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Wang Y, Tu Y, Chen X, Jiang H, Ren H, Lu Q, Wei C, Lv W. Didymellaceae species associated with tea plant ( Camelliasinensis) in China. MycoKeys 2024; 105:217-251. [PMID: 38846425 PMCID: PMC11153891 DOI: 10.3897/mycokeys.105.119536] [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: 02/04/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Tea plant is one of the most important commercial crops worldwide. The Didymellaceae fungi can cause leaf blight disease of tea plant. In this study, 240 isolates were isolated from tea plant leaves of 10 provinces in China. Combined with multi-locus (ITS, LSU, RPB2 and TUB2) phylogenetic analysis and morphological characteristics, these isolates were identified as 25 species of six genera in Didymellaceae, including 19 known species Didymellacoffeae-arabicae, D.pomorum, D.segeticola, D.sinensis, Epicoccumcatenisporum, E.dendrobii, E.draconis, E.italicum, E.latusicollum, E.mackenziei, E.oryzae, E.poaceicola, E.rosae, E.sorghinum, E.tobaicum, Neoascochytamortariensis, Paraboeremialitseae, Remotididymellaanemophila and Stagonosporopsiscaricae, of which 15 species were new record species and six novel species, named D.yunnanensis, E.anhuiense, E.jingdongense, E.puerense, N.yunnanensis and N.zhejiangensis. Amongst all isolates, D.segeticola was the most dominant species. Pathogenicity tests on tea plant leaves showed that E.anhuiense had the strongest virulence, while E.puerense had the weakest virulence. Besides, D.pomorum, D.yunnanensis, E.dendrobii, E.italicum, E.jingdongense, E.mackenziei, E.oryzae, E.rosae, E.tobaicum, N.mortariensis, N.yunnanensis, N.zhejiangensis and R.anemophila were non-pathogenic to the tea plant.
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Affiliation(s)
- Yuchun Wang
- College of Tea Science and Tea Culture, Zhejiang A & F University, Hangzhou 311300, Zhejiang, ChinaZhejiang A & F UniversityHangzhouChina
| | - Yiyi Tu
- College of Tea Science and Tea Culture, Zhejiang A & F University, Hangzhou 311300, Zhejiang, ChinaZhejiang A & F UniversityHangzhouChina
| | - Xueling Chen
- College of Tea Science and Tea Culture, Zhejiang A & F University, Hangzhou 311300, Zhejiang, ChinaZhejiang A & F UniversityHangzhouChina
| | - Hong Jiang
- College of Tea Science and Tea Culture, Zhejiang A & F University, Hangzhou 311300, Zhejiang, ChinaZhejiang A & F UniversityHangzhouChina
| | - Hengze Ren
- College of Tea Science and Tea Culture, Zhejiang A & F University, Hangzhou 311300, Zhejiang, ChinaZhejiang A & F UniversityHangzhouChina
| | - Qinhua Lu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaInstitute of Sericulture and Tea, Zhejiang Academy of Agricultural SciencesHangzhouChina
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, ChinaAnhui Agricultural UniversityHefeiChina
| | - Wuyun Lv
- College of Tea Science and Tea Culture, Zhejiang A & F University, Hangzhou 311300, Zhejiang, ChinaZhejiang A & F UniversityHangzhouChina
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Naumann TA, Dowling NV, Price NPJ, Rose DR. In vitro functional analysis and in silico structural modelling of pathogen-secreted polyglycine hydrolases. Biochem Biophys Res Commun 2024; 706:149746. [PMID: 38461646 DOI: 10.1016/j.bbrc.2024.149746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Polyglycine hydrolases are fungal effectors composed of an N-domain with unique sequence and structure and a C-domain that resembles β-lactamases, with serine protease activity. These secreted fungal proteins cleave Gly-Gly bonds within a polyglycine sequence in corn ChitA chitinase. The polyglycine hydrolase N-domain (PND) function is unknown. In this manuscript we provide evidence that the PND does not directly participate in ChitA cleavage. In vitro analysis of site-directed mutants in conserved residues of the PND of polyglycine hydrolase Es-cmp did not specifically impair protease activity. Furthermore, in silico structural models of three ChitA-bound polyglycine hydrolases created by High Ambiguity Driven protein-protein DOCKing (HADDOCK) did not predict significant interactions between the PND and ChitA. Together these results suggest that the PND has another function. To determine what types of PND-containing proteins exist in nature we performed a computational analysis of Foldseek-identified PND-containing proteins. The analysis showed that proteins with PNDs are present throughout biology as either single domain proteins or fused to accessory domains that are diverse but are usually proteases or kinases.
