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Jia H, Xia R, Zhang R, Liang G, Zhuang Y, Zhou Y, Li D, Wang F. Transcriptome analysis highlights the influence of temperature on hydrolase and traps in nematode-trapping fungi. Front Microbiol 2024; 15:1384459. [PMID: 38774504 PMCID: PMC11106486 DOI: 10.3389/fmicb.2024.1384459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/01/2024] [Indexed: 05/24/2024] Open
Abstract
Pine wilt disease caused by Bursaphelenchus xylophilus poses a serious threat to the economic and ecological value of forestry. Nematode trapping fungi trap and kill nematodes using specialized trapping devices, which are highly efficient and non-toxic to the environment, and are very promising for use as biological control agents. In this study, we isolated several nematode-trapping fungi from various regions and screened three for their high nematocidal efficiency. However, the effectiveness of these fungi as nematicides is notably influenced by temperature and exhibits different morphologies in response to temperature fluctuations, which are categorized as "NA," "thin," "dense," and "sparse." The trend of trap formation with temperature was consistent with the trend of nematocidal efficiency with temperature. Both of which initially increased and then decreased with increasing temperature. Among them, Arthrobotrys cladodes exhibited the highest level of nematocidal activity and trap formation among the tested species. Transcriptome data were collected from A. cladodes with various trap morphologies. Hydrolase activity was significantly enriched according to GO and KEGG enrichment analyses. Eight genes related to hydrolases were found to be consistent with the trend of trap morphology with temperature. Weighted gene co-expression analysis and the Cytoscape network revealed that these 8 genes are associated with either mitosis or autophagy. This suggests that they contribute to the formation of "dense" structures in nematode-trapping fungi. One of these genes is the serine protein hydrolase gene involved in autophagy. This study reveals a potentially critical role for hydrolases in trap formation and nematocidal efficiency. And presents a model where temperature affects trap formation and nematocidal efficiency by influencing the serine protease prb1 involved in the autophagy process.
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Affiliation(s)
- Hanqi Jia
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Rui Xia
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Ruizhi Zhang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Guanjun Liang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Yuting Zhuang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Yantao Zhou
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Danlei Li
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Feng Wang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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2
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Li N, Sun Y, Liu Y, Wei L, Zhang J, Li N, Sun D, Jiao J, Zuo Y, Li R, Cai X, Qiao J, Meng Q. Expression profiles and characterization of microRNAs responding to chitin in Arthrobotrys oligospora. Arch Microbiol 2024; 206:220. [PMID: 38630188 DOI: 10.1007/s00203-024-03949-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/25/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Extracellular proteases, such as chitinases secreted by Arthrobotrys oligospora (A. oligospora), play a crucial role in the process of nematode infection. However, post-transcriptional regulation of gene expression involving microRNAs (miRNAs) in A. oligospora remains scarcely described. Hereto, transcriptome sequencing was carried out to analyze the expression profiles of chitin-responsive miRNAs in A. oligospora. Based on the RNA-seq data, the differential expression of miRNAs (DEmiRNAs) in response to chitin was screened, identified and characterized in A. oligospora. Meanwhile, the potential target genes were predicted by the online tools miRanda and Targetscan, respectively. Furthermore, the interaction of DEmiRNA with it's target gene was validated by a dual-luciferase reporter assay system. Among 85 novel miRNAs identified, 25 miRNAs displayed significant differences in expression in A. oligospora in response to chitin. Gene Ontology (GO) analysis showed that the potential genes targeted by DEmiRNAs were enriched in the biological processes such as bio-degradation, extracellular components and cell cycle. KEGG analysis revealed that the target genes were mainly involved in Hippo, carbon and riboflavin metabolic pathway. Outstandingly, chitinase AOL_s00004g379, which is involved in the hydrolysis metabolic pathway of chitin, was confirmed to be a target gene of differential miR_70. These findings suggest that chitin-responsive miRNAs are involved in the regulation of cell proliferation, predator hyphae growth and chitinase expression through the mechanisms of post-transcriptional regulation, which provides a new perspective to the molecular mechanisms underlying miRNAs-mediated control of gene expression in A. oligospora.
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Affiliation(s)
- Ningxing Li
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Yansen Sun
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Yucheng Liu
- State key laboratory of sheep genetic improvement and healthy breeding, Institute of Animal Science and Veterinary Research, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, Xinjiang, China
| | - Lixiang Wei
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Jiahua Zhang
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Nengxiu Li
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Dianming Sun
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Jian Jiao
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Yufei Zuo
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Ruobing Li
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Xuepeng Cai
- State key laboratory of veterinary etiological biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China.
| | - Qingling Meng
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China.
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3
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Topalović O, Bak F, Santos S, Sikder MM, Sapkota R, Ekelund F, Nicolaisen MH, Vestergård M. Activity of root-knot nematodes associated with composition of a nematode-attached microbiome and the surrounding soil microbiota. FEMS Microbiol Ecol 2023; 99:fiad091. [PMID: 37553158 DOI: 10.1093/femsec/fiad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023] Open
Abstract
We investigated if activity of the pre-infective juveniles (J2s) of root-knot nematodes is linked to the recruitment of a specific microbiome on the nematode surface and/or to the composition of the surrounding microbiota. For this, we determined the J2 activity (active vs. non-motile, which referred to dead and immobile J2s) upon a 3-day incubation in soil suspensions and studied the composition of bacteria, protists, and fungi present on the nematode surface and in the suspensions using amplicon sequencing of the 16S/18S rRNA genes, and ITS region. We also amended suspensions with Pseudomonas protegens strain CHA0 to study its effects on J2 activity and microbial composition. The J2 activity was suppressed in soil suspensions, but increased when suspensions were amended with P. protegens CHA0. The active and non-motile J2s differed in the composition of surface-attached bacteria, which was altered by the presence of P. protegens CHA0 in the soil suspensions. The bacterial genera Algoriphagus, Pedobacter, and Bdellovibrio were enriched on active J2s and may have protected the J2s against antagonists. The incubation time appeared short for attachment of fungi and protists. Altogether, our study is a step forward in disentangling the complex nematode-microbe interactions in soil for more successful nematode control.
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Affiliation(s)
- Olivera Topalović
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
- Department of Terrestrial Ecology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Frederik Bak
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Susana Santos
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
| | - Md Maniruzzaman Sikder
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
- Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, 1342 Savar, Dhaka, Bangladesh
| | - Rumakanta Sapkota
- Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, 4000 Roskilde, Denmark
| | - Flemming Ekelund
- Department of Terrestrial Ecology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
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Bahri BA, Parvathaneni RK, Spratling WT, Saxena H, Sapkota S, Raymer PL, Martinez-Espinoza AD. Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass. Front Genet 2023; 13:1033437. [PMID: 36685867 PMCID: PMC9849252 DOI: 10.3389/fgene.2022.1033437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/21/2022] [Indexed: 01/06/2023] Open
Abstract
Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, Clarireedia monteithiana and C. jacksonii (formerly Sclerotinia homoeocarpa) have been reported so far in the United States To study the Clarireedia genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced via Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as C. aff. paspali, a novel species in the United States Using short and long reads, C. aff. paspali H3 contained 193 contigs with 48.6 Mbp and presented the most completed assembly and annotation among Clarireedia species. Out of the 13,428 protein models from AUGUSTUS, 349 cytoplasmic effectors and 13 apoplastic effectors were identified by EffectorP. To further decipher Clarireedia pathogenicity, C. aff. paspali genomes (H2 and H3), as well as available C. jacksonii (LWC-10 and HRI11), C. monteithiana (DRR09 and RB-19) genomes were screened for fifty-four pathogenesis determinants, previously identified in S. sclerotiorum. Seventeen orthologs of pathogenicity genes have been identified in Clarireedia species involved in oxalic acid production (pac1, nox1), mitogen-activated protein kinase cascade (pka1, smk3, ste12), appressorium formation (caf1, pks13, ams2, rgb1, rhs1) and glycolytic pathway (gpd). Within these genes, 366 species-specific SNPs were recorded between Clarireedia species; twenty-eight were non-synonymous and non-conservative. The predicted protein structure of six of these genes showed superimposition of the models among Clarireedia spp. The genomic variations revealed here could potentially lead to differences in pathogenesis and other physiological functions among Clarireedia species.
