improving the survival rate of conidia in the weak nutrient environment. In addition, all species that form CF produce smaller conidia. Based on this observation, CF may be a strategy to balance the defects (nutrient deficiency) caused by conidia miniaturization.
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Affiliation(s)
- Xinju Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Yaoquan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Faping Zhou
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
- Yunling Back-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
- Key Laboratory of Yunnan State Education Department on Er'hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali 671003, China
| | - Xiaoyan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
- Yunling Back-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
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Zhang F, Yang YQ, Zhou FP, Xiao W, Boonmee S, Yang XY. Morphological and Phylogenetic Characterization of Five Novel Nematode-Trapping Fungi (Orbiliomycetes) from Yunnan, China. J Fungi (Basel) 2023; 9:735. [PMID: 37504724 PMCID: PMC10381634 DOI: 10.3390/jof9070735] [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: 05/26/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023] Open
Abstract
Nematode-trapping fungi are widely studied due to their unique morphological structure, survival strategy, and potential value in the biological control of harmful nematodes. During the identification of carnivorous fungi preserved in our laboratory, five novel nematode-trapping fungi were established and placed in the genera Arthrobotrys and Drehslerella based on morphological and multigene (ITS, TEF, and RPB2) phylogenetic analyses. A. hengjiangensis sp. nov. and A. weixiensis sp. nov. are characterized by producing adhesive networks to catch nematodes. Dr. pengdangensis sp. nov., Dr. tianchiensis sp. nov., and Dr. yunlongensis sp. nov. are characterized by producing constricting rings. Morphological descriptions, illustrations, taxonomic notes, and phylogenetic analysis are provided for all new taxa; a key for Drechslerella species is listed; and some deficiencies in the taxonomy and evolution study of nematode-trapping fungi are also discussed herein.
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Affiliation(s)
- Fa Zhang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Yao-Quan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Fa-Ping Zhou
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
- Yunling Back-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
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9
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Liu Y, Yang X, Zhu M, Bai N, Wang W, Yang J. Involvement of AoMdr1 in the Regulation of the Fluconazole Resistance, Mycelial Fusion, Conidiation, and Trap Formation of Arthrobotrys oligospora. Microorganisms 2023; 11:1612. [PMID: 37375114 DOI: 10.3390/microorganisms11061612] [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: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Multidrug resistance (Mdr) proteins are critical proteins for maintenance of drug resistance in fungi. Mdr1 has been extensively studied in Candida albicans; its role in other fungi is largely unknown. In this study, we identified a homologous protein of Mdr (AoMdr1) in the nematode-trapping (NT) fungus Arthrobotrys oligospora. It was found that the deletion of Aomdr1 resulted in a significant reduction in the number of hyphal septa and nuclei as well as increased sensitivity to fluconazole and resistance to hyperosmotic stress and SDS. The deletion of Aomdr1 also led to a remarkable increase in the numbers of traps and mycelial loops in the traps. Notably, AoMdr1 was able to regulate mycelial fusion under low-nutrient conditions, but not under nutrient-rich conditions. AoMdr1 was also involved in secondary metabolism, and its deletion caused an increase in arthrobotrisins (specific compounds produced by NT fungi). These results suggest that AoMdr1 plays a crucial role in the fluconazole resistance, mycelial fusion, conidiation, trap formation, and secondary metabolism of A. oligospora. Our study contributes to the understanding of the critical role of Mdr proteins in mycelial growth and the development of NT fungi.
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Affiliation(s)
- Yankun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Science, Yunnan University, Kunming 650032, China
| | - Xuewei Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Science, Yunnan University, Kunming 650032, China
| | - Meichen Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Science, Yunnan University, Kunming 650032, China
| | - Na Bai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Science, Yunnan University, Kunming 650032, China
| | - Wenjie Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Science, Yunnan University, Kunming 650032, China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Science, Yunnan University, Kunming 650032, China
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10
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Zhang F, Boonmee S, Yang YQ, Zhou FP, Xiao W, Yang XY. Arthrobotrys blastospora sp. nov. (Orbiliomycetes): A Living Fossil Displaying Morphological Traits of Mesozoic Carnivorous Fungi. J Fungi (Basel) 2023; 9:jof9040451. [PMID: 37108905 PMCID: PMC10144811 DOI: 10.3390/jof9040451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
The evolution of carnivorous fungi in deep time is still poorly understood as their fossil record is scarce. The approximately 100-million-year-old Cretaceous Palaeoanellus dimorphus is the earliest fossil of carnivorous fungi ever discovered. However, its accuracy and ancestral position has been widely questioned because no similar species have been found in modern ecosystems. During a survey of carnivorous fungi in Yunnan, China, two fungal isolates strongly morphologically resembling P. dimorphus were discovered and identified as a new species of Arthrobotrys (Orbiliaceae, Orbiliomycetes), a modern genus of carnivorous fungi. Phylogenetically, Arthrobotrys blastospora sp. nov. forms a sister lineage to A. oligospora. A. blastospora catches nematodes with adhesive networks and produces yeast-like blastospores. This character combination is absent in all other previously known modern carnivorous fungi but is strikingly similar to the Cretaceous P. dimorphus. In this paper, we describe A. blastospora in detail and discuss its relationship to P. dimorphus.
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Affiliation(s)
- Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Yao-Quan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Fa-Ping Zhou
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Key Laboratory of Yunnan State Education Department on Er'hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers from Dali University, Dali University, Dali 671003, China
- Yunling Black-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Key Laboratory of Yunnan State Education Department on Er'hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali 671003, China
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11
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Abstract
Nematode-trapping fungi (NTF) are the majority of carnivorous microbes to capture nematodes through diverse and sophisticated trapping organs derived from hyphae. They can adopt carnivorous lifestyles in addition to saprophytism to obtain extra-nutrition from nematodes. As a special group of fungi, the NTF are not only excellent model organism for studying lifestyle transition of fungi but also natural resources of exploring biological control of nematodes. However, the carnivorous mechanism of NTF remains poorly understood. Nowadays, the omics studies of NTF have provided numerous genes and pathways that are associated with the phenotypes of carnivorous traits, which need molecular tools to verify. Here, we review the development and progress of gene manipulation tools in NTF, including methodology and strategy of transformation, random gene mutagenesis methods and target gene mutagenesis methods. The principle and practical approach for each method was summarized and discussed, and the basic operational flow for each tool was described. This paper offers a clear reference and instruction for researchers who work on NTF as well as other group of fungi.
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Affiliation(s)
- Shunxian Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Xingzhong Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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12
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Chen Y, Liu J, Fan Y, Xiang M, Kang S, Wei D, Liu X. SNARE Protein DdVam7 of the Nematode-Trapping Fungus Drechslerella dactyloides Regulates Vegetative Growth, Conidiation, and the Predatory Process via Vacuole Assembly. Microbiol Spectr 2022; 10:e0187222. [PMID: 36287065 PMCID: PMC9769606 DOI: 10.1128/spectrum.01872-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 01/07/2023] Open
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins play conserved roles in membrane fusion events in eukaryotes and have been documented to be involved in fungal growth and pathogenesis. However, little is known about the roles of SNAREs in trap morphogenesis in nematode-trapping fungi (NTF). Drechslerella dactyloides, one of the constricting ring-forming NTF, captures free-living nematodes via rapid ring cell inflation. Here, we characterized DdVam7 of D. dactyloides, a homolog of the yeast SNARE protein Vam7p. Deletion of DdVam7 significantly suppressed vegetative growth and conidiation. The mutation significantly impaired trap formation and ring cell inflation, resulting in a markedly decreased nematode-trapping ability. A large vacuole could develop in ring cells within ~2.5 s after instant inflation in D. dactyloides. In the ΔDdVam7 mutant, the vacuoles were small and fragmented in hyphae and uninflated ring cells, and the large vacuole failed to form in inflated ring cells. The localization of DdVam7 in vacuoles suggests its involvement in vacuole fusion. In summary, our results suggest that DdVam7 regulates vegetative growth, conidiation, and the predatory process by mediating vacuole assembly in D. dactyloides, and this provides a basis for studying mechanisms of SNAREs in NTF and ring cell rapid inflation. IMPORTANCE D. dactyloides is a nematode-trapping fungus that can capture nematodes through a constricting ring, the most sophisticated trapping device. It is amazing that constricting ring cells can inflate to triple their size within seconds to capture a nematode. A large centrally located vacuole is a unique signature associated with inflated ring cells. However, the mechanism underpinning trap morphogenesis, especially vacuole dynamics during ring cell inflation, remains unclear. Here, we documented the dynamics of vacuole assembly during ring cell inflation via time-lapse imaging for the first time. We characterized a SNARE protein in D. dactyloides (DdVam7) that was involved in vacuole assembly in hyphae and ring cells and played important roles in vegetative growth, conidiation, trap morphogenesis, and ring cell inflation. Overall, this study expands our understanding of biological functions of the SNARE proteins and vacuole assembly in NTF trap morphogenesis and provides a foundation for further study of ring cell rapid inflation mechanisms.
