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Ji S, Liu B, Han J, Kong N, Yang Y, Wang Y, Liu Z. Decrypting biocontrol functions and application modes by genomes data of three Trichoderma Strains/Species. Fungal Genet Biol 2024; 172:103889. [PMID: 38513939 DOI: 10.1016/j.fgb.2024.103889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Trichoderma is an excellent biocontrol agent, but most Trichoderma genomes remained at the scaffold level, which greatly limits the research of biocontrol mechanism. Here, we reported the chromosome-level genome of Trichoderma harzianum CGMCC20739 (Tha739), T. asperellum CGMCC11653 (Tas653) and T. atroviride CGMCC40488 (Tat488), they were assembled into 7 chromosomes, genome size were 40 Mb (10,611 genes), 37.3 Mb (10,102 genes) and 36.3 Mb (9,896 genes), respectively. The positive selected genes of three strains were associated to response to stimulus, signaling transduction, immune system and localization. Furthermore, the number of transcription factors in Tha739, Tas653 and Tat488 strains had significant difference, which may contribute to the differential biocontrol function and stress tolerance. The genes related to signal transduction and gene clusters related to antimicrobial compounds in Tha739 were more than those in Tas653 and Tat488, which showed Tha739 may keenly sense other fungi and quickly secret antimicrobial compounds to inhibit other fungi. Tha739 also contained more genes associated to detoxification, antioxidant and nutrition utilization, indicating it had higher stress-tolerance to hostile environments. And the substrate for synthesizing IAA in Tha739 was mainly 3-indole acetonitrile and indole acetaldehyde, but in Tat488, it was indole-3-acetamide, moreover, Tha739 secreted more phosphatase and phytase and was more related to soil phosphorus metabolism, Tat488 secreted more urease and was more related to soil nitrogen metabolism. These candidate genes related to biocontrol function and stress-tolerance laid foundations for construction of functional strains. All above proved the difference in biocontrol function of Tha739, Tas653 and Tat488 strains, however, the defects in individual strains could be compensated for through Trichoderma-biome during the commercial application process of biocontrol Trichoderma strains.
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Affiliation(s)
- Shida Ji
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China; College of Horticulture, ShenYang Agricultural University, Shenyang 110866, China
| | - Bin Liu
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Jing Han
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Ning Kong
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Yongfeng Yang
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Yucheng Wang
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China; School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Zhihua Liu
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China; School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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John E, Chau MQ, Hoang CV, Chandrasekharan N, Bhaskar C, Ma LS. Fungal Cell Wall-Associated Effectors: Sensing, Integration, Suppression, and Protection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:196-210. [PMID: 37955547 DOI: 10.1094/mpmi-09-23-0142-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The cell wall (CW) of plant-interacting fungi, as the direct interface with host plants, plays a crucial role in fungal development. A number of secreted proteins are directly associated with the fungal CW, either through covalent or non-covalent interactions, and serve a range of important functions. In the context of plant-fungal interactions many are important for fungal development in the host environment and may therefore be considered fungal CW-associated effectors (CWAEs). Key CWAE functions include integrating chemical/physical signals to direct hyphal growth, interfering with plant immunity, and providing protection against plant defenses. In recent years, a diverse range of mechanisms have been reported that underpin their roles, with some CWAEs harboring conserved motifs or functional domains, while others are reported to have novel features. As such, the current understanding regarding fungal CWAEs is systematically presented here from the perspective of their biological functions in plant-fungal interactions. An overview of the fungal CW architecture and the mechanisms by which proteins are secreted, modified, and incorporated into the CW is first presented to provide context for their biological roles. Some CWAE functions are reported across a broad range of pathosystems or symbiotic/mutualistic associations. Prominent are the chitin interacting-effectors that facilitate fungal CW modification, protection, or suppression of host immune responses. However, several alternative functions are now reported and are presented and discussed. CWAEs can play diverse roles, some possibly unique to fungal lineages and others conserved across a broad range of plant-interacting fungi. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Evan John
