1
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Lei H, Zhang G, Zhao P, Li G. Secondary Metabolites from the Nematode-Trapping Fungus Dactylellina haptotyla YMF1.03409. Microorganisms 2023; 11:2693. [PMID: 38004706 PMCID: PMC10672892 DOI: 10.3390/microorganisms11112693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
As a representative nematode-trapping fungus, Dactylellina haptotyla can capture and kill nematodes by producing traps, known as adhesive knobs. In this paper, the strain of D. haptotyla YMF1.03409 was studied by means of medium screening, fermentation, and purification and identification of crude extracts. Eighteen compounds were obtained from D. haptotyla YMF1.03409, including two new metabolites, nosporins C (1) and D (2). The known metabolites were identified to be 3-chloro-4-methoxybenzaldehyde (3), 3-chloro-4-methoxybenzoic acid (4), 2-chloro-1-methoxy-4-(methoxymethyl)benzene (5), 3-hydroxy-3-methyloxindole (6), nicotinic acid (7), succinic acid (8), 3,4-dihydroxybutanoic acid (9), 5'-O-methyladenosine (10), uridine (11), 2'-deoxyuridine (12), thymidine (13), 3-(phenylmethyl)-2,5-morpholinedione (14), methyl-β-D-glucopyranoside (15), 1,2-benzenedicarboxylic acid bis(2-methyl heptyl) ester (16), β-sitosterol (17), and 3β,6α-diol-stigmastane (18). The bioactive assay showed that these compounds had no obvious nematicidal activity against the nematodes Meloidogyne incognita and Panagrellus redivivus.
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Affiliation(s)
| | | | | | - Guohong Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
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2
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Zhao X, Fan Y, Zhang L, Zhang W, Xiang M, Kang S, Wang S, Liu X. Multiple Roles of the Low-Affinity Calcium Uptake System in Drechslerella dactyloides, a Nematode-Trapping Fungus That Forms Constricting Rings. J Fungi (Basel) 2023; 9:975. [PMID: 37888231 PMCID: PMC10607529 DOI: 10.3390/jof9100975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
(1) Background: the low-affinity calcium uptake system (LACS) has been shown to play a crucial role in the conidiation and formation of adhesive nets and knobs by nematode-trapping fungi (NTF), but its involvement in the formation of constricting rings (CRs), mechanical traps to capture free-living nematodes, remains unexplored. (2) Methods: we investigated the function of two LACS genes (DdaFIG_1 and DdaFIG_2) in Drechslerella dactyloides, an NTF that forms CRs. We generated single (DdaFIG_1Ri and DdaFIG_2Ri) and double (DdaFIG_1,2Ri) knockdown mutants via the use of RNA interference (RNAi). (3) Results: suppression of these genes significantly affected conidiation, trap formation, vegetative growth, and response to diverse abiotic stresses. The number of CRs formed by DdaFIG_1Ri, DdaFIG_2Ri, and DdaFIG_1,2Ri decreased to 58.5%, 59.1%, and 38.9% of the wild-type (WT) level, respectively. The ring cell inflation rate also decreased to 73.6%, 60.6%, and 48.8% of the WT level, respectively. (4) Conclusions: the LACS plays multiple critical roles in diverse NTF.
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Affiliation(s)
- Xiaozhou Zhao
- 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 300071, China
| | - Yani Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liao Zhang
- 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 300071, China
| | - Weiwei Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Seogchan Kang
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - 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 300071, 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 300071, China
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3
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Lei HM, Wang JT, Hu QY, Li CQ, Mo MH, Zhang KQ, Li GH, Zhao PJ. 2-Furoic acid associated with the infection of nematodes by Dactylellina haptotyla and its biocontrol potential on plant root-knot nematodes. Microbiol Spectr 2023; 11:e0189623. [PMID: 37754836 PMCID: PMC10580851 DOI: 10.1128/spectrum.01896-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/05/2023] [Indexed: 09/28/2023] Open
Abstract
Dactylellina haptotyla is a typical nematode-trapping fungus that has garnered the attention of many scholars for its highly effective lethal potential for nematodes. Secondary metabolites play an important role in D. haptotyla-nematode interactions, but which metabolites perform which function remains unclear. We report the metabolic functions based on high-quality, chromosome-level genome assembly of wild D. haptotyla YMF1.03409. The results indicate that a large variety of secondary metabolites and their biosynthetic genes were significantly upregulated during the nematode-trapping stage. In parallel, we identified that 2-furoic acid was specifically produced during nematode trapping by D. haptotyla YMF1.03409 and isolated it from fermentation production. 2-Furoic acid demonstrated strong nematicidal activity with an LD50 value of 55.05 µg/mL against Meloidogyne incognita at 48 h. Furthermore, the pot experiment showed that the number of galls of tomato root was significantly reduced in the experimental group treated with 2-furoic acid. The considerable increase in the 2-furoic acid content during the infection process and its virulent nematicidal activity revealed an essential synergistic effect during the process of nematode-trapping fungal infection. IMPORTANCE Dactylellina haptotyla have significant application potential in nematode biocontrol. In this study, we determined the chromosome-level genome sequence of D. haptotyla YMF1.03409 by long-read sequencing technology. Comparative genomic analysis identified a series of pathogenesis-related genes and revealed significant gene family contraction events during the evolution of D. haptotyla YMF1.03409. Combining transcriptomic and metabolomic data as well as in vitro activity test results, a compound with important application potential in nematode biocontrol, 2-furoic acid, was identified. Our result expanded the genetic resource of D. haptotyla and identified a previously unreported nematicidal small molecule, which provides new options for the development of plant biocontrol agents.