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Affiliation(s)
- Yue Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Jia Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Yani Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, Pennsylvania, USA
| | - Dongsheng Wei
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Xingzhong Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
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13
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Zhang F, Boonmee S, Bhat JD, Xiao W, Yang XY. New Arthrobotrys Nematode-Trapping Species (Orbiliaceae) from Terrestrial Soils and Freshwater Sediments in China. J Fungi (Basel) 2022; 8:jof8070671. [PMID: 35887428 PMCID: PMC9317614 DOI: 10.3390/jof8070671] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 11/23/2022] Open
Abstract
Arthrobotrys is the most complex genus of Orbiliaceae nematode-trapping fungi. Its members are widely distributed in various habitats worldwide due to their unique nematode-trapping survival strategies. During a survey of nematophagous fungi in Yunnan Province, China, twelve taxa were isolated from terrestrial soil and freshwater sediment habitats and were identified as six new species in Arthrobotrys based on evidence from morphological and multigene (ITS, TEF, and RPB2) phylogenetic analyses. These new species i.e., Arthrobotrys eryuanensis, A. jinpingensis, A. lanpingensis, A. luquanensis, A. shuifuensis, and A. zhaoyangensis are named in recognition of their places of origin. Morphological descriptions, illustrations, taxonomic notes, and a multilocus phylogenetic analysis are provided for all new taxa. In addition, a key to known species in Arthrobotrys is provided, and the inadequacies in the taxonomic study of nematode-trapping fungi are also discussed.
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Affiliation(s)
- Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (W.X.)
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand;
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand;
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | | | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (W.X.)
- Key Laboratory of Yunnan State Education Department on Er’hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali 671003, China
- Yunling Back-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (W.X.)
- Key Laboratory of Yunnan State Education Department on Er’hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali 671003, China
- Correspondence:
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14
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Al-Ani LKT, Soares FEDF, Sharma A, de los Santos-Villalobos S, Valdivia-Padilla AV, Aguilar-Marcelino L. Strategy of Nematophagous Fungi in Determining the Activity of Plant Parasitic Nematodes and Their Prospective Role in Sustainable Agriculture. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:863198. [PMID: 37746161 PMCID: PMC10512347 DOI: 10.3389/ffunb.2022.863198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/01/2022] [Indexed: 09/22/2023]
Abstract
In this review, we supply a framework for the importance of nematophagous fungi (nematophagous fungi [NF]) and their role in agricultural ecosystems. We characterize the taxonomy, diversity, ecology, and type of NF, depending on their interaction with plant-parasitic nematodes (PPNs). We described potential mechanisms of NF in the control of PPNs, the efficiency and methods of utilization, and the use of nematicides in sustainable agriculture. We explain the utilization of NF in nanotechnology as a new approach. NF are significant in the soil for having the effective potential for use in sustainable agriculture. These types of fungi belong to wide taxa groups, such as Ascomycota, Basidiomycota, and other groups. Diverse NF are available in different kinds of soil, especially in soils that contain high densities of nematodes. There is a relationship between the environment of nematodes and NF. NF can be divided into two types according to the mechanisms that affect nematodes. These types are divided into direct or indirect effects. The direct effects include the following: ectoparasites, endoparasites, cyst, or egg parasites producing toxins, and attack tools as special devices. However, the indirect effect comprises two groups: paralyzing toxins and the effect on the life cycle of nematodes. We explained the molecular mechanisms for determining the suitable conditions in brief and clarified the potential for increasing the efficacy of NF to highly impact sustainable agriculture in two ways: directly and indirectly.
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Affiliation(s)
- Laith Khalil Tawfeeq Al-Ani
- Department of Plant Protection, College of Agriculture, University of Baghdad, Baghdad, Iraq
- School of Biology Science, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | | | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Centre of Bioengineering, Queretaro, Mexico
| | | | | | - Liliana Aguilar-Marcelino
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, INIFAP, Jiutepec, Mexico
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15
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Wang L, Qin Y, Fan Z, Gao K, Zhan J, Xing R, Liu S, Li P. Novel Lead Compound Discovery from Aspergillus fumigatus 1T-2 against Meloidogyne incognita Based on a Chemical Ecology Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4644-4657. [PMID: 35404052 DOI: 10.1021/acs.jafc.1c08147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
To replace biohazardous nematicides, there is an ever-increasing need to identify natural product-based agents to contain root-knot nematodes (RKNs) in agriculture. In this chemical ecology study, an antagonistic fungus Aspergillus fumigatus 1T-2, which could cause the formation of withering of the gut and vacuole-like structures in the nematode body, was isolated based on the gradually increased antagonistic interactions between the soil fungi and RKNs. Based on these typical morphological characteristics, a potent nematode-antagonistic compound 2-furoic acid, which had a simple structure, was successfully identified from 1T-2 fermentation broth by liquid chromatography-mass spectrometry (LC-MS). 2-Furoic acid showed effective mortality activity in vitro, of which the LC50 value to Megalaima incognita at 24 h was 37.75 μg/mL. 2-Furoic acid had similar mortality activity to the positive control fosthiazate at 30 μg/mL. Continuous 2-furoic acid exposure had obvious negative influences on both nematode vitality and egg hatchability. Notably, significant variations were observed in nematodes and eggs with 2-furoic acid treatment, which might be induced by novel nematocidal mechanisms. Furthermore, the 1T-2 fermentation broth and 2-furoic acid had significant control efficacy on M. incognita under the greenhouse test-tube assay. Overall, these findings provide valuable insights into the use of 2-furoic acid with biocontrol potential as a preferable lead structure for the development of innovative nematicides.
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Affiliation(s)
- Linsong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Yukun Qin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Zhaoqian Fan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Kun Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Jiang Zhan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ronge Xing
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Song Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
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16
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Kelley M, Paulines MJ, Yoshida G, Myers R, Jora M, Levoy JP, Addepalli B, Benoit JB, Limbach PA. Ionizing radiation and chemical oxidant exposure impacts on Cryptococcus neoformans transfer RNAs. PLoS One 2022; 17:e0266239. [PMID: 35349591 PMCID: PMC8963569 DOI: 10.1371/journal.pone.0266239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
Cryptococcus neoformans is a fungus that is able to survive abnormally high levels of ionizing radiation (IR). The radiolysis of water by IR generates reactive oxygen species (ROS) such as H2O2 and OH-. C. neoformans withstands the damage caused by IR and ROS through antioxidant production and enzyme-catalyzed breakdown of ROS. Given these particular cellular protein needs, questions arise whether transfer ribonucleic acids molecules (tRNAs) undergo unique chemical modifications to maintain their structure, stability, and/or function under such environmental conditions. Here, we investigated the effects of IR and H2O2 exposure on tRNAs in C. neoformans. We experimentally identified the modified nucleosides present in C. neoformans tRNAs and quantified changes in those modifications upon exposure to oxidative conditions. To better understand these modified nucleoside results, we also evaluated tRNA pool composition in response to the oxidative conditions. We found that regardless of environmental conditions, tRNA modifications and transcripts were minimally affected. A rationale for the stability of the tRNA pool and its concomitant profile of modified nucleosides is proposed based on the lack of codon bias throughout the C. neoformans genome and in particular for oxidative response transcripts. Our findings suggest that C. neoformans can rapidly adapt to oxidative environments as mRNA translation/protein synthesis are minimally impacted by codon bias.