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Affiliation(s)
- Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, USA.
| | - Nicole V Dowling
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Neil P J Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technologies Research Unit, 1815 N. University, Peoria, IL, 61604, USA
| | - David R Rose
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
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Dowling NV, Naumann TA, Price NPJ, Rose DR. Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model. Acta Crystallogr D Struct Biol 2023; 79:168-176. [PMID: 36762862 PMCID: PMC9912923 DOI: 10.1107/s2059798323000311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Polyglycine hydrolases (PGHs) are secreted fungal proteases that cleave the polyglycine linker of Zea mays ChitA, a defensive chitinase, thus overcoming one mechanism of plant resistance to infection. Despite their importance in agriculture, there has been no previous structural characterization of this family of proteases. The objective of this research was to investigate the proteolytic mechanism and other characteristics by structural and biochemical means. Here, the first atomic structure of a polyglycine hydrolase was identified. It was solved by X-ray crystallography using a RoseTTAFold model, taking advantage of recent technical advances in structure prediction. PGHs are composed of two domains: the N- and C-domains. The N-domain is a novel tertiary fold with an as-yet unknown function that is found across all kingdoms of life. The C-domain shares structural similarities with class C β-lactamases, including a common catalytic nucleophilic serine. In addition to insights into the PGH family and its relationship to β-lactamases, the results demonstrate the power of complementing experimental structure determination with new computational techniques.
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Affiliation(s)
- Nicole V. Dowling
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada,Correspondence e-mail:
| | - Todd A. Naumann
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 North University Street, Peoria, IL 61604, USA
| | - Neil P. J. Price
- Renewable Product Technology Research Unit, USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 North University Street, Peoria, IL 61604, USA
| | - David R. Rose
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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Semenova TA, Dunaevsky YE, Beljakova GA, Belozersky MA. Extracellular peptidases of insect-associated fungi and their possible use in biological control programs and as pathogenicity markers. Fungal Biol 2020; 124:65-72. [PMID: 31892378 DOI: 10.1016/j.funbio.2019.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 01/12/2023]
Abstract
This review deals with characteristics of peptidases of fungi whose life cycles are associated with insects to varying degrees. The review examines the characteristic features of the extracellular peptidases of entomopathogenic fungi, the dependence of the specificity of these peptidases on the ecological characteristics of the fungi, and the role of peptidases in the development of the pathogenesis. Data on the properties and physiological role of hydrolytic enzymes of symbiotic fungi in "fungal gardens" are also considered in detail. For the development of representations about mechanisms of control over populations of insect pests, special attention is given to analysis of possibilities of genetic engineering for the creation of entomopathogens with enhanced virulence. Clarification of the role of fungi and their secreted enzymes and careful environmental studies are still required to explain their significance in the composition of the biota and to ensure widespread adoption of these organisms as effective biological control agents. The systematization and comparative analysis of the existing data on extracellular peptidases of insect-associated fungi will help in the planning of further work and the search for markers of pathogenesis and symbiosis.