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Affiliation(s)
- Bochra Amina Bahri
- Department of Plant Pathology, University of Georgia, Griffin, GA, United States,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States,*Correspondence: Bochra Amina Bahri,
| | - Rajiv Krishna Parvathaneni
- Department of Plant Pathology, University of Georgia, Griffin, GA, United States,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States
| | | | - Harshita Saxena
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States
| | - Suraj Sapkota
- Department of Plant Pathology, University of Georgia, Griffin, GA, United States
| | - Paul L. Raymer
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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Ma J, Yang X, Fan W, Zhao C, Li W, Zhou D, Jiang S. Cloning and sequence analysis of a serine protease gene from Rhizoctonia solani Kühn AG5. Biotechnol Appl Biochem 2022; 69:2466-2474. [PMID: 34877711 DOI: 10.1002/bab.2296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
The present study aimed to identify the subtilisin-like proteases (SLPs) of Rhizoctonia solani Kühn potentially involved in the virulence of this phytopathogenic fungus, which has 14 anastomosis groups (AGs) responsible for many crop diseases. Through mycelial microscope observation and strain identification of pathogenic fungus MS-3, it was determined to be R. solani AG-5. Both 5' and 3' rapid amplification of cDNA ends were used to clone the serine protease gene RsSLP from R. solani AG-5. The full-length obtained for RsSLP was 1714 bp with an open reading frame of 1587 bp, encoding a protein of 528 amino acids with a molecular mass of 55.8 kDa. This protein contained a predicted signal peptide for secretion but lacked a transmembrane domain or membrane anchor site. Bioinformatics analysis identified this protein as a serine protease with the Peptidase_S8 and Inhibitor_I9 characteristic domains of SLPs. Phylogenetic analysis suggested that frequent gene duplications of the SLPs occurred in R. solani (RsSLP), and RsSLP shares characteristic sequence features with virulence factors of other phytopathogenic fungi. Because the secretory serine protease RsSLP from R. solani AG5 is similar to the virulence factors of other phytopathogenic fungi, its identification will be helpful in studies considering the roles of these proteases in pathogen virulence.
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Affiliation(s)
- Jing Ma
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Xiling Yang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wenyan Fan
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Changjiang Zhao
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wenshuai Li
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Di Zhou
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Shujun Jiang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
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6
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Falkenberg F, Bott M, Bongaerts J, Siegert P. Phylogenetic survey of the subtilase family and a data-mining-based search for new subtilisins from Bacillaceae. Front Microbiol 2022; 13:1017978. [PMID: 36225363 PMCID: PMC9549277 DOI: 10.3389/fmicb.2022.1017978] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
The subtilase family (S8), a member of the clan SB of serine proteases are ubiquitous in all kingdoms of life and fulfil different physiological functions. Subtilases are divided in several groups and especially subtilisins are of interest as they are used in various industrial sectors. Therefore, we searched for new subtilisin sequences of the family Bacillaceae using a data mining approach. The obtained 1,400 sequences were phylogenetically classified in the context of the subtilase family. This required an updated comprehensive overview of the different groups within this family. To fill this gap, we conducted a phylogenetic survey of the S8 family with characterised holotypes derived from the MEROPS database. The analysis revealed the presence of eight previously uncharacterised groups and 13 subgroups within the S8 family. The sequences that emerged from the data mining with the set filter parameters were mainly assigned to the subtilisin subgroups of true subtilisins, high-alkaline subtilisins, and phylogenetically intermediate subtilisins and represent an excellent source for new subtilisin candidates.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
- *Correspondence: Petra Siegert,
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7
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Sapkota S, Catching KE, Raymer PL, Martinez-Espinoza AD, Bahri BA. New Approaches to an Old Problem: Dollar Spot of Turfgrass. PHYTOPATHOLOGY 2022; 112:469-480. [PMID: 34406790 DOI: 10.1094/phyto-11-20-0505-rvw] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dollar spot, caused by fungal pathogens Clarireedia spp. (formerly Sclerotinia homoeocarpa), is the most common and widely distributed disease of turfgrass worldwide. It can drastically reduce the quality of turfgrass species and affect their aesthetic value and playability. Management of dollar spot typically includes a costly program of multiple application of fungicides within a growing season. Consequently, there have been reported cases of fungicide resistance in populations of Clarireedia spp. Host resistance could be an important component of dollar spot management; however, this approach has been hampered by the lack of sources of resistance because nearly all known warm- and cool-season turfgrass species are susceptible. With the recent advancement in genome sequencing technologies, studies on pathogen genomics and host-pathogen interactions are emerging with the hope of revealing candidate resistance genes in turfgrass and genes for virulence and pathogenicity in Clarireedia spp. Large-scale screening of turfgrass germplasm and quantitative trait locus (QTL) analysis for dollar spot resistance are important for resistance breeding, but only a handful of such studies have been conducted to date. This review summarizes currently available information on the dollar spot pathosystem, taxonomy, pathogen genomics, host-pathogen interaction, genetics of resistance, and QTL mapping and also provides some thoughts for future research prospects to better manage this disease.
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Affiliation(s)
- Suraj Sapkota
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA 30223
| | - Katherine E Catching
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA 30223
| | - Paul L Raymer
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA 30223
- Department of Crop and Soil Science, University of Georgia, Griffin, GA 30223
| | | | - Bochra A Bahri
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA 30223
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Zimmann N, Rada P, Žárský V, Smutná T, Záhonová K, Dacks J, Harant K, Hrdý I, Tachezy J. Proteomic Analysis of Trichomonas vaginalis Phagolysosome, Lysosomal Targeting, and Unconventional Secretion of Cysteine Peptidases. Mol Cell Proteomics 2022; 21:100174. [PMID: 34763061 PMCID: PMC8717582 DOI: 10.1016/j.mcpro.2021.100174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022] Open
Abstract
The lysosome represents a central degradative compartment of eukaryote cells, yet little is known about the biogenesis and function of this organelle in parasitic protists. Whereas the mannose 6-phosphate (M6P)-dependent system is dominant for lysosomal targeting in metazoans, oligosaccharide-independent sorting has been reported in other eukaryotes. In this study, we investigated the phagolysosomal proteome of the human parasite Trichomonas vaginalis, its protein targeting and the involvement of lysosomes in hydrolase secretion. The organelles were purified using Percoll and OptiPrep gradient centrifugation and a novel purification protocol based on the phagocytosis of lactoferrin-covered magnetic nanoparticles. The analysis resulted in a lysosomal proteome of 462 proteins, which were sorted into 21 classes. Hydrolases represented the largest functional class and included proteases, lipases, phosphatases, and glycosidases. Identification of a large set of proteins involved in vesicular trafficking (80) and turnover of actin cytoskeleton rearrangement (29) indicate a dynamic phagolysosomal compartment. Several cysteine proteases such as TvCP2 were previously shown to be secreted. Our experiments showed that secretion of TvCP2 was strongly inhibited by chloroquine, which increases intralysosomal pH, thus indicating that TvCP2 secretion occurs through lysosomes rather than the classical secretory pathway. Unexpectedly, we identified divergent homologues of the M6P receptor TvMPR in the phagolysosomal proteome, although T. vaginalis lacks enzymes for M6P formation. To test whether oligosaccharides are involved in lysosomal targeting, we selected the lysosome-resident cysteine protease CLCP, which possesses two glycosylation sites. Mutation of any of the sites redirected CLCP to the secretory pathway. Similarly, the introduction of glycosylation sites to secreted β-amylase redirected this protein to lysosomes. Thus, unlike other parasitic protists, T. vaginalis seems to utilize glycosylation as a recognition marker for lysosomal hydrolases. Our findings provide the first insight into the complexity of T. vaginalis phagolysosomes, their biogenesis, and role in the unconventional secretion of cysteine peptidases.
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Affiliation(s)
- Nadine Zimmann
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tamara Smutná
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Joel Dacks
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karel Harant
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
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9
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Burchacka E, Pięta P, Łupicka-Słowik A. Recent advances in fungal serine protease inhibitors. Biomed Pharmacother 2021; 146:112523. [PMID: 34902742 DOI: 10.1016/j.biopha.2021.112523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
Four types of antifungal drugs are available that include inhibitors of ergosterol synthesis, of fungal RNA biosynthesis, and of cell wall biosynthesis as well as physiochemical regulators of fungal membrane sterols. Increasing resistance to antifungal drugs can severely limit treatment options of fungal nail infections, vaginal candidiasis, ringworm, blastomycosis, histoplasmosis, and Candida infections of the mouth, throat, and esophagus, among other infections. Development of strategies focused on new fungicides can effectively help tackle troublesome fungal diseases. The virulence and optimal growth of fungi depend on various extracellular secreted factors, among which proteases, such as serine proteases, are of particular interest. A specific extracellular proteolytic system enables fungi to survive and penetrate the tissues. Given the role of fungal proteases in infection, any molecule capable of selectively and specifically inhibiting their activity can lead to the development of potential drugs. Owing to their specific mode of action, fungal protease inhibitors can avoid fungal resistance observed with currently available treatments. Although fungal secreted proteases have been extensively studied as potential virulence factors, our understanding of the substrate specificity of such proteases remains poor. In this review, we summarize the recent advances in the design and development of specific serine protease inhibitors and provide a brief history of the compounds that inhibit fungal serine protease activity.