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Minh-Quang Chau
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Cuong V Hoang
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo UPM, 28223 Pozuelo de Alarcón, Spain
| | | | - Chibbhi Bhaskar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Lay-Sun Ma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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Khan RAA, Najeeb S, Chen J, Wang R, Zhang J, Hou J, Liu T. Insights into the molecular mechanism of Trichoderma stimulating plant growth and immunity against phytopathogens. PHYSIOLOGIA PLANTARUM 2023; 175:e14133. [PMID: 38148197 DOI: 10.1111/ppl.14133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023]
Abstract
Trichoderma species have received significant interest as beneficial fungi for boosting plant growth and immunity against phytopathogens. By establishing a mutualistic relationship with plants, Trichoderma causes a series of intricate signaling events that eventually promote plant growth and improve disease resistance. The mechanisms contain the indirect or direct involvement of Trichoderma in enhancing plant growth by modulating phytohormones signaling pathways, improving uptake and accumulation of nutrients, and increasing soil bioavailability of nutrients. They contribute to plant resistance by stimulating systemic acquired resistance through salicylic acid, jasmonic acid, and ethylene signaling. A cascade of signal transduction processes initiated by the interaction of Trichoderma and plants regulate the expression of defense-related genes, resulting in the synthesis of defense hormones and pathogenesis-related proteins (PRPs), which collectively improve plant resistance. Additionally, advancements in omics technologies has led to the identification of key pathways, their regulating genes, and molecular interactions in the plant defense and growth promotion responses induced by Trichoderma. Deciphering the molecular mechanism behind Trichoderma's induction of plant defense and immunity is essential for harnessing the full plant beneficial potential of Trichoderma. This review article sheds light on the molecular mechanisms that underlie the positive effects of Trichoderma-induced plant immunity and growth and opens new opportunities for developing environmentally friendly and innovative approaches to improve plant immunity and growth.
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Affiliation(s)
- Raja Asad Ali Khan
- Sanya Nanfan Research Institute, Hainan University, Sanya, PR China
- School of Tropical Agriculture and Forestry, Engineering Center of Agricultural Microbial Preparation Research and Development of Hainan, Hainan University, Haikou, PR China
| | - Saba Najeeb
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR, China
| | - Rui Wang
- Sanya Nanfan Research Institute, Hainan University, Sanya, PR China
- School of Tropical Agriculture and Forestry, Engineering Center of Agricultural Microbial Preparation Research and Development of Hainan, Hainan University, Haikou, PR China
| | - Jing Zhang
- Sanya Nanfan Research Institute, Hainan University, Sanya, PR China
- School of Tropical Agriculture and Forestry, Engineering Center of Agricultural Microbial Preparation Research and Development of Hainan, Hainan University, Haikou, PR China
| | - Jumei Hou
- Sanya Nanfan Research Institute, Hainan University, Sanya, PR China
- School of Tropical Agriculture and Forestry, Engineering Center of Agricultural Microbial Preparation Research and Development of Hainan, Hainan University, Haikou, PR China
| | - Tong Liu
- Sanya Nanfan Research Institute, Hainan University, Sanya, PR China
- School of Tropical Agriculture and Forestry, Engineering Center of Agricultural Microbial Preparation Research and Development of Hainan, Hainan University, Haikou, PR China
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Liu H, Wang S, Lang B, Li Y, Wang X, Chen J. Fused expression of Sm1-Chit42 proteins for synergistic mycoparasitic response of Trichoderma afroharzianum on Botrytis cinerea. Microb Cell Fact 2023; 22:156. [PMID: 37592265 PMCID: PMC10433591 DOI: 10.1186/s12934-023-02151-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
Sm1 and Chit42 of Trichoderma have been universally confirmed as crucial biocontrol factors against pathogen infection through induced resistance and mycoparasitism, respectively. However, not enough work has been conducted to understand the novel function of fused expression of these two proteins in Trichoderma. The results of this study demonstrated that Sm1-Chit42 protein (SCf) engineered T. afroharzianum strain OE:SCf exerted synergistic inhibition to Botrytis cinerea growth at multiple stages of mycoparasitic interaction of T. afroharzianum and B. cinerea including chemotropism sensing, hyphal coiling, hydrophobicity modulation, cell wall adhesion, virulence reduction and pathogen killing by ROS. These results highlight a novel mycoparasitic system in Trichoderma strains engineered with Sm1-Chit42 chimeric protein to combat B. cinerea growth and reproduction, which would lay a strong foundation for exploring a new engineered Trichoderma biofungicide created with chimeric proteins in the future.