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Affiliation(s)
- Hong-Mei Lei
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Jun-Tao Wang
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Qian-Yi Hu
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Chun-Qiang Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Ming-He Mo
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Ke-Qin Zhang
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Guo-Hong Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Pei-Ji Zhao
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
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4
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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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5
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Deletion of a Putative GPI-Anchored Protein-Encoding Gene Aog185 Impedes the Growth and Nematode-Trapping Efficiency of Arthrobotrys oligospora by Disrupting Transmembrane Transport Homeostasis. Cell Microbiol 2022. [DOI: 10.1155/2022/8738290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nematode-trapping fungus (NTF) is a crucial predator of nematodes, which can capture nematodes by developing specific trapping devices. However, there is limited understanding of the role and mechanism of cell surface proteins attached to the surface of mycelia or trapping cells. Here, the effects of a putative GPI-anchored protein-encoding gene Aog185 on the growth and nematode-trapping efficiency of A. oligospora were investigated. Compared to the wild-type (WT) strain, the ΔAog185 mutant grew more slowly, exhibited a 20% decrease in conidiation, delayed conidial germination, generated fewer traps, attenuated nematode trapping efficiency, and was more sensitive to chemical stressors. Transcriptomic analysis indicated that a large number of transmembrane transport-related genes were differentially expressed between the WT and ΔAog185 mutant strains. Aog185 deletion could damage the intrinsic components of the membrane and cytoskeleton. Specifically, knockout of Aog185 disrupted transmembrane transport homeostasis during the phagocytosis, cell autophagy, and oxidative phosphorylation processes, which were associated with the fusion of cells and organelle membranes, transport of ions and substrates, and energy metabolism. Hence, the putative GPI-anchored protein-encoding gene Aog185 may contribute to the lifestyle switch of NTF and nematode capture, and the effect of Aog185 gene on cell transmembrane transport is considered key to this process. Our findings provide new insights into the mechanism of Aog185 gene during the process of nematode trapping by NTF.
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6
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Gong S, Meng Q, Qiao J, Huang Y, Zhong W, Zhang G, Zhang K, Li N, Shang Y, Li Z, Cai X. Biological Characteristics of Recombinant Arthrobotrys oligospora Chitinase AO-801. THE KOREAN JOURNAL OF PARASITOLOGY 2022; 60:345-352. [PMID: 36320111 PMCID: PMC9633153 DOI: 10.3347/kjp.2022.60.5.345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2023]
Abstract
Chitinase AO-801 is a hydrolase secreted by Arthrobotrys oligospora during nematode feeding, while its role remained elusive. This study analyzed the molecular characteristics of recombinant chitinase of Arthrobotrys oligospora (reAO-801). AO-801 belongs to the typical glycoside hydrolase 18 family with conserved chitinase sequence and tertiary structure of (α/β)8 triose-phosphate isomerase (TIM) barrel. The molecular weight of reAO-801 was 42 kDa. reAO-801 effectively degraded colloidal and powdered chitin, egg lysate, and stage I larval lysate of Caenorhabditis elegans. The activity of reAO-801 reached its peak at 40˚C and pH values between 4-7. Enzyme activity was inhibited by Zn2+, Ca2+, and Fe3+, whereas Mg2+ and K+ potentiated its activity. In addition, urea, sodium dodecyl sulfate, and 2-mercaptoethanol significantly inhibited enzyme activity. reAO-801 showed complete nematicidal activity against C. elegans stage I larvae. reAO-801 broke down the C. elegans egg shells, causing them to die or die prematurely by hatching the eggs. It also invoked degradation of Haemonchus contortus eggs, resulting in apparent changes in the morphological structure. This study demonstrated the cytotoxic effect of reAO-801, which laid the foundation for further dissecting the mechanism of nematode infestation by A. oligospora.
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Affiliation(s)
- Shasha Gong
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Qingling Meng
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Jun Qiao
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Yunfu Huang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Wenqiang Zhong
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Guowu Zhang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Kai Zhang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Ningxing Li
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Yunxia Shang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Zhiyuan Li
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang 832003,
China
| | - Xuepeng Cai
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046,
China
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7
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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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8
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Ji J, Zhou L, Xu Z, Ma L, Lu Z. Two atypical gram-negative bacteria-binding proteins are involved in the antibacterial response in the pea aphid (Acyrthosiphon pisum). INSECT MOLECULAR BIOLOGY 2021; 30:427-435. [PMID: 33928689 DOI: 10.1111/imb.12708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/26/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
The activation of immune pathways is triggered by the recognition of pathogens by pattern recognition receptors (PRRs). Gram-negative bacteria-binding proteins (GNBPs)/β-1,3-glucan recognition proteins (βGRPs) are a conserved family of PRRs in insects. Two GNBPs are predicted in the genome database of pea aphids; however, little is known about their functions in the aphid immune system. Here, we show that pea aphid GNBPs possess domain architectures and sequence features distinct from those of typical GNBPs/βGRPs and that their expression is induced by bacterial infection. Knockdown of their expression by dsRNA resulted in lower phenoloxidase activity, higher bacterial loads and higher mortality in aphids after infection. Our data suggest that these two atypical GNBPs are involved in the antibacterial response in the pea aphid, likely acting as PRRs in the prophenoloxidase pathway.