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Affiliation(s)
- Melissa Kelley
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Mellie June Paulines
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - George Yoshida
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Ryan Myers
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Joel P. Levoy
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | | | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Patrick A. Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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17
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Dou K, Pang G, Cai F, Chenthamara K, Zhang J, Liu H, Druzhinina IS, Chen J. Functional Genetics of Trichoderma Mycoparasitism. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Wernet N, Wernet V, Fischer R. The small-secreted cysteine-rich protein CyrA is a virulence factor participating in the attack of Caenorhabditis elegans by Duddingtonia flagrans. PLoS Pathog 2021; 17:e1010028. [PMID: 34735554 PMCID: PMC8568293 DOI: 10.1371/journal.ppat.1010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/11/2021] [Indexed: 01/14/2023] Open
Abstract
Nematode-trapping fungi (NTF) are a diverse and intriguing group of fungi that live saprotrophically but can switch to a predatory lifestyle when starving and in the presence of nematodes. NTF like Arthrobotrys oligospora or Duddingtonia flagrans produce adhesive trapping networks to catch and immobilize nematodes. After penetration of the cuticle, hyphae grow and develop inside the worm and secrete large amounts of hydrolytic enzymes for digestion. In many microbial pathogenic interactions small-secreted proteins (SSPs) are used to manipulate the host. The genome of D. flagrans encodes more than 100 of such putative SSPs one of which is the cysteine-rich protein CyrA. We have chosen this gene for further analysis because it is only found in NTF and appeared to be upregulated during the interaction. We show that the cyrA gene was transcriptionally induced in trap cells, and the protein accumulated at the inner rim of the hyphal ring before Caenorhabditis elegans capture. After worm penetration, the protein appeared at the fungal infection bulb, where it is likely to be secreted with the help of the exocyst complex. A cyrA-deletion strain was less virulent, and the time from worm capture to paralysis was extended. Heterologous expression of CyrA in C. elegans reduced its lifespan. CyrA accumulated in C. elegans in coelomocytes where the protein possibly is inactivated. This is the first example that SSPs may be important in predatory microbial interactions.
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Affiliation(s)
- Nicole Wernet
- Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Karlsruhe, Germany
| | - Valentin Wernet
- Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Karlsruhe, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Karlsruhe, Germany
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19
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Zhou D, Xu J, Dong J, Li H, Wang D, Gu J, Zhang KQ, Zhang Y. Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus Arthrobotrys oligospora in China. Microorganisms 2021; 9:1919. [PMID: 34576814 PMCID: PMC8465350 DOI: 10.3390/microorganisms9091919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol agent NTF are geographically and ecologically structured. A previous study reported evidence for ecological adaptation in the model NTF species Arthrobotrys oligospora. However, their large-scale geographic structure, patterns of gene flow, their potential phenotypic diversification, and host specialization remain largely unknown. In this study, we developed a new panel of 20 polymorphic short tandem repeat (STR) markers and analyzed 239 isolates of A. oligospora from 19 geographic populations in China. In addition, DNA sequences at six nuclear gene loci and strain mating types (MAT) were obtained for these strains. Our analyses suggest historical divergence within the A. oligospora population in China. The genetically differentiated populations also showed phenotypic differences that may be related to their ecological adaptations. Interestingly, our analyses identified evidence for recent dispersion and hybridization among the historically subdivided geographic populations in nature. Together, our results indicate a changing population structure of A. oligospora in China and that care must be taken in selecting the appropriate strains as biocontrol agents that can effectively reproduce in agriculture soil while maintaining their nematode-trapping ability.
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Affiliation(s)
- Duanyong Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianyong Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Da Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Juan Gu
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
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20
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The E3-ligase AoUBR1 in N-end rule pathway is involved in the vegetative growth, secretome, and trap formation in Arthrobotrys oligospora. Fungal Biol 2021; 125:532-540. [PMID: 34140149 DOI: 10.1016/j.funbio.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 11/20/2022]
Abstract
The N-end rule pathway is a regulated protein degradation system. Arthrobotrys oligospora, a typical nematode-trapping fungus, switches its life strategies from saprophytism to carnivorism when capturing free-living nematodes by means of adhesive networks. In this study, a putative E3-ligase AoUBR1 involved in N-end rule pathway was characterized in A. oligospora during vegetative growth and trap formation. Expression of AoUBR1 coding gene was down-regulated during trap formation. Compared with wild type, the AoUBR1 knock-out mutants decreased the vegetative growth, formed less traps, and turned to be sensitive to cold stress, while, AoUBR1 overexpression mutants lost the capacity to produce conidia and also formed less traps. A number of genes differentially expressed by knock-out and overexpression of AoUBR1, which lead to the transcriptional responses associated with plasma membrane, transportation, oxidation, and proteolysis. AoUBR1 knock-out also resulted in the down-regulation of numerous secreted proteins associated with carnivorism and nutrient utilization from nematodes. In addition, AoUBR1 homologs were conserved in nematode-trapping fungi based on the genome searching. Therefore, the results suggested AoUBR1 in A. oligospora and its homologs in other trapping fungi are involved in the lifestyle switch between saprophytism and carnivorism.
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21
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Zhang Y, Li S, Li H, Wang R, Zhang KQ, Xu J. Fungi-Nematode Interactions: Diversity, Ecology, and Biocontrol Prospects in Agriculture. J Fungi (Basel) 2020; 6:E206. [PMID: 33020457 PMCID: PMC7711821 DOI: 10.3390/jof6040206] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 01/27/2023] Open
Abstract
Fungi and nematodes are among the most abundant organisms in soil habitats. They provide essential ecosystem services and play crucial roles for maintaining the stability of food-webs and for facilitating nutrient cycling. As two of the very abundant groups of organisms, fungi and nematodes interact with each other in multiple ways. Here in this review, we provide a broad framework of interactions between fungi and nematodes with an emphasis on those that impact crops and agriculture ecosystems. We describe the diversity and evolution of fungi that closely interact with nematodes, including food fungi for nematodes as well as fungi that feed on nematodes. Among the nematophagous fungi, those that produce specialized nematode-trapping devices are especially interesting, and a great deal is known about their diversity, evolution, and molecular mechanisms of interactions with nematodes. Some of the fungi and nematodes are significant pathogens and pests to crops. We summarize the ecological and molecular mechanisms identified so far that impact, either directly or indirectly, the interactions among phytopathogenic fungi, phytopathogenic nematodes, and crop plants. The potential applications of our understanding to controlling phytophagous nematodes and soilborne fungal pathogens in agricultural fields are discussed.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
| | - Shuoshuo Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Ruirui Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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22
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Fonseca PLC, Badotti F, De-Paula RB, Araújo DS, Bortolini DE, Del-Bem LE, Azevedo VA, Brenig B, Aguiar ERGR, Góes-Neto A. Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes. Front Microbiol 2020; 11:765. [PMID: 32411111 PMCID: PMC7202290 DOI: 10.3389/fmicb.2020.00765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/30/2020] [Indexed: 12/24/2022] Open
Abstract
The order Hypocreales (Ascomycota) is composed of ubiquitous and ecologically diverse fungi such as saprobes, biotrophs, and pathogens. Despite their phylogenetic relationship, these species exhibit high variability in biomolecules production, lifestyle, and fitness. The mitochondria play an important role in the fungal biology, providing energy to the cells and regulating diverse processes, such as immune response. In spite of its importance, the mechanisms that shape fungal mitogenomes are still poorly understood. Herein, we investigated the variability and evolution of mitogenomes and its relationship with the divergence time using the order Hypocreales as a study model. We sequenced and annotated for the first time Trichoderma harzianum mitochondrial genome (mtDNA), which was compared to other 34 mtDNAs species that were publicly available. Comparative analysis revealed a substantial structural and size variation on non-coding mtDNA regions, despite the conservation of copy number, length, and structure of protein-coding elements. Interestingly, we observed a highly significant correlation between mitogenome length, and the number and size of non-coding sequences in mitochondrial genome. Among the non-coding elements, group I and II introns and homing endonucleases genes (HEGs) were the main contributors to discrepancies in mitogenomes structure and length. Several intronic sequences displayed sequence similarity among species, and some of them are conserved even at gene position, and were present in the majority of mitogenomes, indicating its origin in a common ancestor. On the other hand, we also identified species-specific introns that advocate for the origin by different mechanisms. Investigation of mitochondrial gene transfer to the nuclear genome revealed that nuclear copies of the nad5 are the most frequent while atp8, atp9, and cox3 could not be identified in any of the nuclear genomes analyzed. Moreover, we also estimated the divergence time of each species and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.