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Affiliation(s)
- Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoqing Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Lang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yaqian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhua Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.
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Silva AC, Oshiquiri LH, de Morais Costa de Jesus LF, Maués DB, Silva RDN. The Cerato-Platanin EPL2 from Trichoderma reesei Is Not Directly Involved in Cellulase Formation but in Cell Wall Remodeling. Microorganisms 2023; 11:1965. [PMID: 37630525 PMCID: PMC10459490 DOI: 10.3390/microorganisms11081965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Trichoderma reesei is a saprophytic fungus that produces large amounts of cellulases and is widely used for biotechnological applications. Cerato-platanins (CPs) are a family of proteins universally distributed among Dikarya fungi and have been implicated in various functions related to fungal physiology and interaction with the environment. In T. reesei, three CPs are encoded in the genome: Trire2_111449, Trire2_123955, and Trire2_82662. However, their function is not fully elucidated. In this study, we deleted the Trire2_123955 gene (named here as epl2) in the wild-type QM6aΔtmus53Δpyr4 (WT) strain and examined the behavior of the Δepl2 strain compared with WT grown for 72 h in 1% cellulose using RNA sequencing. Of the 9143 genes in the T. reesei genome, 760 were differentially expressed, including 260 only in WT, 214 only in Δepl2, and 286 in both. Genes involved in oxidative stress, oxidoreductase activity, antioxidant activity, and transport were upregulated in the Δepl2 mutant. Genes encoding cell wall synthesis were upregulated in the mutant strain during the late growth stage. The Δepl2 mutant accumulated chitin and glucan at higher levels than the parental strain and was more resistant to cell wall stressors. These results suggest a compensatory effect in cell wall remodeling due to the absence of EPL2 in T. reesei. This study is expected to contribute to a better understanding of the role of the EPL2 protein in T. reesei and improve its application in biotechnological fields.
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Affiliation(s)
| | | | | | | | - Roberto do Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (A.C.S.); (L.H.O.); (L.F.d.M.C.d.J.); (D.B.M.)
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Dutta P, Mahanta M, Singh SB, Thakuria D, Deb L, Kumari A, Upamanya GK, Boruah S, Dey U, Mishra AK, Vanlaltani L, VijayReddy D, Heisnam P, Pandey AK. Molecular interaction between plants and Trichoderma species against soil-borne plant pathogens. FRONTIERS IN PLANT SCIENCE 2023; 14:1145715. [PMID: 37255560 PMCID: PMC10225716 DOI: 10.3389/fpls.2023.1145715] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/05/2023] [Indexed: 06/01/2023]
Abstract
Trichoderma spp. (Hypocreales) are used worldwide as a lucrative biocontrol agent. The interactions of Trichoderma spp. with host plants and pathogens at a molecular level are important in understanding the various mechanisms adopted by the fungus to attain a close relationship with their plant host through superior antifungal/antimicrobial activity. When working in synchrony, mycoparasitism, antibiosis, competition, and the induction of a systemic acquired resistance (SAR)-like response are considered key factors in deciding the biocontrol potential of Trichoderma. Sucrose-rich root exudates of the host plant attract Trichoderma. The soluble secretome of Trichoderma plays a significant role in attachment to and penetration and colonization of plant roots, as well as modulating the mycoparasitic and antibiosis activity of Trichoderma. This review aims to gather information on how Trichoderma interacts with host plants and its role as a biocontrol agent of soil-borne phytopathogens, and to give a comprehensive account of the diverse molecular aspects of this interaction.