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Affiliation(s)
- J Ji
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - L Zhou
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Z Xu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - L Ma
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Z Lu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
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9
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Freitas DF, da Rocha IM, Vieira-da-Motta O, de Paula Santos C. The Role of Melanin in the Biology and Ecology of Nematophagous Fungi. J Chem Ecol 2021; 47:597-613. [PMID: 34232439 DOI: 10.1007/s10886-021-01282-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/03/2021] [Accepted: 05/13/2021] [Indexed: 11/24/2022]
Abstract
Melanin is a heteropolymer formed by the polymerization of phenolic and indolic compounds. It occurs in organisms across all biological kingdoms and has a range different of functions, thus indicating its important evolutionary role. The presence of melanin offers several protective advantages, including against ultraviolet radiation, traumatic damage, oxidative stress, extreme temperatures, and pressure. For many species of fungi, melanin also participates directly in the process of virulence and pathogenicity. These organisms can synthesize melanin in two main ways: using a substrate of endogenous origin, involving 1,8-dihydroxynaphthalene (DHN); alternatively, in an exogenous manner with the addition of L-3, 4-dihydroxyphenylalanine (L-DOPA or levodopa). As melanin is an amorphous and complex substance, its study requires expensive and inaccessible technologies and analyses are often difficult to perform with conventional biochemical techniques. As such, details about its chemical structure are not yet fully understood, particularly for nematophagous fungi that remain poorly studied. Thus, this review presents an overview of the different types of melanin, with an emphasis on fungi, and discusses the role of melanin in the biology and ecology of nematophagous fungi.
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Affiliation(s)
- Deivid França Freitas
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Izabelli Martins da Rocha
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Olney Vieira-da-Motta
- Animal Health Laboratory - Infectious Contagious Diseases Sector, State University of North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Clóvis de Paula Santos
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil.
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10
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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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11
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Valette N, Renou J, Boutilliat A, Fernández-González AJ, Gautier V, Silar P, Guyeux C, Charr JC, Cuenot S, Rose C, Gelhaye E, Morel-Rouhier M. OSIP1 is a self-assembling DUF3129 protein required to protect fungal cells from toxins and stressors. Environ Microbiol 2021; 23:1594-1607. [PMID: 33393164 DOI: 10.1111/1462-2920.15381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022]
Abstract
Secreted proteins are key players in fungal physiology and cell protection against external stressing agents and antifungals. Oak stress-induced protein 1 (OSIP1) is a fungal-specific protein with unknown function. By using Podospora anserina and Phanerochaete chrysosporium as models, we combined both in vivo functional approaches and biophysical characterization of OSIP1 recombinant protein. The P. anserina OSIP1Δ mutant showed an increased sensitivity to the antifungal caspofungin compared to the wild type. This correlated with the production of a weakened extracellular exopolysaccharide/protein matrix (ECM). Since the recombinant OSIP1 from P. chrysosporium self-assembled as fibers and was capable of gelation, it is likely that OSIP1 is linked to ECM formation that acts as a physical barrier preventing drug toxicity. Moreover, compared to the wild type, the OSIP1Δ mutant was more sensitive to oak extractives including chaotropic phenols and benzenes. It exhibited a strongly modified secretome pattern and an increased production of proteins associated to the cell-wall integrity signalling pathway, when grown on oak sawdust. This demonstrates that OSIP1 has also an important role in fungal resistance to extractive-induced stress.
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Affiliation(s)
- Nicolas Valette
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Julien Renou
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Alexis Boutilliat
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | | | - Valérie Gautier
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), Paris, 75205, France
| | - Philippe Silar
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), Paris, 75205, France
| | - Christophe Guyeux
- Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, 16 route de Gray, Besançon, 25030, France
| | - Jean-Claude Charr
- Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, 16 route de Gray, Besançon, 25030, France
| | - Stéphane Cuenot
- Institut des Matériaux Jean Rouxel, Université de Nantes, 2 rue de la Houssinière, Nantes Cedex 3, 44322, France
| | - Christophe Rose
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, Nancy, 54000, France
| | - Eric Gelhaye
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Mélanie Morel-Rouhier
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
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12
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Freitas DF, Vieira-Da-Motta O, Mathias LDS, Franco RWDA, Gomes RDS, Vieira RAM, Rocha LOD, Olivares FL, Santos CDP. Synthesis and role of melanin for tolerating in vitro rumen digestion in Duddingtonia flagrans, a nematode-trapping fungus. Mycology 2019; 10:229-242. [PMID: 31632832 PMCID: PMC6781480 DOI: 10.1080/21501203.2019.1631896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 06/07/2019] [Indexed: 01/13/2023] Open
Abstract
We describe the synthesis and a function of melanin in Duddingtonia flagrans, a nematode-trapping fungus. We tested various culture media treated with L-DOPA, glucose and tricyclazole on fungal growth and melanin distribution using infrared spectroscopy (IS), electron paramagnetic resonance (EPR) and transmission electron microscopy (TEM). In vitro rumen digestion was used to test the environmental stress and then to evaluate the capacity of this fungus to trap nematode larvae. The growth and melanization of the fungus after 21 days of incubation at 30°C were best in Sabouraud dextrose medium. IS indicated the presence of melanin in D. flagrans, with similar bands for commercial melanin used as a control, and assigned the values obtained by EPR (g of 2.0051 ± 0.0001) to the production of melanin by the fungus. TEM indicated that melanin was produced in melanosomes but was not totally inhibited by tricyclazole. Within the limits of experimental error, the predatory activity of fungus treated with tricyclazole was drastically affected after 27 h of in vitro anaerobic stress with rumen inoculum. The deposition of melanin particles on the fungal cell wall contributed to the maintenance of D. flagrans predatory abilities after in vitro anaerobic ruminal stress.