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Affiliation(s)
| | - Yakov E Dunaevsky
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
| | | | - Mikhail A Belozersky
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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Naumann TA, Bakota EL, Price NPJ. Recognition of corn defense chitinases by fungal polyglycine hydrolases. Protein Sci 2017; 26:1214-1223. [PMID: 28383143 DOI: 10.1002/pro.3175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/03/2017] [Accepted: 04/03/2017] [Indexed: 11/07/2022]
Abstract
Polyglycine hydrolases (PGH)s are secreted fungal endoproteases that cleave peptide bonds in the polyglycine interdomain linker of ChitA chitinase, an antifungal protein from domesticated corn (Zea mays ssp. mays). These target-specific endoproteases are unusual because they do not cut a specific peptide bond but select one of many Gly-Gly bonds within the polyglycine region. Some Gly-Gly bonds are cleaved frequently while others are never cleaved. Moreover, we have previously shown that PGHs from different fungal pathogens prefer to cleave different Gly-Gly peptide bonds. It is not understood how PGHs selectively cleave the ChitA linker, especially because its polyglycine structure lacks peptide sidechains. To gain insights into this process we synthesized several peptide analogs of ChitA to evaluate them as potential substrates and inhibitors of Es-cmp, a PGH from the plant pathogenic fungus Epicoccum sorghi. Our results showed that part of the PGH recognition site for substrate chitinases is adjacent to the polyglycine linker on the carboxy side. More specifically, four amino acid residues were implicated, each spaced four residues apart on an alpha helix. Moreover, analogous peptides with selective Gly->sarcosine (N-methylglycine) mutations or a specific Ser->Thr mutation retained inhibitor activity but were no longer cleaved by PGH. Additonally, our findings suggest that peptide analogs of ChitA that inhibit PGH activity could be used to strengthen plant defenses.
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Affiliation(s)
- Todd A Naumann
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604
| | - Erica L Bakota
- Renewable Product Technology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604
| | - Neil P J Price
- Functional Foods Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604
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Valueva TA, Zaichik BT, Kudryavtseva NN. Role of proteolytic enzymes in the interaction of phytopathogenic microorganisms with plants. BIOCHEMISTRY (MOSCOW) 2017; 81:1709-1718. [DOI: 10.1134/s0006297916130083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rawlings ND. Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation. Biochimie 2015; 122:5-30. [PMID: 26455268 PMCID: PMC4756867 DOI: 10.1016/j.biochi.2015.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/05/2015] [Indexed: 11/11/2022]
Abstract
One peptidase can usually be distinguished from another biochemically by its action on proteins, peptides and synthetic substrates. Since 1996, the MEROPS database (http://merops.sanger.ac.uk) has accumulated a collection of cleavages in substrates that now amounts to 66,615 cleavages. The total number of peptidases for which at least one cleavage is known is 1700 out of a total of 2457 different peptidases. This paper describes how the cleavages are obtained from the scientific literature, how they are annotated and how cleavages in peptides and proteins are cross-referenced to entries in the UniProt protein sequence database. The specificity profiles of 556 peptidases are shown for which ten or more substrate cleavages are known. However, it has been proposed that at least 40 cleavages in disparate proteins are required for specificity analysis to be meaningful, and only 163 peptidases (6.6%) fulfil this criterion. Also described are the various displays shown on the website to aid with the understanding of peptidase specificity, which are derived from the substrate cleavage collection. These displays include a logo, distribution matrix, and tables to summarize which amino acids or groups of amino acids are acceptable (or not acceptable) in each substrate binding pocket. For each protein substrate, there is a display to show how it is processed and degraded. Also described are tools on the website to help with the assessment of the physiological relevance of cleavages in a substrate. These tools rely on the hypothesis that a cleavage site that is conserved in orthologues is likely to be physiologically relevant, and alignments of substrate protein sequences are made utilizing the UniRef50 database, in which in each entry sequences are 50% or more identical. Conservation in this case means substitutions are permitted only if the amino acid is known to occupy the same substrate binding pocket from at least one other substrate cleaved by the same peptidase.