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Affiliation(s)
- Paula L. C. Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B. De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Daniel S. Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Dener E. Bortolini
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiz-Eduardo Del-Bem
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A. Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R. G. R. Aguiar
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Zhang Y, Yang G, Fang M, Deng C, Zhang KQ, Yu Z, Xu J. Comparative Analyses of Mitochondrial Genomes Provide Evolutionary Insights Into Nematode-Trapping Fungi. Front Microbiol 2020; 11:617. [PMID: 32351475 PMCID: PMC7174627 DOI: 10.3389/fmicb.2020.00617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/19/2020] [Indexed: 01/10/2023] Open
Abstract
Predatory fungi in Orbiliaceae (Ascomycota) have evolved a diversity of trapping devices that enable them to trap and kill nematodes, other small animals, and protozoans. These trapping devices include adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and non-constricting rings. Their diversity and practical importance have attracted significant attention from biologists, making them excellent model organisms for studying adaptative evolution and as biological control agents against parasitic nematodes. The putative origins and evolutionary relationships among these carnivorous fungi have been investigated using nuclear protein-encoding genes, but their patterns of mitogenome relationships and divergences remain unknown. Here we analyze and compare the mitogenomes of 12 fungal strains belonging to eight species, including six species representing all four types of nematode trapping devices and two from related but non-predatory fungi. All 12 analyzed mitogenomes were of circular DNA molecules, with lengths ranging from 146,101 bp to 280,699 bp. Gene synteny analysis revealed several gene rearrangements and intron transfers among the mitogenomes. In addition, the number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among these mitogenomes. The increased number and total size of introns were the main contributors to the length differences among the mitogenomes. Phylogenetic analyses of the protein-coding genes indicated that mitochondrial and nuclear genomes evolved at different rates, and signals of positive selection were found in several genes involved in energy metabolism. Our study provides novel insights into the evolution of nematode-trapping fungi and shall facilitate further investigations of this ecologically and agriculturally important group of fungi.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Guangzhu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Meiling Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Chu Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
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24
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Ji X, Yu Z, Yang J, Xu J, Zhang Y, Liu S, Zou C, Li J, Liang L, Zhang KQ. Expansion of Adhesion Genes Drives Pathogenic Adaptation of Nematode-Trapping Fungi. iScience 2020; 23:101057. [PMID: 32339992 PMCID: PMC7186526 DOI: 10.1016/j.isci.2020.101057] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/12/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2022] Open
Abstract
Understanding how fungi interact with other organisms has significant medical, environmental, and agricultural implications. Nematode-trapping fungi (NTF) can switch to pathogens by producing various trapping devices to capture nematodes. Here we perform comparative genomic analysis of the NTF with four representative trapping devices. Phylogenomic reconstruction of these NTF suggested an evolutionary trend of trapping device simplification in morphology. Interestingly, trapping device simplification was accompanied by expansion of gene families encoding adhesion proteins and their increasing adhesiveness on trap surfaces. Gene expression analysis revealed a consistent up-regulation of the adhesion genes during their lifestyle transition from saprophytic to nematophagous stages. Our results suggest that the expansion of adhesion genes in NTF genomes and consequential increase in trap surface adhesiveness are likely the key drivers of fungal adaptation in trapping nematodes, providing new insights into understanding mechanisms underlying infection and adaptation of pathogenic fungi. Expansion of subtilisin, adhesion protein, and polygalacturonase gene families Trap simplification during evolution of nematode-trapping fungi Connection between trap simplification and expansion of adhesion genes
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Affiliation(s)
- Xinglai Ji
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON L8S 4K1, Canada
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Shuqun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Chenggang Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Lianming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China.
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25
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Zhang Y, Qiao M, Baral HO, Xu J, Zhang KQ, Yu ZF. Morphological and molecular characterization of Orbilia pseudopolybrocha and O. tonghaiensis, two new species of Orbiliaceae from China. Int J Syst Evol Microbiol 2020; 70:2664-2676. [PMID: 32238230 DOI: 10.1099/ijsem.0.004088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
This study examined over 20 fungal specimens of the Orbiliaceae (Orbiliomycetes) from different regions in China. Our analyses based on morphological traits and the ITS rDNA sequences revealed two new Orbilia species with drechslerella-like asexual morphs. These new species are able to trap nematodes with constricting rings. In addition, Orbilia cf. orientalis is reported as a new cryptic Chinese variant of European collections of O. orientalis. All three species are described and illustrated in detail in this paper. Their phylogenetic relationships with other orbiliaceous species were identified based on their ITS sequences.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, PR China
| | - Min Qiao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, PR China
| | - H O Baral
- Blaihofstrasse 42, Germany, D-72074 Tübingen
| | - Jianping Xu
- Department of Biology, McMaster University Hamilton, Ontario, L8S 4K1, Canada.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, PR China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, PR China
| | - Ze-Fen Yu
- School of Life Science, Yunnan University, Kunming, 650032, PR China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, PR China
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26
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Yang CT, Vidal-Diez de Ulzurrun G, Gonçalves AP, Lin HC, Chang CW, Huang TY, Chen SA, Lai CK, Tsai IJ, Schroeder FC, Stajich JE, Hsueh YP. Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi. Proc Natl Acad Sci U S A 2020; 117:6762-6770. [PMID: 32161129 PMCID: PMC7104180 DOI: 10.1073/pnas.1919726117] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nematode-trapping fungi (NTF) are a group of specialized microbial predators that consume nematodes when food sources are limited. Predation is initiated when conserved nematode ascaroside pheromones are sensed, followed by the development of complex trapping devices. To gain insights into the coevolution of this interkingdom predator-prey relationship, we investigated natural populations of nematodes and NTF that we found to be ubiquitous in soils. Arthrobotrys species were sympatric with various nematode species and behaved as generalist predators. The ability to sense prey among wild isolates of Arthrobotrys oligospora varied greatly, as determined by the number of traps after exposure to Caenorhabditis elegans While some strains were highly sensitive to C. elegans and the nematode pheromone ascarosides, others responded only weakly. Furthermore, strains that were highly sensitive to the nematode prey also developed traps faster. The polymorphic nature of trap formation correlated with competency in prey killing, as well as with the phylogeny of A. oligospora natural strains, calculated after assembly and annotation of the genomes of 20 isolates. A chromosome-level genome assembly and annotation were established for one of the most sensitive wild isolates, and deletion of the only G-protein β-subunit-encoding gene of A. oligospora nearly abolished trap formation. In summary, our study establishes a highly responsive A. oligospora wild isolate as a model strain for the study of fungus-nematode interactions and demonstrates that trap formation is a fitness character in generalist predators of the nematode-trapping fungus family.
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Affiliation(s)
- Ching-Ting Yang
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan
| | | | - A Pedro Gonçalves
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan
| | - Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 106, Taiwan
| | - Ching-Wen Chang
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan
| | - Tsung-Yu Huang
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan
| | - Sheng-An Chen
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan
| | - Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei 115, Taiwan
| | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei 115, Taiwan
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan;
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 106, Taiwan
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan
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27
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Ma Y, Yang X, Xie M, Zhang G, Yang L, Bai N, Zhao Y, Li D, Zhang KQ, Yang J. The Arf-GAP AoGlo3 regulates conidiation, endocytosis, and pathogenicity in the nematode-trapping fungus Arthrobotrys oligospora. Fungal Genet Biol 2020; 138:103352. [PMID: 32087364 DOI: 10.1016/j.fgb.2020.103352] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/04/2020] [Accepted: 02/12/2020] [Indexed: 12/18/2022]
Abstract
Small GTPases of the ADP-ribosylation factor (Arf) family and their activating proteins (Arf-GAPs) regulate mycelial development and pathogenicity in yeast and filamentous fungi; however, little is known about their roles in nematode-trapping (NT) fungi. In this study, an ortholog of Arf-GAP Glo3 (AoGlo3) in Saccharomyces cerevisiae was characterized in the NT fungus Arthrobotrys oligospora. Deletion of the Aoglo3 gene resulted in growth defects and an increase in hyphal septum. Meanwhile, the sporulation capacity of the ΔAoglo3 mutant was decreased by 98%, and 67.1-71.2% spores became gourd or claviform in shape (from obovoid), which was accompanied by a significant decrease in the spore germination rate. This reduced sporulation capacity correlated with the transcriptional repression of several sporulation-related genes including fluG, rodA, abaA, medA, and lreA. The ΔAoglo3 mutant was also sensitive to several chemical stressors such as Congo red, NaCl, and sorbitol. Additionally, AoGlo3 was found to be involved in endocytosis, and more myelin figures were observed in the ΔAoglo3 mutant than in the wild-type strain, which was consistent with the presence of more autophagosomes observed in the mutant. Importantly, AoGlo3 affected the production of mycelial traps and serine proteases for nematode predation. In summary, AoGlo3 is involved in the regulation of multiple cellular processes such as mycelial growth, conidiation, environmental adaption, endocytosis, and pathogenicity in A. oligospora.
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Affiliation(s)
- Yuxin Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Xuewei Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Meihua Xie
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Guosheng Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Le Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Na Bai
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Yining Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Dongni Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China.