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Affiliation(s)
- Deivid França Freitas
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Olney Vieira-Da-Motta
- Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Luciana Da Silva Mathias
- Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Roberto Weider De Assis Franco
- Laboratório de Ciências Físicas, Centro de Ciências Tecnológicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Raphael Dos Santos Gomes
- Laboratório de Zootecnia, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Ricardo Augusto Mendonça Vieira
- Laboratório de Zootecnia, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Letícia Oliveira Da Rocha
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Fabio Lopes Olivares
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Clóvis De Paula Santos
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
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13
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Oide S, Tanaka Y, Watanabe A, Inui M. Carbohydrate-binding property of a cell wall integrity and stress response component (WSC) domain of an alcohol oxidase from the rice blast pathogen Pyricularia oryzae. Enzyme Microb Technol 2019; 125:13-20. [DOI: 10.1016/j.enzmictec.2019.02.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/23/2019] [Accepted: 02/23/2019] [Indexed: 11/29/2022]
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14
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Wawra S, Fesel P, Widmer H, Neumann U, Lahrmann U, Becker S, Hehemann JH, Langen G, Zuccaro A. FGB1 and WSC3 are in planta-induced β-glucan-binding fungal lectins with different functions. THE NEW PHYTOLOGIST 2019; 222:1493-1506. [PMID: 30688363 DOI: 10.1111/nph.15711] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
In the root endophyte Serendipita indica, several lectin-like members of the expanded multigene family of WSC proteins are transcriptionally induced in planta and are potentially involved in β-glucan remodeling at the fungal cell wall. Using biochemical and cytological approaches we show that one of these lectins, SiWSC3 with three WSC domains, is an integral fungal cell wall component that binds to long-chain β1-3-glucan but has no affinity for shorter β1-3- or β1-6-linked glucose oligomers. Comparative analysis with the previously identified β-glucan-binding lectin SiFGB1 demonstrated that whereas SiWSC3 does not require β1-6-linked glucose for efficient binding to branched β1-3-glucan, SiFGB1 does. In contrast to SiFGB1, the multivalent SiWSC3 lectin can efficiently agglutinate fungal cells and is additionally induced during fungus-fungus confrontation, suggesting different functions for these two β-glucan-binding lectins. Our results highlight the importance of the β-glucan cell wall component in plant-fungus interactions and the potential of β-glucan-binding lectins as specific detection tools for fungi in vivo.
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Affiliation(s)
- Stephan Wawra
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Philipp Fesel
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Heidi Widmer
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Ulla Neumann
- Central Microscopy (CeMic), Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Urs Lahrmann
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Stefan Becker
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Gregor Langen
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
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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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16
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Random mutagenesis analysis and identification of a novel C 2H 2-type transcription factor from the nematode-trapping fungus Arthrobotrys oligospora. Sci Rep 2017; 7:5640. [PMID: 28717216 PMCID: PMC5514059 DOI: 10.1038/s41598-017-06075-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 06/12/2017] [Indexed: 01/04/2023] Open
Abstract
Arthrobotrys oligospora is a typical nematode-trapping fungus. In this study, 37 transformants of A. oligospora were obtained by REMI (restriction enzyme mediated integration) method and phenotypic properties of nine transformants were analyzed. The nine transformants showed differences in growth, conidiation, trap formation, stress tolerance, and/or pathogenicity among each other and with those of the parental wild-type strain (WT). The insertional sites of the hph cassette were identified in transformants X5 and X13. In X5, the cassette was inserted in the non-coding region between AOL_s00076g273 (76g273) and AOL_s00076g274 (76g274) and the transcription of 76g274, but not 76g273, was enhanced in X5. 76g274p had two conserved domains and was predicted as a nucleoprotein, which we confirmed by its nuclear localization in Saccharomyces cerevisiae using the green fluorescent protein-fused 76g274p. The transcription of 76g274 was stimulated or inhibited by several environmental factors. The sporulation yields of 76g274-deficient mutants were decreased by 70%, and transcription of several sporulation-related genes was severely diminished compared to the WT during the conidiation. In summary, a method for screening mutants was established in A. oligospora and using the method, we identified a novel C2H2-type transcription factor that positively regulates the conidiation of A. oligospora.