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Affiliation(s)
- Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Madhusmita Mahanta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | | | - Dwipendra Thakuria
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Imphal, India
| | - Lipa Deb
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Arti Kumari
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Gunadhya K. Upamanya
- Sarat Chandra Singha (SCS) College of Agriculture, Assam Agricultural University (Jorhat), Dhubri, Assam, India
| | - Sarodee Boruah
- Krishi Vigyan Kendra (KVK)-Tinsukia, Assam Agricultural University (Jorhat), Tinsukia, Assam, India
| | - Utpal Dey
- Krishi Vigyan Kendra (KVK)-Sepahijala, Central Agricultural University (Imphal), Tripura, Sepahijala, India
| | - A. K. Mishra
- Department of Plant Pathology, Dr Rajendra Prasad Central Agricultural University, Bihar, Samastipur, India
| | - Lydia Vanlaltani
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Dumpapenchala VijayReddy
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Punabati Heisnam
- Department of Agronomy, Central Agricultural University (Imphal), Pasighat, India
| | - Abhay K. Pandey
- Department of Mycology and Microbiology, Tea Research Association, North Bengal Regional, R & D Center, Jalpaiguri, West Bengal, India
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Xiao Z, Zhao Q, Li W, Gao L, Liu G. Strain improvement of Trichoderma harzianum for enhanced biocontrol capacity: Strategies and prospects. Front Microbiol 2023; 14:1146210. [PMID: 37125207 PMCID: PMC10134904 DOI: 10.3389/fmicb.2023.1146210] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
In the control of plant diseases, biocontrol has the advantages of being efficient and safe for human health and the environment. The filamentous fungus Trichoderma harzianum and its closely related species can inhibit the growth of many phytopathogenic fungi, and have been developed as commercial biocontrol agents for decades. In this review, we summarize studies on T. harzianum species complex from the perspective of strain improvement. To elevate the biocontrol ability, the production of extracellular proteins and compounds with antimicrobial or plant immunity-eliciting activities need to be enhanced. In addition, resistance to various environmental stressors should be strengthened. Engineering the gene regulatory system has the potential to modulate a variety of biological processes related to biocontrol. With the rapidly developing technologies for fungal genetic engineering, T. harzianum strains with increased biocontrol activities are expected to be constructed to promote the sustainable development of agriculture.
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Affiliation(s)
- Ziyang Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qinqin Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Li
- Shanghai Tobacco Group Beijing Cigarette Factory Co., Ltd., Beijing, China
| | - Liwei Gao
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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The Hydrophobin Gene Family Confers a Fitness Trade-off between Spore Dispersal and Host Colonization in Penicillium expansum. mBio 2022; 13:e0275422. [PMID: 36374077 PMCID: PMC9765440 DOI: 10.1128/mbio.02754-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Hydrophobins are small amphipathic surface proteins found exclusively in fungi. In filamentous ascomycetes, one conserved role of a subset of hydrophobins is their requirement for spore dispersal. Other contributions of these proteins to fungal biology are less clear and vary across genera. To determine the functions of hydrophobins in the biology and virulence of this fungus, we created seven single mutants and a septuple-deletion mutant (Δsep) of the entire putative P. expansum hydrophobin gene family. One spore hydrophobin, HfbA, shared 72.56% sequence identity to the Aspergillus fumigatus spore hydrophobin RodA and was required for efficient spore dispersion in P. expansum. The Δsep mutant was likewise reduced in spore dispersal, hypothesized to be due to the aberrant shape and clumping of the Δsep conidia and conidiophores. Additionally, the Δsep mutant presented several differences in physiological traits, including decreased survival in extreme cold temperatures and increased production of several toxic secondary metabolites. Most striking was the unexpected fitness advantage that the Δsep strain displayed in competitive passaging with the wild-type strain on host apple where the mutant significantly increased in percentage of the colonizing population. This work uncovers potential ecological trade-offs of hydrophobin presence in filamentous fungi. IMPORTANCE Hydrophobins are amphipathic secreted proteins uniquely found in filamentous fungi. These proteins self-assemble and constitute the outer most layer of fungal surfaces thus mediating multiple aspects of fungal interactions with their environments. Hydrophobins facilitate spore dispersal, yet a full understanding of the function and need for multiple hydrophobins in fungal species remains elusive. To address the role of this protein family in Penicillium expansum, the causative agent of blue mold disease in pome fruit, all seven putative hydrophobin genes were deleted and the mutant assessed for numerous physiological traits and virulence on fruit. Despite showing a decrease in spore dispersal, the septuple-deletion mutant was more fit than the wild type in competitive pathogenicity tests on apple. Our findings suggest this gene family illustrates a functional trade-off between dispersal and host colonization in P. expansum.