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28
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Kumar KK. Fungi: A Bio-resource for the Control of Plant Parasitic Nematodes. Fungal Biol 2020. [DOI: 10.1007/978-3-030-48474-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Xie M, Wang Y, Tang L, Yang L, Zhou D, Li Q, Niu X, Zhang KQ, Yang J. AoStuA, an APSES transcription factor, regulates the conidiation, trap formation, stress resistance and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora. Environ Microbiol 2019; 21:4648-4661. [PMID: 31433890 DOI: 10.1111/1462-2920.14785] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 01/30/2023]
Abstract
The APSES protein family comprises a conserved class of fungus-specific transcriptional regulators. Some members have been identified in partial ascomycetes. In this study, the APSES protein StuA (AoStuA) of the nematode-trapping fungus Arthrobotrys oligospora was characterized. Compared with the wild-type (WT) strain, three ΔAoStuA mutants grew relatively slowly, displayed a 96% reduction in sporulation capacity and a delay in conidial germination. The reduced sporulation capacity correlated with transcriptional repression of several sporulation-related genes. The mutants were also more sensitive to chemical stressors than the WT strain. Importantly, the mutants were unable to produce mycelial traps for nematode predation. Moreover, peroxisomes and Woronin bodies were abundant in the WT cells but hardly found in the cells of those mutants. The lack of such organelles correlated with transcriptional repression of some genes involved in the biogenesis of peroxisomes and Woronin bodies. The transcript levels of several genes involved in the cAMP/PKA signalling pathway were also significantly reduced in the mutants versus the WT strain, implicating a regulatory role of AoStuA in the transcription of genes involved in the cAMP/PKA signalling pathway that regulates an array of cellular processes and events. In particular, AoStuA is indispensable for A. oligospora trap formation and virulence.
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Affiliation(s)
- Meihua Xie
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Department of Chemistry and Life Science, Chuxiong Normal University, Chuxiong, 675000, P. R. China
| | - Yunchuan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Liyan Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Le Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Duanxu Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Qing Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Xuemei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
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30
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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31
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Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J, Cai F, Kopchinskiy AG, Kubicek EM, Kuo A, Baroncelli R, Sarrocco S, Noronha EF, Vannacci G, Shen Q, Grigoriev IV, Druzhinina IS. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 2019; 20:485. [PMID: 31189469 PMCID: PMC6560777 DOI: 10.1186/s12864-019-5680-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. RESULTS We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. CONCLUSIONS Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.
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Affiliation(s)
- Christian P Kubicek
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- , Vienna, Austria
| | - Andrei S Steindorff
- Departamento de Biologia Celular, Universidade de Brasília, Brasíla, DF, Brazil
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Komal Chenthamara
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Gelsomina Manganiello
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", Naples, Portici, Italy
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jian Zhang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Alexey G Kopchinskiy
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | | | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Riccardo Baroncelli
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | | | - Giovanni Vannacci
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
| | - Irina S Druzhinina
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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32
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Zhang J, Miao Y, Rahimi MJ, Zhu H, Steindorff A, Schiessler S, Cai F, Pang G, Chenthamara K, Xu Y, Kubicek CP, Shen Q, Druzhinina IS. Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi. Environ Microbiol 2019; 21:2644-2658. [PMID: 30815928 PMCID: PMC6850483 DOI: 10.1111/1462-2920.14575] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 12/01/2022]
Abstract
When resources are limited, the hypocrealean fungus Trichoderma guizhouense can overgrow another hypocrealean fungus Fusarium oxysporum, cause sporadic cell death and arrest growth. A transcriptomic analysis of this interaction shows that T. guizhouense undergoes a succession of metabolic stresses while F. oxysporum responded relatively neutrally but used the constitutive expression of several toxin‐encoding genes as a protective strategy. Because of these toxins, T. guizhouense cannot approach it is potential host on the substrate surface and attacks F. oxysporum from above. The success of T. guizhouense is secured by the excessive production of hydrogen peroxide (H2O2), which is stored in microscopic bag‐like guttation droplets hanging on the contacting hyphae. The deletion of NADPH oxidase nox1 and its regulator, nor1 in T. guizhouense led to a substantial decrease in H2O2 formation with concomitant loss of antagonistic activity. We envision the role of NOX proteins in the antagonism of T. guizhouense as an example of metabolic exaptation evolved in this fungus because the primary function of these ancient proteins was probably not linked to interfungal relationships. In support of this, F. oxysporum showed almost no transcriptional response to T. guizhouense Δnox1 strain indicating the role of NOX/H2O2 in signalling and fungal communication.
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Affiliation(s)
- Jian Zhang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Mohammad Javad Rahimi
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Hong Zhu
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Andrei Steindorff
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sabine Schiessler
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Guan Pang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Komal Chenthamara
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Yu Xu
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Christian P Kubicek
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.,Steinschoetelgasse 7,1100, Vienna, Austria
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Irina S Druzhinina
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
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33
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Youssar L, Wernet V, Hensel N, Yu X, Hildebrand HG, Schreckenberger B, Kriegler M, Hetzer B, Frankino P, Dillin A, Fischer R. Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans. PLoS Genet 2019; 15:e1008029. [PMID: 30917129 PMCID: PMC6453484 DOI: 10.1371/journal.pgen.1008029] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/08/2019] [Accepted: 02/18/2019] [Indexed: 11/21/2022] Open
Abstract
Nematode-trapping fungi (NTF) are a large and diverse group of fungi, which may switch from a saprotrophic to a predatory lifestyle if nematodes are present. Different fungi have developed different trapping devices, ranging from adhesive cells to constricting rings. After trapping, fungal hyphae penetrate the worm, secrete lytic enzymes and form a hyphal network inside the body. We sequenced the genome of Duddingtonia flagrans, a biotechnologically important NTF used to control nematode populations in fields. The 36.64 Mb genome encodes 9,927 putative proteins, among which are more than 638 predicted secreted proteins. Most secreted proteins are lytic enzymes, but more than 200 were classified as small secreted proteins (< 300 amino acids). 117 putative effector proteins were predicted, suggesting interkingdom communication during the colonization. As a first step to analyze the function of such proteins or other phenomena at the molecular level, we developed a transformation system, established the fluorescent proteins GFP and mCherry, adapted an assay to monitor protein secretion, and established gene-deletion protocols using homologous recombination or CRISPR/Cas9. One putative virulence effector protein, PefB, was transcriptionally induced during the interaction. We show that the mature protein is able to be imported into nuclei in Caenorhabditis elegans cells. In addition, we studied trap formation and show that cell-to-cell communication is required for ring closure. The availability of the genome sequence and the establishment of many molecular tools will open new avenues to studying this biotechnologically relevant nematode-trapping fungus. Nematode-trapping fungi are fascinating microorganisms, because they are able to switch from saprotrophic growth to a predatory lifestyle. Duddingtonia flagrans forms adhesive trap systems and conidia and resistant chlamydospores. Chlamydospores are ideal for dissemination in the environment to control nematode populations in the field. We show that D. flagrans is able to catch C. elegans but also the very large wine-pathogenic nematode Xiphinema index. We sequenced the D. flagrans genome and show that it encodes about 10,000 genes with a large proportion of secreted proteins. We hypothesize that virulence effector proteins are involved in the interkingdom organismic interaction and identified more than 100 candidates. In order to investigate the molecular biology of D. flagrans and its interaction with nematodes, we established a transformation system and several molecular tools. We show that cell-to-cell communication and hyphal fusion are required for trap formation. Finally, we show that one putative virulence effector protein targets nuclei when expressed in C. elegans.
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Affiliation(s)
- Loubna Youssar
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Valentin Wernet
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Nicole Hensel
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Xi Yu
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Heinz-Georg Hildebrand
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Birgit Schreckenberger
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Marius Kriegler
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | | | - Phillip Frankino
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of Berkeley, Berkeley, California, United States of America
| | - Andrew Dillin
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of Berkeley, Berkeley, California, United States of America
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
- * E-mail:
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34
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Davis WJ, Amses KR, Benny GL, Carter-House D, Chang Y, Grigoriev I, Smith ME, Spatafora JW, Stajich JE, James TY. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). Mol Phylogenet Evol 2019; 133:152-163. [PMID: 30639767 DOI: 10.1016/j.ympev.2019.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/25/2018] [Accepted: 01/04/2019] [Indexed: 11/26/2022]
Abstract
Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.
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Affiliation(s)
- William J Davis
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Kevin R Amses
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Gerald L Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Derreck Carter-House
- Department of Microbiology and Plant Pathology, University of California-Riverside, United States
| | - Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Igor Grigoriev
- United States of America Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, United States
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States.