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Affiliation(s)
- Neil D Rawlings
- Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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Naumann TA, Naldrett MJ, Ward TJ, Price NPJ. Polyglycine hydrolases: Fungal β-lactamase-like endoproteases that cleave polyglycine regions within plant class IV chitinases. Protein Sci 2015; 24:1147-57. [PMID: 25966977 DOI: 10.1002/pro.2705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/23/2015] [Accepted: 04/26/2015] [Indexed: 11/11/2022]
Abstract
Polyglycine hydrolases are secreted fungal proteases that cleave glycine-glycine peptide bonds in the inter-domain linker region of specific plant defense chitinases. Previously, we reported the catalytic activity of polyglycine hydrolases from the phytopathogens Epicoccum sorghi (Es-cmp) and Cochliobolus carbonum (Bz-cmp). Here we report the identity of their encoding genes and the primary amino acid sequences of the proteins responsible for these activities. Peptides from a tryptic digest of Es-cmp were analyzed by LC-MS/MS and the spectra obtained were matched to a draft genome sequence of E. sorghi. From this analysis, a 642 amino acid protein containing a predicted β-lactamase catalytic region of 280 amino acids was identified. Heterologous strains of the yeast Pichia pastoris were created to express this protein and its homolog from C. carbonum from their cDNAs. Both strains produced recombinant proteins with polyglycine hydrolase activity as shown by SDS-PAGE and MALDI-MS based assays. Site directed mutagenesis was used to mutate the predicted catalytic serine of Es-cmp to glycine, resulting in loss of catalytic activity. BLAST searching of publicly available fungal genomes identified full-length homologous proteins in 11 other fungi of the class Dothideomycetes, and in three fungi of the related class Sordariomycetes while significant BLAST hits extended into the phylum Basidiomycota. Multiple sequence alignment led to the identification of a network of seven conserved tryptophans that surround the β-lactamase-like region. This is the first report of a predicted β-lactamase that is an endoprotease.
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Affiliation(s)
- Todd A Naumann
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agriculture Utilization Research, Peoria, Illinois, 61604
| | - Michael J Naldrett
- Proteomics and Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, Missouri, 63132
| | - Todd J Ward
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agriculture Utilization Research, Peoria, Illinois, 61604
| | - Neil P J Price
- Renewable Product Technology Research Unit, National Center for Agriculture Utilization Research, Peoria, Illinois, 61604
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Jashni MK, Mehrabi R, Collemare J, Mesarich CH, de Wit PJGM. The battle in the apoplast: further insights into the roles of proteases and their inhibitors in plant-pathogen interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:584. [PMID: 26284100 PMCID: PMC4522555 DOI: 10.3389/fpls.2015.00584] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/13/2015] [Indexed: 05/06/2023]
Abstract
Upon host penetration, fungal pathogens secrete a plethora of effectors to promote disease, including proteases that degrade plant antimicrobial proteins, and protease inhibitors (PIs) that inhibit plant proteases with antimicrobial activity. Conversely, plants secrete proteases and PIs to protect themselves against pathogens or to mediate recognition of pathogen proteases and PIs, which leads to induction of defense responses. Many examples of proteases and PIs mediating effector-triggered immunity in host plants have been reported in the literature, but little is known about their role in compromising basal defense responses induced by microbe-associated molecular patterns. Recently, several reports appeared in literature on secreted fungal proteases that modify or degrade pathogenesis-related proteins, including plant chitinases or PIs that compromise their activities. This prompted us to review the recent advances on proteases and PIs involved in fungal virulence and plant defense. Proteases and PIs from plants and their fungal pathogens play an important role in the arms race between plants and pathogens, which has resulted in co-evolutionary diversification and adaptation shaping pathogen lifestyles.
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Affiliation(s)
- Mansoor Karimi Jashni
- Laboratory of Phytopathology, Wageningen University and Research Centre, Wageningen, Netherlands
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
| | - Rahim Mehrabi
- Laboratory of Phytopathology, Wageningen University and Research Centre, Wageningen, Netherlands
- Cereal Research Department, Seed and Plant Improvement Institute, Karaj, Iran
| | - Jérôme Collemare
- Laboratory of Phytopathology, Wageningen University and Research Centre, Wageningen, Netherlands
- UMR1345, IRHS-INRA, Beaucouzé, France
| | - Carl H. Mesarich
- Laboratory of Phytopathology, Wageningen University and Research Centre, Wageningen, Netherlands
- Bioprotection Technologies, The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, New Zealand
| | - Pierre J. G. M. de Wit
- Laboratory of Phytopathology, Wageningen University and Research Centre, Wageningen, Netherlands
- *Correspondence: Pierre J. G. M. de Wit, Laboratory of Phytopathology, Wageningen University and Research Centre, Droevendaalsesteeg 9, Wageningen 6708 PB, Netherlands,
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