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17
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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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18
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RNA-Seq reveals the molecular mechanism of trapping and killing of root-knot nematodes by nematode-trapping fungi. World J Microbiol Biotechnol 2017; 33:65. [DOI: 10.1007/s11274-017-2232-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 02/17/2017] [Indexed: 12/22/2022]
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19
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Zhang L, Zhou Z, Guo Q, Fokkens L, Miskei M, Pócsi I, Zhang W, Chen M, Wang L, Sun Y, Donzelli BGG, Gibson DM, Nelson DR, Luo JG, Rep M, Liu H, Yang S, Wang J, Krasnoff SB, Xu Y, Molnár I, Lin M. Insights into Adaptations to a Near-Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniospora. Sci Rep 2016; 6:23122. [PMID: 26975455 PMCID: PMC4792172 DOI: 10.1038/srep23122] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/29/2016] [Indexed: 12/18/2022] Open
Abstract
Nematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, and endoparasitism. While endoparasites play key roles in controlling nematode populations in nature, their application for integrated pest management is hindered by the limited understanding of their biology. We present a comparative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endoparasitic nematophagous fungus, integrated with a transcriptomic study. Adaptation of D. coniospora to its almost completely obligate endoparasitic lifestyle led to the simplification of many orthologous gene families involved in the saprophytic trophic mode, while maintaining orthologs of most known fungal pathogen-host interaction proteins, stress response circuits and putative effectors of the small secreted protein type. The need to adhere to and penetrate the host cuticle led to a selective radiation of surface proteins and hydrolytic enzymes. Although the endoparasite has a simplified secondary metabolome, it produces a novel peptaibiotic family that shows antibacterial, antifungal and nematicidal activities. Our analyses emphasize the basic malleability of the D. coniospora genome: loss of genes advantageous for the saprophytic lifestyle; modulation of elements that its cohort species utilize for entomopathogenesis; and expansion of protein families necessary for the nematode endoparasitic lifestyle.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengfu Zhou
- Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China
| | - Qiannan Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Like Fokkens
- Molecular Plant Pathology, University of Amsterdam, Amsterdam, the Netherlands
| | - Márton Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Hungary
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Hungary
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Wang
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yamin Sun
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Bruno G. G. Donzelli
- Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Donna M. Gibson
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jian-Guang Luo
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Martijn Rep
- Molecular Plant Pathology, University of Amsterdam, Amsterdam, the Netherlands
| | - Hang Liu
- Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China
| | - Shengnan Yang
- Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China
| | - Jing Wang
- Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China
| | - Stuart B. Krasnoff
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Yuquan Xu
- Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, China
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Kim KT, Jeon J, Choi J, Cheong K, Song H, Choi G, Kang S, Lee YH. Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association. FRONTIERS IN PLANT SCIENCE 2016; 7:186. [PMID: 26925088 PMCID: PMC4759460 DOI: 10.3389/fpls.2016.00186] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 02/03/2016] [Indexed: 05/18/2023]
Abstract
Fungal secretome consists of various functional groups of proteins, many of which participate in nutrient acquisition, self-protection, or manipulation of the environment and neighboring organisms. The least characterized component of the secretome is small secreted proteins (SSPs). Some SSPs have been reported to function as effectors, but most remain to be characterized. The composition of major secretome components, such as carbohydrate-active enzymes, proteases, lipases, and oxidoreductases, appear to reflect the lifestyle and ecological niche of individual species. We hypothesize that many SSPs participate in manipulating plants as effectors. Obligate biotrophs likely encode more and diverse effector-like SSPs to suppress host defense compared to necrotrophs, which generally use cell wall degrading enzymes and phytotoxins to kill hosts. Because different secretome prediction workflows have been used in different studies, available secretome data are difficult to integrate for comprehensive comparative studies to test this hypothesis. In this study, SSPs encoded by 136 fungal species were identified from data archived in Fungal Secretome Database (FSD) via a refined secretome workflow. Subsequently, compositions of SSPs and other secretome components were compared in light of taxa and lifestyles. Those species that are intimately associated with host cells, such as biotrophs and symbionts, usually have higher proportion of species-specific SSPs (SSSPs) than hemibiotrophs and necrotrophs, but the latter groups displayed higher proportions of secreted enzymes. Results from our study established a foundation for functional studies on SSPs and will also help understand genomic changes potentially underpinning different fungal lifestyles.
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Affiliation(s)
- Ki-Tae Kim
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Department of Agricultural Biotechnology, Seoul National UniversitySeoul, South Korea
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Jaeyoung Choi
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State UniversityUniversity Park, PA, USA
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Department of Agricultural Biotechnology, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
- Center for Fungal Genetic Resources, Center for Fungal Pathogenesis, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
- *Correspondence: Yong-Hwan Lee
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Loshaj-Shala A, Regazzoni L, Daci A, Orioli M, Brezovska K, Panovska AP, Beretta G, Suturkova L. Guillain Barré syndrome (GBS): new insights in the molecular mimicry between C. jejuni and human peripheral nerve (HPN) proteins. J Neuroimmunol 2015; 289:168-76. [DOI: 10.1016/j.jneuroim.2015.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/05/2015] [Accepted: 11/07/2015] [Indexed: 12/19/2022]
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22
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Transcriptome analysis of genes involved in defence response in Polyporus umbellatus with Armillaria mellea infection. Sci Rep 2015; 5:16075. [PMID: 26526032 PMCID: PMC4630638 DOI: 10.1038/srep16075] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022] Open
Abstract
Polyporus umbellatus, a species symbiotic with Armillaria mellea and it also exhibits substantial defence response to Armillaria mellea infection. There are no genomics resources databases for understanding the molecular mechanism underlying the infection stress of P. umbellatus. Therefore, we performed a large-scale transcriptome sequencing of this fungus with A. mellea infection using Illumina sequencing technology. The assembly of the clean reads resulted in 120,576 transcripts, including 38,444 unigenes. Additionally, we performed a gene expression profiling analysis upon infection treatment. The results indicated significant differences in the gene expression profiles between the control and the infection group. In total, 10933 genes were identified between the two groups. Based on the differentially expressed genes, a Gene Ontology annotation analysis showed many defence-relevant categories. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways. Furthermore, the expression patterns of 13 putative genes that are involved in defence response resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The sequenced genes covered a considerable proportion of the P. umbellatus transcriptome, and the expression results may be useful to strengthen the knowledge on the defence response of this fungus defend against Armillaria mellea invasion.