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35
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Tong SM, Feng MG. Insights into regulatory roles of MAPK-cascaded pathways in multiple stress responses and life cycles of insect and nematode mycopathogens. Appl Microbiol Biotechnol 2018; 103:577-587. [PMID: 30448905 DOI: 10.1007/s00253-018-9516-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 11/24/2022]
Abstract
Fungal entomopathogenicity may have evolved at least 200 million years later than carnivorism of nematophagous fungi on Earth. This mini-review focuses on the composition and regulatory roles of mitogen-activated protein kinase (MAPK) cascades, which act as stress-responsive signaling pathways. Unveiled by genomic comparison, three MAPK cascades of these mycopathogens consist of singular MAPKs (Fus3/Hog1/Slt2), MAPK kinases (Ste7/Pbs2/Mkk1), and MAPK kinase kinases (Ste11/Ssk2/Bck1). All cascaded components characterized in fungal entomopathogens play conserved and special roles in regulating multiple stress responses and phenotypes associated with biological control potential. Fus3-cascaded components are indispensable for fungal growth on oligotrophic substrata and virulence, and mediate cell tolerance to Na+/K+ toxicity, which is often misinterpreted as hyperosmotic effect but readily clarified by transcriptional changes of Na+/K+ ATPase genes and/or cell responses to osmotic polyols. Hog1-cascaded components regulate osmotolerance positively and phenylpyrrole-type fungicide resistance negatively, and also play differential roles in cell growth, conidiation, virulence, and responses to other stress cues. Ste11 has no stress-responsive role in the Beauveria Hog1 cascade despite an essential role in branched yeast Hog1 cascade. Slt2-cascaded components are required for mediation of cell wall integrity and repair of cell wall damage. A crosstalk between Hog1 and Slt2 cascades ensures fungal osmotolerance inside or outside insect. In nematode-trapping fungi, Slt2 is indispensable for cell wall integrity, conidiation, and mycelial trap formation, suggesting that the Slt2 cascade could have evolved along a distinct trajectory required for fungal carnivorism and dispersal/survival in nematode habitats. Altogether, the MAPK cascades are major parts of signaling network that regulate fungal adaptation to insects and nematodes and their habitats.
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Affiliation(s)
- Sen-Miao Tong
- College of Agricultural and Food Science, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China. .,Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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36
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Zhen Z, Zhang G, Yang L, Ma N, Li Q, Ma Y, Niu X, Zhang KQ, Yang J. Characterization and functional analysis of calcium/calmodulin-dependent protein kinases (CaMKs) in the nematode-trapping fungus Arthrobotrys oligospora. Appl Microbiol Biotechnol 2018; 103:819-832. [PMID: 30417308 DOI: 10.1007/s00253-018-9504-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 12/19/2022]
Abstract
Ca2+/calmodulin-dependent protein kinases (CaMKs) are unique second-messenger molecules that impact almost all cellular processes in eukaryotes. In this study, five genes encoding different CaMKs were characterized in the nematode-trapping fungus Arthrobotrys oligospora. These CaMKs, which were retrieved from the A. oligospora genome according to their orthologs in fungi such as Aspergillus nidulans and Neurospora crassa, were expressed at a low level in vitro during mycelial growth stages. Five deletion mutants corresponding to these CaMKs led to growth defects in different media and increased sensitivity to several environmental stresses, including H2O2, menadione, SDS, and Congo red; they also reduced the ability to produce conidia and traps, thus causing a deficiency in nematicidal ability as well. In addition, the transcriptional levels of several typical sporulation-related genes, such as MedA, VelB, and VeA, were down-regulated in all ΔCaMK mutants compared with the wild-type (WT) strain. Moreover, these mutants exhibited hypersensitivity to heat shock and ultraviolet-radiation stresses compared with the WT strain. These results suggest that the five CaMKs in A. oligospora are involved in regulating multiple cellular processes, such as growth, environmental stress tolerance, conidiation, trap formation, and virulence.
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Affiliation(s)
- Zhengyi Zhen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Guosheng Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ni Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Qing Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Yuxin Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Xuemei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China.
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Qu J, Zhou Y, Yu J, Zhang J, Han Y, Zou X. Estimated divergence times of Hirsutella (asexual morphs) in Ophiocordyceps provides insight into evolution of phialide structure. BMC Evol Biol 2018; 18:111. [PMID: 30005592 DOI: 10.1186/s12862-018-1223-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/27/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Hirsutella Pat genus, the asexual morphs of the Ophiocordyceps Sung, is globally distributed entomopathogenic fungi, which infect a variety of arthropods, mites and nematodes. The fungal species also have shown potential application in the field of biological control, bio-medicine and food development. Although these fungi are synonymized under Ophiocordyceps, formal taxonomic assignments remain necessary for classification of species in Hirsutella. However, due to the heterogeneity and complexity of Hirsutella genus, more detailed taxonomic and phylogenetic analyses are required to address the following subjects: (1) the relationships between the phialide morphological characteristics and phylogenetic information of Hirsutella with asexual morphs, (2) the origin and evolution of the phialide structure, and (3) host specificity and fungal pathogenicity. RESULTS Five typical phialide structures are summarized, in which the variation in phialide characteristics overlaps well with phylogenetic information. A new member of the special twisted neck clade in the Hirsutella-like group, Ophiocordyceps retorta, was reported based on these analyses. The molecular clock calibration analysis based on one fossil record revealed that Hirsutella (asexual morph) species originated from a common ancestor approximately 102 million years ago (Mya) (Early Cretaceous, Lower Albian) and then resolved into two major lineages. One lineage was typically phialidic, which was a larger shape, including H. guyana, H. nodulosa and H. sinensis clades (86.9 Mya, 95% highest posterior density (HPD): 69.1-101.4 Mya). Another main lineage of the phialides was more diversified and smaller than the former, which included H. citriformis and H. thompsonii clades (71.9 Mya, 95% HPD: 41.8-99.6 Mya). CONCLUSIONS Our results showed that certain phialide characteristics of Hirsutella were phylogenetically informative for two groups of taxa. The differentiation of the phialides structures in the major clades demonstrated a clear evolutionary path of Hirsutella (asexual morph) species, which exhibited two trends depending on the host size. Fungi in one of the groups displayed elongated conidiogenous cells with increased complexity of auxiliary structures from the mycelia. The species in another group reduced the volume of phialides and spores, which might be due to an energy-efficient strategy. These results suggested that a common origin allowed for diversification of given clades into separate niches. The distinct parallel evolutionary path combined with the specific phialides structure might result in the host specificity of Hirsutella (asexual morphs). A direct relationship between Hirsutella (asexual morphs) and the Cretaceous-Tertiary extinction was not found, which suggested that the diversity of phialides is more likely to be caused by long-term environmental adaptation and evolution rather than dramatic extinction events. This evolutionary result might correspond to the background of important biological and geological events in the late Cretaceous occurring near the divergence times of Hirsutella (asexual morphs).
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Affiliation(s)
- Jiaojiao Qu
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China.,Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yeming Zhou
- Institute of Entomology, Guizhou University, Guiyang, 550025, China
| | - Jianping Yu
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Jian Zhang
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yanfeng Han
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Xiao Zou
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China.
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38
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Devi G. Utilization of Nematode Destroying Fungi for Management of Plant-Parasitic Nematodes-A Review. ACTA ACUST UNITED AC 2018. [DOI: 10.13005/bbra/2642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nematode destroying fungi are potential biocontrol agent for management of plant-parasitic nematodes. They inhibit nematode population through trapping devices or by means of enzymes and metabolic products. They regulate nematode behavior by interfering plant-nematode recognition, and promote plant growth. For more effective biocontrol, thorough understanding of the biology of nematode destroying fungi, targeted nematode pest and the soil ecology and environmental condition in the field is necessary. This review highlights different types of nematode destroying fungi, their mode of action as well as commercial products based on reports published in this area of research.
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Affiliation(s)
- Gitanjali Devi
- Department of Nematology, Assam Agricultural University, Jorhat-785013, Assam, India
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39
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Zhen Z, Xing X, Xie M, Yang L, Yang X, Zheng Y, Chen Y, Ma N, Li Q, Zhang KQ, Yang J. MAP kinase Slt2 orthologs play similar roles in conidiation, trap formation, and pathogenicity in two nematode-trapping fungi. Fungal Genet Biol 2018; 116:42-50. [PMID: 29702229 DOI: 10.1016/j.fgb.2018.04.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/20/2018] [Accepted: 04/21/2018] [Indexed: 11/29/2022]
Abstract
Mitogen-activated protein (MAP) kinase Slt2 is a key player in the cell-wall integrity pathway of budding yeast. In this study, we functionally characterized Slt2 orthologs AoSlt2 and MhSlt2 from the nematode-trapping fungi Arthrobotrys oligospora and Monacrosporium haptotylum, respectively. We found that disruption of AoSlt2 and MhSlt2 led to reduced mycelial growth, increased sensitivity to environmental stresses such as sodium dodecyl sulfate, Congo red, and H2O2, and an inability to produce conidia and nematode-trapping structures. Real-time polymerase chain reaction-based analyses showed that the transcription of sporulation-related (AbaA, Sep2, and MedA) and cell wall synthesis-related (Chs, Glu, and Gfpa) genes was down-regulated in the mutants compared with the wild-type strains. Moreover, the mutant strains showed reduced extracellular proteolytic activity and decreased transcription of three homologous serine protease-encoding genes. These results show for the first time that MAP kinase Slt2 orthologs play similar roles in regulating mycelial growth, conidiation, trap formation, stress resistance, and pathogenicity in the divergent nematode-trapping fungal species A. oligospora and M. haptotylum.