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Affiliation(s)
- E Burchacka
- Faculty of Chemistry, Department of Organic and Medicinal Chemistry, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St, 50-370 Wrocław, Poland.
| | - P Pięta
- Department of Bionic and Medical Experimental Biology, Poznań University of Medical Sciences, Parkowa 2 St, 60-775 Poznań, Poland
| | - A Łupicka-Słowik
- Faculty of Chemistry, Department of Organic and Medicinal Chemistry, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St, 50-370 Wrocław, Poland
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Šečić E, Zanini S, Wibberg D, Jelonek L, Busche T, Kalinowski J, Nasfi S, Thielmann J, Imani J, Steinbrenner J, Kogel KH. A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis. BMC Biol 2021; 19:171. [PMID: 34429124 PMCID: PMC8385953 DOI: 10.1186/s12915-021-01104-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silvia Zanini
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, 35392, Giessen, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Sabrine Nasfi
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jennifer Thielmann
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jens Steinbrenner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
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11
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Gao BJ, Mou YN, Tong SM, Ying SH, Feng MG. Subtilisin-like Pr1 proteases marking the evolution of pathogenicity in a wide-spectrum insect-pathogenic fungus. Virulence 2021; 11:365-380. [PMID: 32253991 PMCID: PMC7199741 DOI: 10.1080/21505594.2020.1749487] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Subtilisin-like Pr1 proteases of insect-pathogenic fungi are a large family of extracellular cuticle-degrading enzymes that presumably determine a capability of hyphal invasion into insect hemocoel through normal cuticle infection, but remain poorly understood although often considered as virulence factors for genetic improvement of fungal potential against pests. Here, we report that not all of 11 Pr1 family members necessarily function in Beauveria bassiana, an ancient wide-spectrum pathogen evolved insect pathogenicity ~200 million years ago. These Pr1 proteases are phylogenetically similar to or distinct from 11 homologues (Pr1A–K) early named in Metarhizium anisopliae complex, a young entomopathogen lineage undergoing molecular evolution toward Pr1 diversification, and hence renamed Pr1A1/A2, Pr1B1–B3, Pr1 C, Pr1F1–F4,4 and Pr1 G, respectively. Multiple analyses of all single gene-deleted and rescued mutants led to the recognition of five conserved members (Pr1C, Pr1G, Pr1A2, Pr1B1, and Pr1B2) contributing significantly to the fungal pathogenicity to insect. The conserved Pr1 proteases were proven to function only in cuticle degradation, individually contribute 19–29% to virulence, but play no role in post-infection cellular events critical for fungal killing action. Six other Pr1 proteases were not functional at all in either cuticle degradation during host infection or virulence-related cellular events post-infection. Therefore, only the five conserved proteases are collectively required for, and hence mark evolution of, insect pathogenicity in B. bassiana. These findings provide the first referable base for insight into the evolution of Pr1 family members in different lineages of fungal insect pathogens.
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Affiliation(s)
- Ben-Jie Gao
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ya-Ni Mou
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sen-Miao Tong
- College of Agricultural and Food Science, Zhejiang A and F University, Lin'an, Zhejiang, China
| | - Sheng-Hua Ying
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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12
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Muturi SM, Muthui LW, Njogu PM, Onguso JM, Wachira FN, Opiyo SO, Pelle R. Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PLoS One 2021; 16:e0244755. [PMID: 33395690 PMCID: PMC7781671 DOI: 10.1371/journal.pone.0244755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022] Open
Abstract
The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.
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Affiliation(s)
- Samuel Mwangangi Muturi
- Department of Biological Sciences, University of Eldoret, Eldoret, Kenya
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Lucy Wangui Muthui
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Paul Mwangi Njogu
- Institute for Energy and Environmental Technology, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Justus Mong’are Onguso
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | | | - Stephen Obol Opiyo
- OARDC, Molecular and Cellular Imaging Center-Columbus, Ohio State University, Columbus, Ohio, United States of America
- The University of Sacread Heart, Gulu, Uganda
| | - Roger Pelle
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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13
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Kim HM, Jeong SG, Choi IS, Yang JE, Lee KH, Kim J, Kim JC, Kim JS, Park HW. Mechanisms of Insecticidal Action of Metarhizium anisopliae on Adult Japanese Pine Sawyer Beetles ( Monochamus alternatus). ACS OMEGA 2020; 5:25312-25318. [PMID: 33043210 PMCID: PMC7542838 DOI: 10.1021/acsomega.0c03585] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/14/2020] [Indexed: 05/31/2023]
Abstract
Pine wilt disease, caused by Bursaphelenchus xylophilus (pine wood nematode), leads to severe environmental and economic damage. Here, we report the results of experiments on the biological control of pine wilt disease through termination of the insect vector of the nematode and the mechanism of the insecticidal action of Metarhizium anisopliae JEF-279 against Monochamus alternatus (Japanese pine sawyer). A combined treatment with a fungal conidia suspension and a fungal protease-containing culture filtrate caused 75.8% mortality of the insect vector. Additionally, the presence of destruxins was confirmed in the dead Japanese pine sawyer adults, and half of the 10 protein spots in proteomic analysis were identified as an actin related to muscle contraction. Based on proteomic and microscopic analyses, the infection cycle of the Japanese pine sawyer by M. anisopliae JEF-279 was inferred to proceed in the following sequence: (1) host adhesion and germination, (2) epicuticle degradation, (3) growth as blastospore, (4) killing by various fungal toxins (insecticidal metabolites), (5) immune response as defense mechanism, and (6) hyphal extrusion and conidiation. Consequently, the combined fungal conidia suspension and protease-containing culture filtrate treatment may be applied as an insecticidal agent, and flaccid paralysis is likely a major mechanism underlying the insecticidal action of M. anisopliae JEF-279 on host insects.
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Affiliation(s)
- Ho Myeong Kim
- R&D
Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - Seul-Gi Jeong
- R&D
Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - In Seong Choi
- R&D
Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - Jung Eun Yang
- R&D
Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - Kwang Ho Lee
- Center
for Research Facilities, Chonnam National
University, Gwangju 61186, Republic of Korea
| | - Junheon Kim
- National
Institute of Forest Science, Seoul 02455, Republic
of Korea
| | - Jong Cheol Kim
- Department
of Agricultural Biology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea
| | - Jae Su Kim
- Department
of Agricultural Biology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea
| | - Hae Woong Park
- R&D
Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
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14
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Zhang Y, Li S, Li H, Wang R, Zhang KQ, Xu J. Fungi-Nematode Interactions: Diversity, Ecology, and Biocontrol Prospects in Agriculture. J Fungi (Basel) 2020; 6:E206. [PMID: 33020457 PMCID: PMC7711821 DOI: 10.3390/jof6040206] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 01/27/2023] Open
Abstract
Fungi and nematodes are among the most abundant organisms in soil habitats. They provide essential ecosystem services and play crucial roles for maintaining the stability of food-webs and for facilitating nutrient cycling. As two of the very abundant groups of organisms, fungi and nematodes interact with each other in multiple ways. Here in this review, we provide a broad framework of interactions between fungi and nematodes with an emphasis on those that impact crops and agriculture ecosystems. We describe the diversity and evolution of fungi that closely interact with nematodes, including food fungi for nematodes as well as fungi that feed on nematodes. Among the nematophagous fungi, those that produce specialized nematode-trapping devices are especially interesting, and a great deal is known about their diversity, evolution, and molecular mechanisms of interactions with nematodes. Some of the fungi and nematodes are significant pathogens and pests to crops. We summarize the ecological and molecular mechanisms identified so far that impact, either directly or indirectly, the interactions among phytopathogenic fungi, phytopathogenic nematodes, and crop plants. The potential applications of our understanding to controlling phytophagous nematodes and soilborne fungal pathogens in agricultural fields are discussed.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
| | - Shuoshuo Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Ruirui Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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15
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Wang L, Li Y, Jin X, Liu L, Dai X, Liu Y, Zhao L, Zheng P, Wang X, Liu Y, Lin D, Qin Y. Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development. Commun Biol 2020; 3:500. [PMID: 32913289 PMCID: PMC7483743 DOI: 10.1038/s42003-020-01235-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/12/2020] [Indexed: 11/12/2022] Open
Abstract
Proper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific transcriptomic profiles. Pairwise comparisons and weighted gene co-expression network analysis successfully identified ovule-, stamen-, petal- and fruit-specific modules as well as hub genes involved in ovule, fruit and petal development. In situ hybridization confirmed the enriched expression of six genes in developing ovules and stamens. Mutant characterization and complementation analysis revealed the important role of the subtilase gene AcSBT1.8 in petal development. This work provides an important genomic resource for functional analysis of pineapple floral organ growth and fruit development and sheds light on molecular networks underlying pineapple reproductive organ growth.
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Affiliation(s)
- Lulu Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xingyue Jin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liping Liu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaozhuan Dai
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanhui Liu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lihua Zhao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ping Zheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China
| | - Yeqiang Liu
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China
| | - Deshu Lin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Qin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China.