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Pang G, Sun T, Ding M, Li J, Zhao Z, Shen Q, Cai FM. Characterization of an Exceptional Fungal Mutant Enables the Discovery of the Specific Regulator of a Silent PKS-NRPS Hybrid Biosynthetic Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11769-11781. [PMID: 36084284 DOI: 10.1021/acs.jafc.2c03550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Filamentous fungi produce a great variety of bioactive secondary metabolites essential for their biotic interactions. Here, we characterized an exceptional Trichoderma mutant overproducing harzianic acids (HAs) with exclusively highly antifungal activity against numerous fungi from different ecological groups. Interestingly, two transcription factors (TFs) were identified in this HA biosynthetic gene cluster (hac BGC), with HacI regulating the biosynthetic genes and HacF being likely responsible for the product transportation essential for the self-detoxification of the fungus from the produced HAs. Evolutionary analysis suggested that the sparse distribution of hac BGC in many environmental opportunistic fungi including several species from Trichoderma, Penicillium, and Aspergillus could result from lateral gene transfers and pervasive gene losses in different lineages of Pezizomycotina. Taken together, we propose that the production of HAs by fungi is to inhibit the growth of the surrounding partners to secure an exclusive position in a competitive community.
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Affiliation(s)
- Guan Pang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Sun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyue Ding
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Zheng Zhao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng M Cai
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
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Schalamun M, Schmoll M. Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1002161. [PMID: 37746224 PMCID: PMC10512326 DOI: 10.3389/ffunb.2022.1002161] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/25/2022] [Indexed: 09/26/2023]
Abstract
The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.
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Affiliation(s)
- Miriam Schalamun
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Monika Schmoll
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
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11
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Lopes da Silva F, Aquino EN, Costa da Cunha D, Vieira Hamann PR, Magalhães TB, Steindorff AS, Ulhoa CJ, Noronha EF. Analysis of Trichoderma harzianum TR 274 secretome to assign candidate proteins involved in symbiotic interactions with Phaseolus vulgaris. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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13
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Dautt-Castro M, Jijón-Moreno S, Gómez-Hernández N, del Carmen González-López M, Hernández-Hernández EJ, Rosendo-Vargas MM, Rebolledo-Prudencio OG, Casas-Flores S. New Insights on the Duality of Trichoderma as a Phytopathogen Killer and a Plant Protector Based on an Integrated Multi-omics Perspective. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cai F, Dou K, Wang P, Chenthamara K, Chen J, Druzhinina IS. The Current State of Trichoderma Taxonomy and Species Identification. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Landeta-Salgado C, Cicatiello P, Stanzione I, Medina D, Berlanga Mora I, Gomez C, Lienqueo ME. The growth of marine fungi on seaweed polysaccharides produces cerato-platanin and hydrophobin self-assembling proteins. Microbiol Res 2021; 251:126835. [PMID: 34399103 DOI: 10.1016/j.micres.2021.126835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/08/2021] [Accepted: 07/28/2021] [Indexed: 01/15/2023]
Abstract
The marine fungi Paradendryphiela salina and Talaromyces pinophilus degrade and assimilate complex substrates from plants and seaweed. Additionally, these fungi secrete surface-active proteins, identified as cerato-platanins and hydrophobins. These hydrophobic proteins have the ability to self-assemble forming amyloid-like aggregates and play an essential role in the growth and development of the filamentous fungi. It is the first time that one cerato-platanin (CP) is identified and isolated from P. salina (PsCP) and two Class I hydrophobins (HFBs) from T. pinophilus (TpHYD1 and TpHYD2). Furthermore, it is possible to extract cerato-platanins and hydrophobins using marine fungi that can feed on seaweed biomass, and through a submerged liquid fermentation process. The propensity to aggregate of these proteins has been analyzed using different techniques such as Thioflavin T fluorescence assay, Fourier-transform Infrared Spectroscopy, and Atomic Force Microscopy. Here, we show that the formation of aggregates of PsCP and TpHYD, was influenced by the carbon source from seaweed. This study highlighted the potential of these self-assembling proteins generated from a fermentation process with marine fungi and with promising properties such as conformational plasticity with extensive applications in biotechnology, pharmacy, nanotechnology, and biomedicine.