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Affiliation(s)
- Zhengyi Zhen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Xinjing Xing
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Meihua Xie
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Le Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Xuewei Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Yaqing Zheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Yuanli Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Ni Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Qing Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China.
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Yang X, Ma N, Yang L, Zheng Y, Zhen Z, Li Q, Xie M, Li J, Zhang KQ, Yang J. Two Rab GTPases play different roles in conidiation, trap formation, stress resistance, and virulence in the nematode-trapping fungus Arthrobotrys oligospora. Appl Microbiol Biotechnol 2018; 102:4601-4613. [PMID: 29616315 DOI: 10.1007/s00253-018-8929-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/10/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022]
Abstract
Rab GTPases are the largest group of the small GTPases family, which play a pivotal role in the secretion of proteins. Arthrobotrys oligospora is a representative nematode-trapping fungus that can produce adhesive networks to capture nematodes. In this study, the roles of two Rab GTPases AoRab-7A and AoRab-2 were characterized by gene knockout in the fungus A. oligospora. The disruption of AoRab-7A hindered the mycelial growth in different media, the conidiation of ΔAoRab-7A transformants was almost abolished, and the transcription of four sporulation-related genes (AbaA, FluG, Hyp1, and VosA) was downregulated compared to the wild-type strain (WT). Furthermore, the tolerance of the ΔAoRab-7A mutants to sodium dodecyl sulfate (SDS) and H2O2 was also significantly reduced compared to the WT, and the transcription of several genes related to environmental resistance, such as genes for catalase and trehalose synthase, was downregulated. Similarly, the extracellular proteolytic activity was decreased. Importantly, the ΔAoRab-7A mutants were unable to produce traps and capture nematodes. However, the disruption of gene AoRab-2 only affected the conidiation slightly but non-significantly, while other phenotypic traits were unaffected. Moreover, the gene AoRab-7A was also involved in the autophagy induced by nitrogen deprivation in A. oligospora. Our results revealed for the first time that the Rab GTPases are involved in the regulation of mycelial growth, conidiation, trap formation, stress resistance, and pathogenicity in the nematode-trapping fungus A. oligospora.
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Affiliation(s)
- Xuewei Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ni Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Yaqing Zheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Zhengyi Zhen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Qing Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meihua Xie
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China. .,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China. .,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, People's Republic of China.
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Predator-prey interactions of nematode-trapping fungi and nematodes: both sides of the coin. Appl Microbiol Biotechnol 2018. [PMID: 29523933 DOI: 10.1007/s00253-018-8897-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nematode-trapping fungi develop complex trapping devices to capture and consume nematodes. The dynamics of these organisms is especially important given the pathogenicity of nematodes and, consequently, the potential application of nematode-trapping fungi as biocontrol agents. Furthermore, both the nematodes and nematode-trapping fungi can be easily grown in laboratories, making them a unique manipulatable predator-prey system to study their coevolution. Several different aspects of these fungi have been studied, such as their genetics and the different factors triggering trap formation. In this review, we use the nematode-trapping fungus Arthrobotrys oligospora (which forms adhesive nets) as a model to describe the trapping process. We divide this process into several stages; namely attraction, recognition, trap formation, adhesion, penetration, and digestion. We summarize the latest findings in the field and current knowledge on the interactions between nematodes and nematode-trapping fungi, representing both sides of the predator-prey interaction.
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42
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Expansion of Arthropod Herbivory in Late Triassic South Africa: The Molteno Biota, Aasvoëlberg 411 Site and Developmental Biology of a Gall. TOPICS IN GEOBIOLOGY 2018. [DOI: 10.1007/978-3-319-68009-5_14] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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43
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Corsaro D, Köhsler M, Wylezich C, Venditti D, Walochnik J, Michel R. New insights from molecular phylogenetics of amoebophagous fungi (Zoopagomycota, Zoopagales). Parasitol Res 2017; 117:157-167. [PMID: 29170872 DOI: 10.1007/s00436-017-5685-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 11/15/2017] [Indexed: 12/21/2022]
Abstract
Amoebophagous fungi are represented in all fungal groups: Basidiomycota, Ascomycota, Zygomycota, and Chytridiomycota. The amoebophagous fungi, within the zygomycota (Zoopagales, Zoopagomycota), mainly affect naked amoebae as ectoparasites or endoparasites. It is rather difficult to isolate members of the Zoopagales, because of their parasitic lifestyle, and to bring them into culture. Consequently, gene sequences of this group are undersampled, and its species composition and phylogeny are relatively unknown. In the present study, we were able to isolate amoebophagous fungi together with their amoeba hosts from various habitats (moss, pond, bark, and soil). Altogether, four fungal strains belonging to the genera Acaulopage and Stylopage plus one unidentified isolate were detected. Sequences of the 18S rDNA and the complete ITS region and partial 28S (LSU) rDNA were generated. Subsequent phylogenetic analyses showed that all new isolates diverge at one branch together with two environmental clonal sequences within the Zoopagomycota. Here, we provide the first molecular characterization of the genus Stylopage. Stylopage is closely related to the genus Acaulopage. In addition, taxonomy and phylogeny of amoebophagous fungi and their ecological importance are reviewed based on new sequence data, which includes environmental clonal sequences.
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Affiliation(s)
- Daniele Corsaro
- Chlamydia Research Association (CHLAREAS), 12 rue du Maconnais, F-54500, Vandoeuvre-lès-Nancy, France.
| | - Martina Köhsler
- Molecular Parasitology, Institute for Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Danielle Venditti
- Chlamydia Research Association (CHLAREAS), 12 rue du Maconnais, F-54500, Vandoeuvre-lès-Nancy, France.,TREDI Research Department, Faculty of Medicine, Technopôle de Nancy-Brabois, 9, Avenue de la Forêt de Haye, B.P. 184, 54505, Vandœuvre-lès-Nancy, France
| | - Julia Walochnik
- Molecular Parasitology, Institute for Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Rolf Michel
- Central Institute of the Federal Armed Forces Medical Services, P.O. Box 7340, D 56070, Koblenz, Germany
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44
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Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0595-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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45
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Ashrafi S, Helaly S, Schroers HJ, Stadler M, Richert-Poeggeler KR, Dababat AA, Maier W. Ijuhya vitellina sp. nov., a novel source for chaetoglobosin A, is a destructive parasite of the cereal cyst nematode Heterodera filipjevi. PLoS One 2017; 12:e0180032. [PMID: 28700638 PMCID: PMC5507501 DOI: 10.1371/journal.pone.0180032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/07/2017] [Indexed: 01/17/2023] Open
Abstract
Cyst nematodes are globally important pathogens in agriculture. Their sedentary lifestyle and long-term association with the roots of host plants render cyst nematodes especially good targets for attack by parasitic fungi. In this context fungi were specifically isolated from nematode eggs of the cereal cyst nematode Heterodera filipjevi. Here, Ijuhya vitellina (Ascomycota, Hypocreales, Bionectriaceae), encountered in wheat fields in Turkey, is newly described on the basis of phylogenetic analyses, morphological characters and life-style related inferences. The species destructively parasitises eggs inside cysts of H. filipjevi. The parasitism was reproduced in in vitro studies. Infected eggs were found to harbour microsclerotia produced by I. vitellina that resemble long-term survival structures also known from other ascomycetes. Microsclerotia were also formed by this species in pure cultures obtained from both, solitarily isolated infected eggs obtained from fields and artificially infected eggs. Hyphae penetrating the eggshell colonised the interior of eggs and became transformed into multicellular, chlamydospore-like structures that developed into microsclerotia. When isolated on artificial media, microsclerotia germinated to produce multiple emerging hyphae. The specific nature of morphological structures produced by I. vitellina inside nematode eggs is interpreted as a unique mode of interaction allowing long-term survival of the fungus inside nematode cysts that are known to survive periods of drought or other harsh environmental conditions. Generic classification of the new species is based on molecular phylogenetic inferences using five different gene regions. I. vitellina is the only species of the genus known to parasitise nematodes and produce microsclerotia. Metabolomic analyses revealed that within the Ijuhya species studied here, only I. vitellina produces chaetoglobosin A and its derivate 19-O-acetylchaetoglobosin A. Nematicidal and nematode-inhibiting activities of these compounds have been demonstrated suggesting that the production of these compounds may represent an adaptation to nematode parasitism.