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16
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Xu L, Wang H, Zhang C, Wang J, Chen A, Chen Y, Ma Z. System-wide characterization of subtilases reveals that subtilisin-like protease FgPrb1 of Fusarium graminearum regulates fungal development and virulence. Fungal Genet Biol 2020; 144:103449. [PMID: 32890707 DOI: 10.1016/j.fgb.2020.103449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/30/2022]
Abstract
Subtilases represent the second largest subfamily of serine proteases, and are important for various biological processes. However, the biological function of subtilases has not been systematically characterized in plant pathogens. In present study, 32 subtilases were identified in the genome of wheat scab fungus Fusarium graminearum, a devastating cereal plant pathogen. Deletion mutants of each subtilase were obtained and functionally characterized. Among them, the deletion of FgPrb1 resulted in greatly reduced virulence of F. graminearum. The regulatory mechanisms of FgPrb1 in virulence were investigated in details. Our results showed that the loss of FgPrb1 led to defects in deoxynivalenol (DON) production, responses to environmental stimuli, and lipid metabolism. Additionally, we found that FgPrb1 was involved in autophagy regulation. Taken together, the systematic functional characterization of subtilases showed that the FgPrb1 of F. graminearum is critical for plant infection by regulating multiple different cellular processes.
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Affiliation(s)
- Luona Xu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Chengqi Zhang
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Jinli Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Ahai Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China.
| | - Yun Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
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17
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The Subtilisin-Like Protease Bcser2 Affects the Sclerotial Formation, Conidiation and Virulence of Botrytis cinerea. Int J Mol Sci 2020; 21:ijms21020603. [PMID: 31963451 PMCID: PMC7013506 DOI: 10.3390/ijms21020603] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
Botrytis cinerea, a ubiquitous necrotrophic plant-pathogenic fungus, is responsible for grey mold and rot disease in a very wide range of plant species. Subtilisin-like proteases (or subtilases) are a very diverse family of serine proteases present in many organisms and are reported to have a broad spectrum of biological functions. Here, we identified two genes encoding subtilisin-like proteases (Bcser1 and Bcser2) in the genome of B. cinerea, both of which contain an inhibitor I9 domain and a peptidase S8 domain. The expression levels of Bcser1 and Bcser2 increased during the sclerotial forming stage, as well as during a later stage of hyphal infection on Arabidopsis thaliana leaves, but the up-regulation of Bcser1 was significantly higher than that of Bcser2. Interestingly, deletion of Bcser1 had no effect on the fungal development or virulence of B. cinerea. However, deletion of Bcser2 or double deletion of Bcser1 and Bcser2 severely impaired the hyphal growth, sclerotial formation and conidiation of B. cinerea. We also found that ∆Bcser2 and ∆Bcser1/2 could not form complete infection cushions and then lost the ability to infect intact plant leaves of Arabidopsis and tomato but could infect wounded plant tissues. Taken together, our results indicate that the subtilisin-like protease Bcser2 is crucial for the sclerotial formation, conidiation, and virulence of B. cinerea.
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18
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Moonjely S, Zhang X, Fang W, Bidochka MJ. Metarhizium robertsii ammonium permeases (MepC and Mep2) contribute to rhizoplane colonization and modulates the transfer of insect derived nitrogen to plants. PLoS One 2019; 14:e0223718. [PMID: 31618269 PMCID: PMC6795453 DOI: 10.1371/journal.pone.0223718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022] Open
Abstract
The endophytic insect pathogenic fungi (EIPF) Metarhizium promotes plant growth through symbiotic association and the transfer of insect-derived nitrogen. However, little is known about the genes involved in this association and the transfer of nitrogen. In this study, we assessed the involvement of six Metarhizium robertsii genes in endophytic, rhizoplane and rhizospheric colonization with barley roots. Two ammonium permeases (MepC and Mep2) and a urease, were selected since homologous genes in arbuscular mycorrhizal fungi were reported to play a pivotal role in nitrogen mobilization during plant root colonization. Three other genes were selected on the basis on RNA-Seq data that showed high expression levels on bean roots, and these encoded a hydrophobin (Hyd3), a subtilisin-like serine protease (Pr1A) and a hypothetical protein. The root colonization assays revealed that the deletion of urease, hydrophobin, subtilisin-like serine protease and hypothetical protein genes had no impact on endophytic, rhizoplane and rhizospheric colonization at 10 or 20 days. However, the deletion of MepC resulted in significantly increased rhizoplane colonization at 10 days whereas ΔMep2 showed increased rhizoplane colonization at 20 days. In addition, the nitrogen transporter mutants also showed significantly higher 15N incorporation of insect derived nitrogen in barley leaves in the presence of nutrients. Insect pathogenesis assay revealed that disruption of MepC, Mep2, urease did not reduce virulence toward insects. The enhanced rhizoplane colonization of ΔMep2 and ΔMepC and insect derived nitrogen transfer to plant hosts suggests the role of MepC and Mep2 in Metarhizium-plant symbiosis.
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Affiliation(s)
- Soumya Moonjely
- Department of Biological Sciences, Brock University, St. Catharines, ON Canada
| | - Xing Zhang
- Institute of Microbiology, Zhejiang University, Hangzhou, China
| | - Weiguo Fang
- Institute of Microbiology, Zhejiang University, Hangzhou, China
| | - Michael J Bidochka
- Department of Biological Sciences, Brock University, St. Catharines, ON Canada
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19
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Genome sequence of Isaria javanica and comparative genome analysis insights into family S53 peptidase evolution in fungal entomopathogens. Appl Microbiol Biotechnol 2019; 103:7111-7128. [PMID: 31273397 DOI: 10.1007/s00253-019-09997-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/18/2019] [Accepted: 06/22/2019] [Indexed: 12/17/2022]
Abstract
The fungus Isaria javanica is an important entomopathogen that parasitizes various insects and is effective for pest control. In this study, we sequenced and assembled the genomes (IJ1G and IJ2G) of two I. javanica strains isolated from different insects. The genomes were approximately 35 Mb in size with 11,441 and 11,143 protein-coding genes, respectively. Using a phylogenomic approach, we evaluated genome evolution across five entomopathogenic fungi in Cordycipitaceae. By comparative genome analysis, it was found that family S53 serine peptidases were expanded in Cordycipitaceae entomopathogens, particularly in I. javanica. Gene duplication events were identified based on phylogenetic relationships inferred from 82 S53 peptidases within six entomopathogenic fungal genomes. Moreover, we found that carbohydrate-active enzymes and proteinases were the largest secretory protein groups encoded in the I. javanica genome, especially chitinases (GH18), serine and aspartic peptidases (S53, S08, S10, A01). Pathogenesis-related genes and genes for bacterial-like toxins and secondary metabolites were also identified. By comparative transcriptome analysis, differentially expressed genes in response to insect nutrients (in vitro) were identified. Moreover, most S53 peptidases were detected to be significantly upregulated during the initial fungal infection process in insects (in vivo) by RT-qPCR. Our results provide new clues about understanding evolution of pathogenic proteases and may suggest that abundant S53 peptidases in the I. javanica genome may contribute to its effective parasitism on various insects.