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Affiliation(s)
- Catalina Landeta-Salgado
- Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef 851, 8370456, Chile; Center for Biotechnology and Bioengineering (CeBiB), Santiago, Beauchef 851, 8370456, Chile
| | - Paola Cicatiello
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 4, I-80126 Naples, Italy
| | - Ilaria Stanzione
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 4, I-80126 Naples, Italy
| | - David Medina
- Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef 851, 8370456, Chile; Center for Biotechnology and Bioengineering (CeBiB), Santiago, Beauchef 851, 8370456, Chile
| | - Isadora Berlanga Mora
- Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef 851, 8370456, Chile
| | - Carlos Gomez
- Chemistry Department, University of Valle-Yumbo, Valle del Cauca, 760501, Colombia
| | - María Elena Lienqueo
- Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef 851, 8370456, Chile; Center for Biotechnology and Bioengineering (CeBiB), Santiago, Beauchef 851, 8370456, Chile.
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16
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Zhao Z, Cai F, Gao R, Ding M, Jiang S, Chen P, Pang G, Chenthamara K, Shen Q, Bayram Akcapinar G, Druzhinina IS. At least three families of hyphosphere small secreted cysteine-rich proteins can optimize surface properties to a moderately hydrophilic state suitable for fungal attachment. Environ Microbiol 2021; 23:5750-5768. [PMID: 33538393 PMCID: PMC8596622 DOI: 10.1111/1462-2920.15413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/11/2022]
Abstract
The secretomes of filamentous fungi contain a diversity of small secreted cysteine‐rich proteins (SSCPs) that have a variety of properties ranging from toxicity to surface activity. Some SSCPs are recognized by other organisms as indicators of fungal presence, but their function in fungi is not fully understood. We detected a new family of fungal surface‐active SSCPs (saSSCPs), here named hyphosphere proteins (HFSs). An evolutionary analysis of the HFSs in Pezizomycotina revealed a unique pattern of eight single cysteine residues (C‐CXXXC‐C‐C‐C‐C‐C) and a long evolutionary history of multiple gene duplications and ancient interfungal lateral gene transfers, suggesting their functional significance for fungi with different lifestyles. Interestingly, recombinantly produced saSSCPs from three families (HFSs, hydrophobins and cerato‐platanins) showed convergent surface‐modulating activity on glass and on poly(ethylene‐terephthalate), transforming their surfaces to a moderately hydrophilic state, which significantly favoured subsequent hyphal attachment. The addition of purified saSSCPs to the tomato rhizosphere had mixed effects on hyphal attachment to roots, while all tested saSSCPs had an adverse effect on plant growth in vitro. We propose that the exceptionally high diversity of saSSCPs in Trichoderma and other fungi evolved to efficiently condition various surfaces in the hyphosphere to a fungal‐beneficial state.
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Affiliation(s)
- Zheng Zhao
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Feng Cai
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China.,Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Renwei Gao
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Mingyue Ding
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Siqi Jiang
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Peijie Chen
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Guan Pang
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Komal Chenthamara
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Qirong Shen
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Günseli Bayram Akcapinar
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irina S Druzhinina
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China.,Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
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17
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Abstract
The production of biofuels from plant biomass is dependent on the availability of enzymes that can hydrolyze the plant cell wall polysaccharides to their monosaccharides. These enzyme mixtures are formed by microorganisms but their native compositions and properties are often not ideal for application. Genetic engineering of these microorganisms is therefore necessary, in which introduction of DNA is an essential precondition. The filamentous fungus Trichoderma reesei-the main producer of plant-cell-wall-degrading enzymes for biofuels and other industries-has been subjected to intensive genetic engineering toward this goal and has become one of the iconic examples of the successful genetic improvement of fungi. However, the genetic manipulation of other enzyme-producing Trichoderma species is frequently less efficient and, therefore, rarely managed. In this chapter, we therefore describe the two potent methods of Trichoderma transformation mediated by either (a) polyethylene glycol (PEG) or (b) Agrobacterium. The methods are optimized for T. reesei but can also be applied for such transformation-resilient species as T. harzianum and T. guizhouense, which are putative upcoming alternatives for T. reesei in this field. The protocols are simple, do not require extensive training or special equipment, and can be further adjusted for T. reesei mutants with particular properties.
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Affiliation(s)
- Feng Cai
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.,FungiG, Fungal Genomics Laboratory, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Christian P Kubicek
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Irina S Druzhinina
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria. .,FungiG, Fungal Genomics Laboratory, Nanjing Agricultural University, Nanjing, People's Republic of China.
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