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Su H, Zhao Y, Zhou J, Feng H, Jiang D, Zhang KQ, Yang J. Trapping devices of nematode-trapping fungi: formation, evolution, and genomic perspectives. Biol Rev Camb Philos Soc 2015; 92:357-368. [PMID: 26526919 DOI: 10.1111/brv.12233] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 11/29/2022]
Abstract
Nematode-trapping fungi (NTF) are potential biological control agents against plant- and animal-parasitic nematodes. These fungi produce diverse trapping devices (traps) to capture, kill, and digest nematodes as food sources. Most NTF can live as both saprophytes and parasites. Traps are not only the weapons that NTF use to capture and infect nematodes, but also an important indicator of their switch from a saprophytic to a predacious lifestyle. Formation of traps and their numbers are closely related to the nematicidal activity of NTF, so the mechanisms governing trap formation have become a focus of research on NTF. Recently, much progress has been made in our understanding of trap formation, evolution, and the genome, proteome and transcriptome of NTF. Here we provide a comprehensive overview of recent advances in research on traps of NTF. Various inducers of trap formation, trap development, structural properties and evolution of traps are summarized and discussed. We specifically discuss the latest studies of NTF based on genomic, proteomic and transcriptomic analyses.
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Affiliation(s)
- Hao Su
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, No. 2 North Cuihu Road, Kunming, 650091, China
| | - Yong Zhao
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, No. 2 North Cuihu Road, Kunming, 650091, China
| | - Jing Zhou
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, No. 2 North Cuihu Road, Kunming, 650091, China
| | - Huihua Feng
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, No. 2 North Cuihu Road, Kunming, 650091, China
| | - Dewei Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, China
| | - Ke-Qin Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, No. 2 North Cuihu Road, Kunming, 650091, China
| | - Jinkui Yang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, No. 2 North Cuihu Road, Kunming, 650091, China
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Zhao H, Qiao J, Meng Q, Gong S, Chen C, Liu T, Tian L, Cai X, Luo J, Chen C. Expression of serine proteinase P186 of Arthrobotrys oligospora and analysis of its nematode-degrading activity. Antonie van Leeuwenhoek 2015; 108:1485-1494. [PMID: 26419902 DOI: 10.1007/s10482-015-0595-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/21/2015] [Indexed: 11/25/2022]
Abstract
The nematode-trapping fungi possess a unique capability of predating and invading nematodes. As a representative nematode-trapping fungus, Arthrobotrys oligospora has been widely used to study the interactions between nematode-trapping fungi and their hosts. Serine proteinase is one of the important virulence factors during process of invasion of the nematode-trapping fungi into nematodes. In this study, using reverse transcription polymerase chain reaction, we amplified the gene sequence of serine proteinase 186 from A. oligospora, cloned it into pPIC9K vector and expressed it in the yeast Pichia pastoris. The expressed recombinant serine proteinase186 (reP186) was purified via Ni-affinity chromatography. The in vitro nematode-degrading activity of reP186 was analyzed. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blot analysis revealed that reP186 with molecular weight of 33 kDa was successfully obtained. ReP186 was capable of degrading a series of protein substrates including casein, gelatin, bovine serum albumin, denatured collagen and nematode cortical layer. The reP186 exhibited the maximal activity at pH 8.0 and 55 °C and was highly sensitive to the inhibitor, phenylmethanesulfonylfluoride. Treatment of Caenorhabditis elegans and Haemonchus contortus with reP186 for 12, 24 and 36 h, respectively, resulted in 62, 88 and 100 % of killing rates for C. elegans, and 52, 65 and 84 % of killing rates for H. contortus, respectively, indicating a relatively strong nematode-degrading bioactivity of reP186.
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Affiliation(s)
- Hailong Zhao
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Jun Qiao
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Qingling Meng
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China.
| | - Shasha Gong
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Cheng Chen
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Tianli Liu
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Lulu Tian
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Xuepeng Cai
- State Key Lab of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Jianxun Luo
- State Key Lab of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Chuangfu Chen
- Key Laboratory of Control and Prevention of Animal Disease of Xinjiang Production & Construction Corps, College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
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Ramesh P, Reena P, Amitbikram M, Chaitanya J, Anju K. Insight into the transcriptome of Arthrobotrys conoides using high throughput sequencing. J Basic Microbiol 2015; 55:1394-405. [PMID: 26301953 DOI: 10.1002/jobm.201500237] [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: 05/07/2015] [Accepted: 07/20/2015] [Indexed: 11/09/2022]
Abstract
Arthrobotrys conoides is a nematode-trapping fungus belonging to Orbiliales, Ascomycota group, and traps prey nematodes by means of adhesive network. Fungus has a potential to be used as a biocontrol agent against plant parasitic nematodes. In the present study, we characterized the transcriptome of A. conoides using high-throughput sequencing technology and characterized its virulence unigenes. Total 7,255 cDNA contigs with an average length of 425 bp were generated and 6184 (61.81%) transcripts were functionally annotated and characterized. Majority of unigenes were found analogous to the genes of plant pathogenic fungi. A total of 1749 transcripts were found to be orthologous with eukaryotic proteins of KOG database. Several carbohydrate active enzymes and peptidases were identified. We also analyzed classically and nonclassically secreted proteins and confirmed by BLASTP against fungal secretome database. A total of 916 contigs were analogous to 556 unique proteins of Pathogen Host Interaction (PHI) database. Further, we identified 91 unigenes homologous to the database of fungal virulence factor (DFVF). A total of 104 putative protein kinases coding transcripts were identified by BLASTP against KinBase database, which are major players in signaling pathways. This study provides a comprehensive look at the transcriptome of A. conoides and the identified unigenes might have a role in catching and killing prey nematodes by A. conoides.