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20
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Andreis FC, Schrank A, Thompson CE. Molecular evolution of Pr1 proteases depicts ongoing diversification in Metarhizium spp. Mol Genet Genomics 2019; 294:901-917. [DOI: 10.1007/s00438-019-01546-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
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21
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Iqbal M, Dubey M, Gudmundsson M, Viketoft M, Jensen DF, Karlsson M. Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea. BMC Evol Biol 2018; 18:171. [PMID: 30445903 PMCID: PMC6240243 DOI: 10.1186/s12862-018-1291-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Background The ascomycete fungus Clonostachys rosea (order Hypocreales) can control several important plant diseases caused by plant pathogenic fungi and nematodes. Subtilisin-like serine proteases are considered to play an important role in pathogenesis in entomopathogenic, mycoparasitic, and nematophagous fungi used for biological control. In this study, we analysed the evolutionary histories of protease gene families, and investigated sequence divergence and regulation of serine protease genes in C. rosea. Results Proteases of selected hypocrealean fungal species were classified into families based on the MEROPS peptidase database. The highest number of protease genes (590) was found in Fusarium solani, followed by C. rosea with 576 genes. Analysis of gene family evolution identified non-random changes in gene copy numbers in the five serine protease gene families S1A, S8A, S9X, S12 and S33. Four families, S1A, S8A, S9X, and S33, displayed gene gains in C. rosea. A gene-tree / species-tree reconciliation analysis of the S8A family revealed that the gene copy number increase in C. rosea was primarily associated with the S08.054 (proteinase K) subgroup. In addition, regulatory and predicted structural differences, including twelve sites evolving under positive selection, among eighteen C. rosea S8A serine protease paralog genes were also observed. The C. rosea S8A serine protease gene prs6 was induced during interaction with the plant pathogenic species F. graminearum. Conclusions Non-random increases in S8A, S9X and S33 serine protease gene numbers in the mycoparasitic species C. rosea, Trichoderma atroviride and T. virens suggests an involvement in fungal-fungal interactions. Regulatory and predicted structural differences between C. rosea S8A paralogs indicate that functional diversification is driving the observed increase in gene copy numbers. The induction of prs6 expression in C. rosea during confrontation with F. graminearum suggests an involvement of the corresponding protease in fungal-fungal interactions. The results pinpoint the importance of serine proteases for ecological niche adaptation in C. rosea, including a potential role in the mycoparasitic attack on fungal prey. Electronic supplementary material The online version of this article (10.1186/s12862-018-1291-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mudassir Iqbal
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
| | - Maria Viketoft
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, SE-75007, Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
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22
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Krishnan P, Ma X, McDonald BA, Brunner PC. Widespread signatures of selection for secreted peptidases in a fungal plant pathogen. BMC Evol Biol 2018; 18:7. [PMID: 29368587 PMCID: PMC5784588 DOI: 10.1186/s12862-018-1123-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungal plant pathogens secrete a large arsenal of hydrolytic enzymes during the course of infection, including peptidases. Secreted peptidases have been extensively studied for their role as effectors. In this study, we combined transcriptomics, comparative genomics and evolutionary analyses to investigate all 39 secreted peptidases in the fungal wheat pathogen Zymoseptoria tritici and its close relatives Z. pseudotritici and Z. ardabiliae. RESULTS RNA-seq data revealed that a majority of the secreted peptidases displayed differential transcription during the course of Z. tritici infection, indicative of specialization for different stages in the life cycle. Evolutionary analyses detected widespread evidence of adaptive evolution acting on at least 28 of the peptidases. A few peptidases displayed lineage-specific rates of molecular evolution, suggesting altered selection pressure in Z. tritici following host specialization on domesticated wheat. The peptidases belonging to MEROPS families A1 and G1 emerged as a particularly interesting group that may play key roles in host-pathogen co-evolution, host adaptation and pathogenicity. Sister genes in the A1 and G1 families showed accelerated substitution rates after gene duplications. CONCLUSIONS These results suggest widespread evolution of secreted peptidases leading to novel gene functions, consistent with predicted models of "escape from adaptive conflict" and "neo-functionalization". Our analyses identified candidate genes worthy of functional analyses that may encode effector functions, for example by suppressing plant defenses during the biotrophic phase of infection.
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Affiliation(s)
- Parvathy Krishnan
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Patrick C Brunner
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland.
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23
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Wang R, Dong L, He R, Wang Q, Chen Y, Qu L, Zhang YA. Comparative genomic analyses reveal the features for adaptation to nematodes in fungi. DNA Res 2018; 25:4791394. [PMID: 29315395 PMCID: PMC6014366 DOI: 10.1093/dnares/dsx053] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/06/2017] [Indexed: 12/20/2022] Open
Abstract
Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application.
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Affiliation(s)
- Ruizhen Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Botany, Beijing Botanical Garden, Beijing 100093, China
| | - Leiming Dong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Ran He
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Botany, Beijing Botanical Garden, Beijing 100093, China
| | - Qinghua Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yuequ Chen
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Forestry Resources Protection Institute, Jilin Provincial Academy of Forestry Sciences, Changchun 130031, China
| | - Liangjian Qu
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yong-An Zhang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
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Lysøe E, Dees MW, Brurberg MB. A Three-Way Transcriptomic Interaction Study of a Biocontrol Agent (Clonostachys rosea), a Fungal Pathogen (Helminthosporium solani), and a Potato Host (Solanum tuberosum). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:646-655. [PMID: 28585451 DOI: 10.1094/mpmi-03-17-0062-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Helminthosporium solani causes silver scurf, which affects the quality of potato. The biocontrol agent Clonostachys rosea greatly limited the severity of silver scurf symptoms and amount of H. solani genomic DNA in laboratory experiments. Transcriptomic analysis during interaction showed that H. solani gene expression was highly reduced when coinoculated with the biocontrol agent C. rosea, whereas gene expression of C. rosea was clearly boosted as a response to the pathogen. The most notable upregulated C. rosea genes were those encoding proteins involved in cellular response to oxidative stress, proteases, G-protein signaling, and the methyltransferase LaeA. The most notable potato response to both fungi was downregulation of defense-related genes and mitogen-activated protein kinase kinase kinases. At a later stage, this shifted, and most potato defense genes were turned on, especially those involved in terpenoid biosynthesis when H. solani was present. Some biocontrol-activated defense-related genes in potato were upregulated during early interaction with C. rosea alone that were not triggered by H. solani alone. Our results indicate that the reductions of silver scurf using C. rosea are probably due to a combination of mechanisms, including mycoparasitism, biocontrol-activated stimulation of plant defense mechanisms, microbial competition for nutrients, space, and antibiosis.
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Affiliation(s)
- Erik Lysøe
- 1 Norwegian Institute of Bioeconomy Research, Division of Biotechnology and Plant Health, Høgskoleveien 7, 1430 Ås, Norway; and
| | - Merete W Dees
- 1 Norwegian Institute of Bioeconomy Research, Division of Biotechnology and Plant Health, Høgskoleveien 7, 1430 Ås, Norway; and
| | - May Bente Brurberg
- 1 Norwegian Institute of Bioeconomy Research, Division of Biotechnology and Plant Health, Høgskoleveien 7, 1430 Ås, Norway; and
- 2 Norwegian University of Life Sciences, Department of Plant Sciences, 1432 Ås, Norway
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25
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Wang Y, Song J, Marquez-Lago TT, Leier A, Li C, Lithgow T, Webb GI, Shen HB. Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites. Sci Rep 2017; 7:5755. [PMID: 28720874 PMCID: PMC5515926 DOI: 10.1038/s41598-017-06219-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/08/2017] [Indexed: 11/24/2022] Open
Abstract
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8. To fill this gap, we propose a new knowledge-transfer computational framework which effectively utilizes the hidden shared knowledge from some MMP types to enhance predictions of other, distinct target substrate-cleavage sites. Our computational framework uses support vector machines combined with transfer machine learning and feature selection. To demonstrate the value of the model, we extracted a variety of substrate sequence-derived features and compared the performance of our method using both 5-fold cross-validation and independent tests. The results show that our transfer-learning-based method provides a robust performance, which is at least comparable to traditional feature-selection methods for prediction of MMP-2, -3, -7, -8, -9 and -12 substrate-cleavage sites on independent tests. The results also demonstrate that our proposed computational framework provides a useful alternative for the characterization of sequence-level determinants of MMP-substrate specificity.
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Affiliation(s)
- Yanan Wang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jiangning Song
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana T Marquez-Lago
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - André Leier
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Chen Li
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
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26
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Li J, Gu F, Wu R, Yang J, Zhang KQ. Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi. Sci Rep 2017; 7:45456. [PMID: 28358043 PMCID: PMC5371821 DOI: 10.1038/srep45456] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/28/2017] [Indexed: 01/10/2023] Open
Abstract
Subtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal kingdom. Our comparative genomic analyses of the subtilase superfamily indicated that extensive gene duplications, losses and functional diversifications have occurred in fungi, and that the four families of subtilase enzymes in fungi, including proteinase K-like, Pyrolisin, kexin and S53, have distinct evolutionary histories which may have facilitated the adaptation of fungi to a broad array of life strategies. Our study provides new insights into the evolution of the subtilase superfamily in fungi and expands our understanding of the evolution of fungi with different lifestyles.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Fei Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Runian Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - JinKui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
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27
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Varshney D, Jaiswar A, Adholeya A, Prasad P. Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales. BMC Evol Biol 2016; 16:220. [PMID: 27756202 PMCID: PMC5069783 DOI: 10.1186/s12862-016-0793-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 10/07/2016] [Indexed: 11/15/2022] Open
Abstract
Background Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales. Results A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales. Conclusions Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0793-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deepti Varshney
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India
| | - Akanksha Jaiswar
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India
| | - Alok Adholeya
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India
| | - Pushplata Prasad
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India.
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Moonjely S, Barelli L, Bidochka MJ. Insect Pathogenic Fungi as Endophytes. ADVANCES IN GENETICS 2016; 94:107-35. [PMID: 27131324 DOI: 10.1016/bs.adgen.2015.12.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this chapter, we explore some of the evolutionary, ecological, molecular genetics, and applied aspects of a subset of insect pathogenic fungi that also have a lifestyle as endophytes and we term endophytic insect pathogenic fungi (EIPF). We focus particularly on Metarhizium spp. and Beauveria bassiana as EIPF. The discussion of the evolution of EIPF challenges a view that these fungi were first and foremost insect pathogens that eventually evolved to colonize plants. Phylogenetic evidence shows that the lineages of EIPF are most closely related to grass endophytes that diverged c. 100MYA. We discuss the relationship between genes involved in "insect pathogenesis" and those involved in "endophytism" and provide examples of genes with potential importance in lifestyle transitions toward insect pathogenicity. That is, some genes for insect pathogenesis may have been coopted from genes involved in endophytic colonization. Other genes may be multifunctional and serve in both lifestyle capacities. The interactions of EIPF with their host plants are discussed in some detail. The genetic basis for rhizospheric competence, plant communication, and nutrient exchange is examined and we highlight, with examples, the benefits of EIPF to plants, and the potential reservoir of secondary metabolites hidden within these beneficial symbioses.