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Affiliation(s)
- Samad Ashrafi
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI)—Federal Research Centre for Cultivated Plants, Braunschweig, Germany
- Department of Ecological Plant Protection, Faculty of Organic Agricultural Sciences, University of Kassel, Witzenhausen, Germany
| | - Soleiman Helaly
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany
- Department of Chemistry, Faculty of Science, Aswan University, Aswan, Egypt
| | | | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany
| | - Katja R. Richert-Poeggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI)—Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Abdelfattah A. Dababat
- CIMMYT (International Maize and Wheat Improvement Centre), P.K.39 06511 Emek, Ankara, Turkey
| | - Wolfgang Maier
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI)—Federal Research Centre for Cultivated Plants, Braunschweig, Germany
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Abstract
Nematode-trapping fungi are a unique and intriguing group of carnivorous microorganisms that can trap and digest nematodes by means of specialized trapping structures. They can develop diverse trapping devices, such as adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and nonconstricting rings. Nematode-trapping fungi have been found in all regions of the world, from the tropics to Antarctica, from terrestrial to aquatic ecosystems. They play an important ecological role in regulating nematode dynamics in soil. Molecular phylogenetic studies have shown that the majority of nematode-trapping fungi belong to a monophyletic group in the order Orbiliales (Ascomycota). Nematode-trapping fungi serve as an excellent model system for understanding fungal evolution and interaction between fungi and nematodes. With the development of molecular techniques and genome sequencing, their evolutionary origins and divergence, and the mechanisms underlying fungus-nematode interactions have been well studied. In recent decades, an increasing concern about the environmental hazards of using chemical nematicides has led to the application of these biological control agents as a rapidly developing component of crop protection.
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47
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Phylogenic analysis of adhesion related genes Mad1 revealed a positive selection for the evolution of trapping devices of nematode-trapping fungi. Sci Rep 2016; 6:22609. [PMID: 26941065 PMCID: PMC4778117 DOI: 10.1038/srep22609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/17/2016] [Indexed: 12/27/2022] Open
Abstract
Adhesions, the major components of the extracellular fibrillar polymers which accumulate on the outer surface of adhesive traps of nematode-trapping fungi, are thought to have played important roles during the evolution of trapping devices. Phylogenetic analyses based on the genes related to adhesive materials can be of great importance for understanding the evolution of trapping devices. Recently, AoMad1, one homologous gene of the entomopathogenic fungus Metarhizium anisopliae cell wall protein MAD1, has been functionally characterized as involved in the production of adhesions in the nematode-trapping fungus Arthrobotrys oligospora. In this study, we cloned Mad1 homologous genes from nematode-trapping fungi with various trapping devices. Phylogenetic analyses suggested that species which formed nonadhesive constricting ring (CR) traps more basally placed and species with adhesive traps evolved along two lineages. Likelihood ratio tests (LRT) revealed that significant positive selective pressure likely acted on the ancestral trapping devices including both adhesive and mechanical traps, indicating that the Mad1 genes likely played important roles during the evolution of nematode-trapping fungi. Our study provides new insights into the evolution of trapping devices of nematode-trapping fungi and also contributes to understanding the importance of adhesions during the evolution of nematode-trapping fungi.
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48
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Zhang W, Cheng X, Liu X, Xiang M. Genome Studies on Nematophagous and Entomogenous Fungi in China. J Fungi (Basel) 2016; 2:jof2010009. [PMID: 29376926 PMCID: PMC5753090 DOI: 10.3390/jof2010009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/24/2016] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous fungi, including nematode-trapping fungi (Arthrobotrys oligospora and Drechslerella stenobrocha), nematode endoparasite (Hirsutella minnesotensis), insect pathogens (Beauveria bassiana and Metarhizium spp.) and Chinese medicinal fungi (Ophiocordyceps sinensis and Cordyceps militaris), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper.
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Affiliation(s)
- Weiwei Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China.
| | - Xiaoli Cheng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China.
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China.
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China.
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Degenkolb T, Vilcinskas A. Metabolites from nematophagous fungi and nematicidal natural products from fungi as an alternative for biological control. Part I: metabolites from nematophagous ascomycetes. Appl Microbiol Biotechnol 2015; 100:3799-812. [PMID: 26715220 PMCID: PMC4824826 DOI: 10.1007/s00253-015-7233-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/29/2015] [Accepted: 12/02/2015] [Indexed: 11/29/2022]
Abstract
Plant-parasitic nematodes are estimated to cause global annual losses of more than US$ 100 billion. The number of registered nematicides has declined substantially over the last 25 years due to concerns about their non-specific mechanisms of action and hence their potential toxicity and likelihood to cause environmental damage. Environmentally beneficial and inexpensive alternatives to chemicals, which do not affect vertebrates, crops, and other non-target organisms, are therefore urgently required. Nematophagous fungi are natural antagonists of nematode parasites, and these offer an ecophysiological source of novel biocontrol strategies. In this first section of a two-part review article, we discuss 83 nematicidal and non-nematicidal primary and secondary metabolites found in nematophagous ascomycetes. Some of these substances exhibit nematicidal activities, namely oligosporon, 4',5'-dihydrooligosporon, talathermophilins A and B, phomalactone, aurovertins D and F, paeciloxazine, a pyridine carboxylic acid derivative, and leucinostatins. Blumenol A acts as a nematode attractant. Other substances, such as arthrosporols and paganins, play a decisive role in the life cycle of the producers, regulating the formation of reproductive or trapping organs. We conclude by considering the potential applications of these beneficial organisms in plant protection strategies.
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Affiliation(s)
- Thomas Degenkolb
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany. .,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchester Strasse 2, 35394, Giessen, Germany.
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Van der Nest MA, Steenkamp ET, McTaggart AR, Trollip C, Godlonton T, Sauerman E, Roodt D, Naidoo K, Coetzee MPA, Wilken PM, Wingfield MJ, Wingfield BD. Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose. BMC Evol Biol 2015; 15:273. [PMID: 26643441 PMCID: PMC4672557 DOI: 10.1186/s12862-015-0550-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/25/2015] [Indexed: 11/25/2022] Open
Abstract
Background Proteins in the Glycoside Hydrolase family 32 (GH32) are carbohydrate-active enzymes known as invertases that hydrolyse the glycosidic bonds of complex saccharides. Fungi rely on these enzymes to gain access to and utilize plant-derived sucrose. In fungi, GH32 invertase genes are found in higher copy numbers in the genomes of pathogens when compared to closely related saprophytes, suggesting an association between invertases and ecological strategy. The aim of this study was to investigate the distribution and evolution of GH32 invertases in the Ceratocystidaceae using a comparative genomics approach. This fungal family provides an interesting model to study the evolution of these genes, because it includes economically important pathogenic species such as Ceratocystis fimbriata, C. manginecans and C. albifundus, as well as saprophytic species such as Huntiella moniliformis, H. omanensis and H. savannae. Results The publicly available Ceratocystidaceae genome sequences, as well as the H. savannae genome sequenced here, allowed for the identification of novel GH32-like sequences. The de novo assembly of the H. savannae draft genome consisted of 28.54 megabases that coded for 7 687 putative genes of which one represented a GH32 family member. The number of GH32 gene family members appeared to be related to the ecological adaptations of these fungi. The pathogenic Ceratocystis species all contained two GH32 family genes (a putative cell wall and a putative vacuolar invertase), while the saprophytic Huntiella species had only one of these genes (a putative cell wall invertase). Further analysis showed that the evolution of the GH32 gene family in the Ceratocystidaceae involved transposable element-based retro-transposition and translocation. As an example, the activity of a Fot5-like element likely facilitated the assembly of the genomic regions harbouring the GH32 family genes in Ceratocystis. Conclusions This study provides insight into the evolutionary history of the GH32 gene family in Ceratocystidaceae. Our findings suggest that transposable elements shaped the evolution of the GH32 gene family, which in turn determines the sucrolytic activities and related ecological strategies of the Ceratocystidaceae species that harbour them. The study also provides insights into the role of carbohydrate-active enzymes in plant-fungal interactions and adds to our understanding of the evolution of these enzymes and their role in the life style of these fungi. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0550-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M A Van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - E T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - A R McTaggart
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - C Trollip
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - T Godlonton
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - E Sauerman
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - D Roodt
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - K Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - M P A Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - P M Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - M J Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - B D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
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