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Affiliation(s)
- Pandit Ramesh
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India.,Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Patel Reena
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India
| | - Mohapatra Amitbikram
- Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Joshi Chaitanya
- Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Kunjadia Anju
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India
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Cruz DG, Costa LM, Rocha LO, Retamal CA, Vieira RAM, Seabra SH, Silva CP, DaMatta RA, Santos CP. Serine proteases activity is important for the interaction of nematophagous fungus Duddingtonia flagrans with infective larvae of trichostrongylides and free-living nematodes Panagrellus spp. Fungal Biol 2015; 119:672-8. [PMID: 26228558 DOI: 10.1016/j.funbio.2015.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 11/26/2022]
Abstract
The nematode-trapping fungus Duddingtonia flagrans has been studied as a possible control method for gastrointestinal nematodes of livestock animals. These fungi capture and infect the nematode by cuticle penetration, immobilization, and digestion of the internal contents. It has been suggested that this sequence of events occurs by a combination of physical and enzymatical activities. The aim of this study was to investigate the participation of proteolytic enzymatic activity during the interaction of the nematophagous fungus D. flagrans with infective larvae of trichostrongylides and the free-living nematode Panagrellus spp. Protease inhibitors used interfered in the predatory activity of D. flagrans. However, only PMSF significantly reduced the mean number of Panagrellus spp. captured by D. flagrans in comparison with the control. The experiment with fluorogenic substrate showed that maximum urokinase activity during the interaction of the fungus with the infective larvae of trichostrongylides or Panagrellus spp. occurred within 7 or 1 h of incubation, respectively. The protease activity, especially of the serine class, may be important during the interaction between the fungus and nematodes.
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Affiliation(s)
- Daniela G Cruz
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Parque Califórnia, CEP 28013602, Campos dos Goytacazes, Rio de Janeiro, Brazil; Laboratório de Tecnologia em Bioquímica e Microscopia, Centro de Ciências Biológicas e da Saúde, Centro Universitário Estadual da Zona Oeste, Avenida Manuel Caldeira de Alvarenga, 1203, Campo Grande, Rio de Janeiro, RJ, CEP 23070-200, Brazil
| | - Luana M Costa
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Parque Califórnia, CEP 28013602, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Letícia O Rocha
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Parque Califórnia, CEP 28013602, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Claudio A Retamal
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Parque Califórnia, CEP 28013602, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Ricardo A M Vieira
- Laboratório de Zootecnia e Nutrição Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Parque Califórnia, CEP 28013602, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Sergio H Seabra
- Laboratório de Tecnologia em Bioquímica e Microscopia, Centro de Ciências Biológicas e da Saúde, Centro Universitário Estadual da Zona Oeste, Avenida Manuel Caldeira de Alvarenga, 1203, Campo Grande, Rio de Janeiro, RJ, CEP 23070-200, Brazil
| | - Carlos P Silva
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Reitor João David Ferreira Lima, s/n, Trindade, CEP 88040-900, Florianópolis, Santa Catarina, Brazil
| | - Renato A DaMatta
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Parque Califórnia, CEP 28013602, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Clóvis P Santos
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Parque Califórnia, CEP 28013602, Campos dos Goytacazes, Rio de Janeiro, Brazil.
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Andersson KM, Kumar D, Bentzer J, Friman E, Ahrén D, Tunlid A. Interspecific and host-related gene expression patterns in nematode-trapping fungi. BMC Genomics 2014; 15:968. [PMID: 25384908 PMCID: PMC4237727 DOI: 10.1186/1471-2164-15-968] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 09/24/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host preferences. To provide insights into the genetic basis for this variation, we compared the transcriptome expressed by three species of nematode-trapping fungi (Arthrobotrys oligospora, Monacrosporium cionopagum and Arthrobotrys dactyloides, which use adhesive nets, adhesive branches or constricting rings, respectively, to trap nematodes) during infection of two different plant-pathogenic nematode hosts (the root knot nematode Meloidogyne hapla and the sugar beet cyst nematode Heterodera schachtii). RESULTS The divergence in gene expression between the fungi was significantly larger than that related to the nematode species being infected. Transcripts predicted to encode secreted proteins and proteins with unknown function (orphans) were overrepresented among the highly expressed transcripts in all fungi. Genes that were highly expressed in all fungi encoded endopeptidases, such as subtilisins and aspartic proteases; cell-surface proteins containing the carbohydrate-binding domain WSC; stress response proteins; membrane transporters; transcription factors; and transcripts containing the Ricin-B lectin domain. Differentially expressed transcripts among the fungal species encoded various lectins, such as the fungal fruit-body lectin and the D-mannose binding lectin; transcription factors; cell-signaling components; proteins containing a WSC domain; and proteins containing a DUF3129 domain. A small set of transcripts were differentially expressed in infections of different host nematodes, including peptidases, WSC domain proteins, tyrosinases, and small secreted proteins with unknown function. CONCLUSIONS This is the first study on the variation of infection-related gene expression patterns in nematode-trapping fungi infecting different host species. A better understanding of these patterns will facilitate the improvements of these fungi in biological control programs, by providing molecular markers for screening programs and candidates for genetic manipulations of virulence and host preferences.
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Affiliation(s)
- Karl-Magnus Andersson
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Dharmendra Kumar
- />Department of Genetics and Plant Breeding, College of Agriculture, Narendra Deva University of Agriculture and Technology, Kumarganj, Faizabad, 224229 Uttar Pradesh (U.P.) India
| | - Johan Bentzer
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Eva Friman
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Dag Ahrén
- />Department of Biology, BILS Bioinformatics Infrastructure for Life Sciences, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Anders Tunlid
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
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Lai Y, Liu K, Zhang X, Zhang X, Li K, Wang N, Shu C, Wu Y, Wang C, Bushley KE, Xiang M, Liu X. Comparative genomics and transcriptomics analyses reveal divergent lifestyle features of nematode endoparasitic fungus Hirsutella minnesotensis. Genome Biol Evol 2014; 6:3077-93. [PMID: 25359922 PMCID: PMC4255773 DOI: 10.1093/gbe/evu241] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism.