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Affiliation(s)
- S Moonjely
- Brock University, St. Catharines, ON, Canada
| | - L Barelli
- Brock University, St. Catharines, ON, Canada
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29
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Prasad P, Varshney D, Adholeya A. Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum. BMC Genomics 2015; 16:1004. [PMID: 26607873 PMCID: PMC4658809 DOI: 10.1186/s12864-015-2229-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/18/2015] [Indexed: 01/11/2023] Open
Abstract
Background The fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes. This research article consists of genomic annotation of the first draft of whole genome sequence of P. lilacinum. The study aims to decipher the putative genetic components of the fungus involved in nematode pathogenesis by performing comparative genomic analysis with nine closely related fungal species in Hypocreales. Results de novo genomic assembly was done and a total of 301 scaffolds were constructed for P. lilacinum genomic DNA. By employing structural genome prediction models, 13, 266 genes coding for proteins were predicted in the genome. Approximately 73 % of the predicted genes were functionally annotated using Blastp, InterProScan and Gene Ontology. A 14.7 % fraction of the predicted genes shared significant homology with genes in the Pathogen Host Interactions (PHI) database. The phylogenomic analysis carried out using maximum likelihood RAxML algorithm provided insight into the evolutionary relationship of P. lilacinum. In congruence with other closely related species in the Hypocreales namely, Metarhizium spp., Pochonia chlamydosporia, Cordyceps militaris, Trichoderma reesei and Fusarium spp., P. lilacinum has large gene sets coding for G-protein coupled receptors (GPCRs), proteases, glycoside hydrolases and carbohydrate esterases that are required for degradation of nematode-egg shell components. Screening of the genome by Antibiotics & Secondary Metabolite Analysis Shell (AntiSMASH) pipeline indicated that the genome potentially codes for a variety of secondary metabolites, possibly required for adaptation to heterogeneous lifestyles reported for P. lilacinum. Significant up-regulation of subtilisin-like serine protease genes in presence of nematode eggs in quantitative real-time analyses suggested potential role of serine proteases in nematode pathogenesis. Conclusions The data offer a better understanding of Purpureocillium lilacinum genome and will enhance our understanding on the molecular mechanism involved in nematophagy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2229-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pushplata Prasad
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari,Faridabad Road, Gurgaon, Haryana, 122 001, India.
| | - Deepti Varshney
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari,Faridabad Road, Gurgaon, Haryana, 122 001, India.
| | - Alok Adholeya
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari,Faridabad Road, Gurgaon, Haryana, 122 001, India.
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30
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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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Huang Y, Busk PK, Herbst FA, Lange L. Genome and secretome analyses provide insights into keratin decomposition by novel proteases from the non-pathogenic fungus Onygena corvina. Appl Microbiol Biotechnol 2015; 99:9635-49. [PMID: 26177915 PMCID: PMC4628079 DOI: 10.1007/s00253-015-6805-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/24/2015] [Accepted: 06/29/2015] [Indexed: 11/26/2022]
Abstract
Poultry processing plants and slaughterhouses produce huge quantities of feathers and hair/bristle waste annually. These keratinaceous wastes are highly resistant to degradation. Onygena corvina, a non-pathogenic fungus, grows specifically on feathers, hooves, horn, and hair in nature. Hence, the proteases secreted by O. corvina are interesting in view of their potential relevance for industrial decomposition of keratinaceous wastes. We sequenced and assembled the genome of O. corvina and used a method called peptide pattern recognition to identify 73 different proteases. Comparative genome analysis of proteases in keratin-degrading and non-keratin-degrading fungi indicated that 18 putative secreted proteases from four protease families (M36, M35, M43, and S8) may be responsible for keratin decomposition. Twelve of the 18 predicted protease genes could be amplified from O. corvina grown on keratinaceous materials and were transformed into Pichia pastoris. One of the recombinant proteases belonging to the S8 family showed high keratin-degrading activity. Furthermore, 29 different proteases were identified by mass spectrometry in the culture broth of O. corvina grown on feathers and bristle. The culture broth was fractionated by ion exchange chromatography to isolate active fractions with five novel proteases belonging to three protease families (S8, M28, and M3). Enzyme blends composed of three of these five proteases, one from each family, showed high degree of degradation of keratin in vitro. A blend of novel proteases, such as those we discovered, could possibly find a use for degrading keratinaceous wastes and provide proteins, peptides, and amino acids as valuable ingredients for animal feed.
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Affiliation(s)
- Yuhong Huang
- Department of Chemistry and Bioscience, Aalborg University Copenhagen, 2450, Copenhagen, SV, Denmark
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800, Kgs. Lyngby, Denmark
| | - Peter Kamp Busk
- Department of Chemistry and Bioscience, Aalborg University Copenhagen, 2450, Copenhagen, SV, Denmark
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800, Kgs. Lyngby, Denmark
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg East, Denmark
| | - Lene Lange
- Department of Chemistry and Bioscience, Aalborg University Copenhagen, 2450, Copenhagen, SV, Denmark.
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800, Kgs. Lyngby, Denmark.
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Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome. Proc Natl Acad Sci U S A 2015; 112:7478-83. [PMID: 25944934 DOI: 10.1073/pnas.1507082112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pseudogymnoascus destructans is the causative agent of white-nose syndrome, a disease that has caused the deaths of millions of bats in North America. This psychrophilic fungus proliferates at low temperatures and targets hibernating bats, resulting in their premature arousal from stupor with catastrophic consequences. Despite the impact of white-nose syndrome, little is known about the fungus itself or how it infects its mammalian host. P. destructans is not amenable to genetic manipulation, and therefore understanding the proteins involved in infection requires alternative approaches. Here, we identify hydrolytic enzymes secreted by P. destructans, and use a novel and unbiased substrate profiling technique to define active peptidases. These experiments revealed that endopeptidases are the major proteolytic activities secreted by P. destructans, and that collagen, the major structural protein in mammals, is actively degraded by the secretome. A serine endopeptidase, hereby-named Destructin-1, was subsequently identified, and a recombinant form overexpressed and purified. Biochemical analysis of Destructin-1 showed that it mediated collagen degradation, and a potent inhibitor of peptidase activity was identified. Treatment of P. destructans-conditioned media with this antagonist blocked collagen degradation and facilitated the detection of additional secreted proteolytic activities, including aminopeptidases and carboxypeptidases. These results provide molecular insights into the secretome of P. destructans, and identify serine endopeptidases that have the clear potential to facilitate tissue invasion and pathogenesis in the mammalian host.
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Li J, Zou C, Xu J, Ji X, Niu X, Yang J, Huang X, Zhang KQ. Molecular mechanisms of nematode-nematophagous microbe interactions: basis for biological control of plant-parasitic nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:67-95. [PMID: 25938277 DOI: 10.1146/annurev-phyto-080614-120336] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant-parasitic nematodes cause significant damage to a broad range of vegetables and agricultural crops throughout the world. As the natural enemies of nematodes, nematophagous microorganisms offer a promising approach to control the nematode pests. Some of these microorganisms produce traps to capture and kill the worms from the outside. Others act as internal parasites to produce toxins and virulence factors to kill the nematodes from within. Understanding the molecular basis of microbe-nematode interactions provides crucial insights for developing effective biological control agents against plant-parasitic nematodes. Here, we review recent advances in our understanding of the interactions between nematodes and nematophagous microorganisms, with a focus on the molecular mechanisms by which nematophagous microorganisms infect nematodes and on the nematode defense against pathogenic attacks. We conclude by discussing several key areas for future research and development, including potential approaches to apply our recent understandings to develop effective biocontrol strategies.
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Affiliation(s)
- Juan Li
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, China;
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Wang X, Guan T, Zhang L, Li H. Cloning of a serine protease gene from the nematophagous fungus Esteya vermicola and expressed activity of the recombinant enzyme against Bursaphelenchus xylophilus. NEMATOLOGY 2015. [DOI: 10.1163/15685411-00002924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A serine protease geneEvspwas cloned from the nematophagous fungusEsteya vermicolawith strong virulence againstBursaphelenchus xylophilus. The full-length cDNA ofEvspcontains 2280 nucleotides with a 1656 bp ORF encoding a protein with 551 amino acids. The genomicEvspincludes two exons (396 bp and 1260 bp) separated by an intron (207 bp). There is only one copy ofEvspgene in the fungal genome. The deduced amino acids sequences ofEvspshowed highly homology with the catalytic domains in subtilisin serine proteases. Phylogenetic analyses based on the protein sequences revealed thatE. vermicolais separated from nematode-trapping fungi but close to other nematophagous and entomopathogenic fungi. The recombinant serine protease rEvsp was induced inEscherichia coliwith expression vector pET28a(+). The tests of protease and nematicidal activities for the purified and refolded rEvsp indicated it is possibly involved in the fungal infection process againstB. xylophilus.
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Affiliation(s)
- Xuan Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Tinglong Guan
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Long Zhang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Hongmei Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, P.R. China
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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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Page AP, Stepek G, Winter AD, Pertab D. Enzymology of the nematode cuticle: A potential drug target? INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2014; 4:133-41. [PMID: 25057463 PMCID: PMC4095051 DOI: 10.1016/j.ijpddr.2014.05.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 11/16/2022]
Abstract
All nematodes possess an external structure known as the cuticle, which is crucial for their development and survival. This structure is composed primarily of collagen, which is secreted from the underlying hypodermal cells. Extensive studies using the free-living nematode Caenorhabditis elegans demonstrate that formation of the cuticle requires the activity of an extensive range of enzymes. Enzymes are required both pre-secretion, for synthesis of component proteins such as collagen, and post-secretion, for removal of the previous developmental stage cuticle, in a process known as moulting or exsheathment. The excretion/secretion products of numerous parasitic nematodes contain metallo-, serine and cysteine proteases, and these proteases are conserved across the nematode phylum and many are involved in the moulting/exsheathment process. This review highlights the enzymes required for cuticle formation, with a focus on the post-secretion moulting events. Where orthologues of the C. elegans enzymes have been identified in parasitic nematodes these may represent novel candidate targets for future drug/vaccine development.
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Affiliation(s)
- Antony P Page
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Gillian Stepek
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Alan D Winter
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - David Pertab
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
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Kooij PW, Rogowska-Wrzesinska A, Hoffmann D, Roepstorff P, Boomsma JJ, Schiøtt M. Leucoagaricus gongylophorus uses leaf-cutting ants to vector proteolytic enzymes towards new plant substrate. THE ISME JOURNAL 2014; 8:1032-40. [PMID: 24401858 PMCID: PMC3996701 DOI: 10.1038/ismej.2013.231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 11/09/2022]
Abstract
The mutualism between leaf-cutting ants and their fungal symbionts revolves around processing and inoculation of fresh leaf pulp in underground fungus gardens, mediated by ant fecal fluid deposited on the newly added plant substrate. As herbivorous feeding often implies that growth is nitrogen limited, we cloned and sequenced six fungal proteases found in the fecal fluid of the leaf-cutting ant Acromyrmex echinatior and identified them as two metalloendoproteases, two serine proteases and two aspartic proteases. The metalloendoproteases and serine proteases showed significant activity in fecal fluid at pH values of 5-7, but the aspartic proteases were inactive across a pH range of 3-10. Protease activity disappeared when the ants were kept on a sugar water diet without fungus. Relative to normal mycelium, both metalloendoproteases, both serine proteases and one aspartic protease were upregulated in the gongylidia, specialized hyphal tips whose only known function is to provide food to the ants. These combined results indicate that the enzymes are derived from the ingested fungal tissues. We infer that the five proteases are likely to accelerate protein extraction from plant cells in the leaf pulp that the ants add to the fungus garden, but regulatory functions such as activation of proenzymes are also possible, particularly for the aspartic proteases that were present but without showing activity. The proteases had high sequence similarities to proteolytic enzymes of phytopathogenic fungi, consistent with previous indications of convergent evolution of decomposition enzymes in attine ant fungal symbionts and phytopathogenic fungi.
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Affiliation(s)
- Pepijn W Kooij
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Adelina Rogowska-Wrzesinska
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Daniel Hoffmann
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Roepstorff
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Nematicidal enzymes from microorganisms and their applications. Appl Microbiol Biotechnol 2013; 97:7081-95. [DOI: 10.1007/s00253-013-5045-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/05/2013] [Accepted: 06/07/2013] [Indexed: 01/07/2023]
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Junwei W, Qingling M, Jun Q, Weisheng W, Shuangqing C, Jianxun L, Chunguang Z, Chuangfu C. The recombinant serine proteaseXAoz1ofArthrobotrys oligosporaexhibits potent nematicidal activity againstCaenorhabditis elegansandHaemonchus contortus. FEMS Microbiol Lett 2013; 344:53-9. [DOI: 10.1111/1574-6968.12154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/24/2013] [Accepted: 04/04/2013] [Indexed: 01/09/2023] Open
Affiliation(s)
- Wang Junwei
- Key Lab of Preventive Veterinary; College of Animal Science and Technology; Shihezi University; Shihezi; Xinjiang; China
| | - Meng Qingling
- Key Lab of Preventive Veterinary; College of Animal Science and Technology; Shihezi University; Shihezi; Xinjiang; China
| | - Qiao Jun
- Key Lab of Preventive Veterinary; College of Animal Science and Technology; Shihezi University; Shihezi; Xinjiang; China
| | - Wang Weisheng
- Key Lab of Preventive Veterinary; College of Animal Science and Technology; Shihezi University; Shihezi; Xinjiang; China
| | - Chen Shuangqing
- Key Lab of Preventive Veterinary; College of Animal Science and Technology; Shihezi University; Shihezi; Xinjiang; China
| | - Luo Jianxun
- State Key Lab of Veterinary Etiological Biology; Key Laboratory of Veterinary Parasitology of Gansu Province; Lanzhou Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Lanzhou; Gansu; China
| | - Zhao Chunguang
- Key Lab of Preventive Veterinary; College of Animal Science and Technology; Shihezi University; Shihezi; Xinjiang; China
| | - Chen Chuangfu
- Key Lab of Preventive Veterinary; College of Animal Science and Technology; Shihezi University; Shihezi; Xinjiang; China
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Yang J, Yu Y, Li J, Zhu W, Geng Z, Jiang D, Wang Y, Zhang KQ. Characterization and functional analyses of the chitinase-encoding genes in the nematode-trapping fungus Arthrobotrys oligospora. Arch Microbiol 2013; 195:453-62. [PMID: 23661195 DOI: 10.1007/s00203-013-0894-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/08/2013] [Accepted: 04/11/2013] [Indexed: 01/17/2023]
Abstract
Nematode-trapping fungi can secrete many extracellular hydrolytic enzymes such as serine proteases and chitinases to digest and penetrate nematode/egg-cuticles. However, little is known about the structure and function of chitinases in these fungi. In this study, 16 ORFs encoding putative chitinases, which all belong to glycoside hydrolase (GH) family 18, were identified from the Arthrobotrys oligospora genome. Bioinformatics analyses showed that these 16 putative chitinases differ in their functional domains, molecular weights and pI. Phylogenetic analysis grouped these A. oligospora chitinases into four clades: clades I, II, III and IV, respectively, including an A. oligospora-specific subclade (Clade IV-B) that contained high-molecular weight chitinases (≥100 kDa). Transcriptional analysis of A. oligospora chitinases suggested that the expression of most chitinases was repressed by carbon starvation, and all chitinases were up-regulated under nitrogen starvation. However, chitinase AO-190 was up-regulated under carbon and/or nitrogen starvation. Moreover, several chitinases (such as AO-59, AO-190 and AO-801) were up-regulated in the presence of chitinous substrates or a plant pathogenic fungus, indicating that they could play a role in biocontrol applications of A. oligospora. Our results provided a basis for further understanding the functions, diversities and evolutionary relationships between chitinase genes in nematode-trapping fungi.
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Affiliation(s)
- Jinkui Yang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, People's Republic of China.
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41
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Orshinsky AM, Hu J, Opiyo SO, Reddyvari-Channarayappa V, Mitchell TK, Boehm MJ. RNA-Seq analysis of the Sclerotinia homoeocarpa--creeping bentgrass pathosystem. PLoS One 2012; 7:e41150. [PMID: 22905098 PMCID: PMC3414504 DOI: 10.1371/journal.pone.0041150] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/18/2012] [Indexed: 11/25/2022] Open
Abstract
Sclerotinia homoeocarpa causes dollar spot disease, the predominate disease on highly-maintained turfgrass. Currently, there are major gaps in our understanding of the molecular interactions between S. homoeocarpa and creeping bentgrass. In this study, 454 sequencing technology was used in the de novo assembly of S. homoeocarpa and creeping bentgrass transcriptomes. Transcript sequence data obtained using Illumina's first generation sequencing-by-synthesis (SBS) were mapped to the transcriptome assemblies to estimate transcript representation in different SBS libraries. SBS libraries included a S. homoeocarpa culture control, a creeping bentgrass uninoculated control, and a library for creeping bentgrass inoculated with S. homoeocarpa and incubated for 96 h. A Fisher's exact test was performed to determine transcripts that were significantly different during creeping bentgrass infection with S. homoeocarpa. Fungal transcripts of interest included glycosyl hydrolases, proteases, and ABC transporters. Of particular interest were the large number of glycosyl hydrolase transcripts that target a wide range of plant cell wall compounds, corroborating the suggested wide host range and saprophytic abilities of S. homoeocarpa. Several of the multidrug resistance ABC transporters may be important for resistance to both fungicides and plant defense compounds. Creeping bentgrass transcripts of interest included germins, ubiquitin transcripts involved in proteasome degradation, and cinnamoyl reductase, which is involved in lignin production. This analysis provides an extensive overview of the S. homoeocarpa-turfgrass pathosystem and provides a starting point for the characterization of potential virulence factors and host defense responses. In particular, determination of important host defense responses may assist in the development of highly resistant creeping bentgrass varieties.