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Affiliation(s)
- Yiling Lai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Keke Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Niuniu Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Chi Shu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Yunpeng Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Malate synthase gene AoMls in the nematode-trapping fungus Arthrobotrys oligospora contributes to conidiation, trap formation, and pathogenicity. Appl Microbiol Biotechnol 2013; 98:2555-63. [PMID: 24323290 DOI: 10.1007/s00253-013-5432-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/16/2013] [Accepted: 11/20/2013] [Indexed: 10/25/2022]
Abstract
Malate synthase (Mls), a key enzyme in the glyoxylate cycle, is required for virulence in microbial pathogens. In this study, we identified the AoMls gene from the nematode-trapping fungus Arthobotrys oligospora. The gene contains 4 introns and encodes a polypeptide of 540 amino acids. To characterize the function of AoMls in A. oligospora, we disrupted it by homologous recombination, and the ΔAoMls mutants were confirmed by PCR and Southern blot analyses. The growth rate and colony morphology of the ΔAoMls mutants showed no obvious difference from the wild-type strains on potato dextrose agar (PDA) plate. However, the disruption of gene AoMls led to a significant reduction in conidiation, failure to utilize fatty acids and sodium acetate for growth, and its conidia were unable to germinate on minimal medium supplemented with sodium oleate. In addition, the trap formation was retarded in the ΔAoMls mutants, which only produced immature traps containing one or two rings. Moreover, the nematicidal activity of the ΔAoMls mutants was significantly decreased. Our results suggest that the gene AoMls plays an important role in conidiation, trap formation and pathogenicity of A. oligospora.
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Islam MT, Mohamedali A, Garg G, Khan JM, Gorse AD, Parsons J, Marshall P, Ranganathan S, Baker MS. Unlocking the puzzling biology of the black Périgord truffle Tuber melanosporum. J Proteome Res 2013; 12:5349-56. [PMID: 24147936 DOI: 10.1021/pr400650c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The black Périgord truffle (Tuber melanosporum Vittad.) is a highly prized food today, with its unique scent (i.e., perfume) and texture. Despite these attributes, it remains relatively poorly studied, lacking "omics" information to characterize its biology and biochemistry, especially changes associated with freshness and the proteins/metabolites responsible for its organoleptic properties. In this study, we have functionally annotated the truffle proteome from the 2010 T. melanosporum genome comprising 12,771 putative nonredundant proteins. Using sequential BLAST search strategies, we identified homologues for 2587 proteins with 2486 (96.0%) fungal homologues (available from http://biolinfo.org/protannotator/blacktruffle.php). A combined 1D PAGE and high-accuracy LC-MS/MS proteomic study was employed to validate the results of the functional annotation and identified 836 (6.5%) proteins, of which 47.5% (i.e., 397) were present in our bioinformatics studies. Our study, functionally annotating 6487 black Périgord truffle proteins and confirming 836 by proteomic experiments, is by far the most comprehensive study to date contributing significantly to the scientific community. This study has resulted in the functional characterization of novel proteins to increase our biological understanding of this organism and to uncover potential biomarkers of authenticity, freshness, and perfume maturation.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Macquarie University , NSW 2109, Australia
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Meerupati T, Andersson KM, Friman E, Kumar D, Tunlid A, Ahrén D. Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi. PLoS Genet 2013; 9:e1003909. [PMID: 24244185 PMCID: PMC3828140 DOI: 10.1371/journal.pgen.1003909] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/09/2013] [Indexed: 01/12/2023] Open
Abstract
Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.
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Affiliation(s)
- Tejashwari Meerupati
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Karl-Magnus Andersson
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Eva Friman
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Dharmendra Kumar
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
- Department of Genetics and Plant Breeding, N.D. University of Agriculture and Technology, Faizabad, India
| | - Anders Tunlid
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Dag Ahrén
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
- BILS Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Ecology Building, Lund, Sweden
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Liang L, Wu H, Liu Z, Shen R, Gao H, Yang J, Zhang K. Proteomic and transcriptional analyses of Arthrobotrys oligospora cell wall related proteins reveal complexity of fungal virulence against nematodes. Appl Microbiol Biotechnol 2013; 97:8683-92. [PMID: 23948728 DOI: 10.1007/s00253-013-5178-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
The nematode-trapping fungus Arthrobotrys oligospora is the best-studied fungus for understanding the interaction between fungi and nematodes. The fungus uses three-dimensional adhesive networks to capture nematodes and then penetrates into the worms through their cuticle. Here we examine the effects of fungal cell wall related proteins on morphogenesis and virulence of the fungi. We focused on the changes in its proteomic and transcriptional profiles during its transition from saprophytic to predatory phase. Isobaric tags for relative and absolute quantitation (iTRAQ) proteomics using the liquid chromatography/mass spectrometry (LC/MS) method revealed an extended set of virulence related proteins, such as adhesins and serine proteases, on the cell wall of A. oligospora. Transcription analyses of their coding genes revealed an important set of candidate virulence factors. Our analyses also show that glycosyl hydrolases likely play important roles in trap formation of A. oligospora. The adhesins on the three-dimensional adhesive networks may have two functions: to enable the mycelia to stick to nematodes and to serve as important constituents of the extracellular matrix that harbors many secreted virulence related proteins. This study is the first to systematically identify cell wall related proteins that are important in the trap formation and infection of the fungus against nematode hosts.
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Affiliation(s)
- Lianming Liang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
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