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Affiliation(s)
- Angela M Orshinsky
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, United States of America.
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Yang E, Xu L, Yang Y, Zhang X, Xiang M, Wang C, An Z, Liu X. Origin and evolution of carnivorism in the Ascomycota (fungi). Proc Natl Acad Sci U S A 2012; 109:10960-5. [PMID: 22715289 PMCID: PMC3390824 DOI: 10.1073/pnas.1120915109] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550-600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian-Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198-208 Mya, which was within the time frame of the Triassic-Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous-Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.
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Affiliation(s)
- Ence Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingling Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Biotechnology, Xi'an University of Arts and Science, Xi'an 710065, China
| | - Ying Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, 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 200032, China; and
| | - Zhiqiang An
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Larriba E, Martín-Nieto J, Lopez-Llorca LV. Gene cloning, molecular modeling, and phylogenetics of serine protease P32 and serine carboxypeptidase SCP1 from nematophagous fungi Pochonia rubescens and Pochonia chlamydosporia. Can J Microbiol 2012; 58:815-27. [PMID: 22690687 DOI: 10.1139/w2012-054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The fungi Pochonia chlamydosporia and Pochonia rubescens are parasites of nematode eggs and thus are biocontrol agents of nematodes. Proteolytic enzymes such as the S8 proteases VCP1 and P32, secreted during the pathogenesis of nematode eggs, are major virulence factors in these fungi. Recently, expression of these enzymes and of SCP1, a new putative S10 carboxypeptidase, was detected during endophytic colonization of barley roots by these fungi. In our study, we cloned the genomic and mRNA sequences encoding P32 from P. rubescens and SCP1 from P. chlamydosporia. P32 showed a high homology with the serine proteases Pr1A from the entomopathogenic fungus Metarhizium anisopliae and VCP1 from P. chlamydosporia (86% and 76% identity, respectively). However, the catalytic pocket of P32 showed differences in the amino acids of the substrate-recognition sites compared with the catalytic pockets of Pr1A and VCP1 proteases. Phylogenetic analysis of P32 suggests a common ancestor with protease Pr1A. SCP1 displays the characteristic features of a member of the S10 family of serine proteases. Phylogenetic comparisons show that SCP1 and other carboxypeptidases from filamentous fungi have an origin different from that of yeast vacuolar serine carboxypeptidases. Understanding protease genes from nematophagous fungi is crucial for enhancing the biocontrol potential of these organisms.
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Affiliation(s)
- Eduardo Larriba
- Department of Marine Sciences and Applied Biology, University of Alicante, Spain.
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Yang J, Wang L, Ji X, Feng Y, Li X, Zou C, Xu J, Ren Y, Mi Q, Wu J, Liu S, Liu Y, Huang X, Wang H, Niu X, Li J, Liang L, Luo Y, Ji K, Zhou W, Yu Z, Li G, Liu Y, Li L, Qiao M, Feng L, Zhang KQ. Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation. PLoS Pathog 2011; 7:e1002179. [PMID: 21909256 PMCID: PMC3164635 DOI: 10.1371/journal.ppat.1002179] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 06/09/2011] [Indexed: 12/18/2022] Open
Abstract
Nematode-trapping fungi are "carnivorous" and attack their hosts using specialized trapping devices. The morphological development of these traps is the key indicator of their switch from saprophytic to predacious lifestyles. Here, the genome of the nematode-trapping fungus Arthrobotrys oligospora Fres. (ATCC24927) was reported. The genome contains 40.07 Mb assembled sequence with 11,479 predicted genes. Comparative analysis showed that A. oligospora shared many more genes with pathogenic fungi than with non-pathogenic fungi. Specifically, compared to several sequenced ascomycete fungi, the A. oligospora genome has a larger number of pathogenicity-related genes in the subtilisin, cellulase, cellobiohydrolase, and pectinesterase gene families. Searching against the pathogen-host interaction gene database identified 398 homologous genes involved in pathogenicity in other fungi. The analysis of repetitive sequences provided evidence for repeat-induced point mutations in A. oligospora. Proteomic and quantitative PCR (qPCR) analyses revealed that 90 genes were significantly up-regulated at the early stage of trap-formation by nematode extracts and most of these genes were involved in translation, amino acid metabolism, carbohydrate metabolism, cell wall and membrane biogenesis. Based on the combined genomic, proteomic and qPCR data, a model for the formation of nematode trapping device in this fungus was proposed. In this model, multiple fungal signal transduction pathways are activated by its nematode prey to further regulate downstream genes associated with diverse cellular processes such as energy metabolism, biosynthesis of the cell wall and adhesive proteins, cell division, glycerol accumulation and peroxisome biogenesis. This study will facilitate the identification of pathogenicity-related genes and provide a broad foundation for understanding the molecular and evolutionary mechanisms underlying fungi-nematodes interactions.
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Affiliation(s)
- Jinkui Yang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Xinglai Ji
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Yun Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Xiaomin Li
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Chenggang Zou
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Yan Ren
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Qili Mi
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
- Yunnan Academy of Tobacco Science, Kunming, P. R. China
| | - Junli Wu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Shuqun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Yu Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Xiaowei Huang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Haiyan Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
| | - Xuemei Niu
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Juan Li
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Lianming Liang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Yanlu Luo
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Kaifang Ji
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Wei Zhou
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Zefen Yu
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Guohong Li
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Yajun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Lei Li
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Min Qiao
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. 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, Kunming, P. R. China
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Liang L, Liu S, Yang J, Meng Z, Lei L, Zhang K. Comparison of homology models and crystal structures of cuticle-degrading proteases from nematophagous fungi: structural basis of nematicidal activity. FASEB J 2011; 25:1894-902. [PMID: 21350115 DOI: 10.1096/fj.10-175653] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cuticle-degrading proteases secreted by nematophagous fungi can degrade nematode cuticle during infection. Alkaline proteases from nematode-parasitic fungi show stronger nematicidal activity in vitro than neutral proteases from nematode-trapping fungi. Sequence alignment of these proteases revealed that the active-site residues were much conserved. Disulfide bridges in alkaline proteases not only contribute to the thermal stability of enzyme structure but also increase the flexibility of S1 and S4 pockets located at the substrate-binding site. Molecular electrostatic potential surfaces of these proteases change gradually from negative to positive while arranging in the order from neutral to alkaline proteases, possibly contributing to the distinct extent of substrate (nematode cuticle) attraction by proteases. The differences in flexibility of substrate-binding site and in electrostatic surface potential distribution between neutral and alkaline cuticle-degrading proteases are associated with the changes of their catalytic activities and nematicidal activities with fungal species. Our results indicate that nematode-parasitic and nematode-trapping fungi have evolved for distinct adaptation under selective pressure.
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Affiliation(s)
- Lianming Liang
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming 650091, China
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Yang J, Zhao X, Liang L, Xia Z, Lei L, Niu X, Zou C, Zhang KQ. Overexpression of a cuticle-degrading protease Ver112 increases the nematicidal activity of Paecilomyces lilacinus. Appl Microbiol Biotechnol 2010; 89:1895-903. [PMID: 21110018 DOI: 10.1007/s00253-010-3012-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 11/07/2010] [Accepted: 11/14/2010] [Indexed: 11/24/2022]
Abstract
Due to their ability to degrade the proteins in nematode cuticle, serine proteases play an important role in the pathogenicity of nematophagous fungi against nematodes. The serine protease Ver112 was identified from the nematophagous fungus Lecanicillium psalliotae capable of degrading the nematode cuticle and killing nematodes effectively. In this study, the gene ver112 was introduced into the commercial biocontrol fungal agent Paecilomyces lilacinus by the restriction enzyme-mediated integration transformation. Compared to the wild strain, the transformant P. lilacinus 112 showed significantly greater protease activity, with nematicidal activities increased by 79% and 96% to Panagrellus redivivus and Caenorhabditis elegans at the second day, respectively. The crude protein extract isolated from the culture filtrate of P. lilacinus 112 also showed 20-25% higher nematicidal activity than that of the wild-type strain. Reverse transcription PCR results showed that the expression of gene ver112 in P. lilacinus 112 was correlated to protease activity of the culture filtrate. Our results demonstrated the first successful transfer of a virulence gene from one nematophagous fungus to another nematophagous fungus, and improved the pathogenicity of the recipient fungus against pest nematodes.
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Affiliation(s)
- Jinkui Yang
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, People's Republic of China
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