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Elsherbiny AS, Galal A, Ghoneem KM, Salahuddin NA. Graphene oxide-based nanocomposites for outstanding eco-friendly antifungal potential against tomato phytopathogens. BIOMATERIALS ADVANCES 2024; 160:213863. [PMID: 38642516 DOI: 10.1016/j.bioadv.2024.213863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 04/01/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
To obtain the collaborative antifungal potential of nanocomposites conjugated with graphene oxide (GO), a combination of GO with chitosan (CS/GO) and GO with chitosan (CS) and polyaniline (PANI/CS/GO) was carried out. The synthesized GO-nanocomposites were recognized by several techniques. Vanillin (Van.) and cinnamaldehyde (Cinn.) were loaded on the prepared nanocomposites as antioxidants through a batch adsorption process. In vitro release study of Van. and Cinn. from the nanocomposites was accomplished at pH 7 and 25°C. The antimicrobial activity of GO, CS/GO, and PANI/CS/GO was studied against tomato Fusarium oxysporum (FOL) and Pythium debaryanum (PYD) pathogens. The loaded ternary composite PANI/CS/GO exhibited the best percent of reduction against the two pathogens in vitro studies. The Greenhouse experiment revealed that seedlings' treatment by CS/GO/Van. and PANI/CS/GO/Van significantly lowered both disease index and disease incidence. The loaded CS/GO and PANI/CS/GO nanocomposites had a positive effect on lengthening shoots. Additionally, when CS/GO/Cinn., CS/GO/Van. and PANI/CS/GO/Van. were used, tomato seedlings' photosynthetic pigments dramatically increased as compared to infected control. The results show that these bio-nanocomposites can be an efficient, sustainable, nontoxic, eco-friendly, and residue-free approach for fighting fungal pathogens and improving plant growth.
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Affiliation(s)
- Abeer S Elsherbiny
- Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Alyaa Galal
- Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Khalid M Ghoneem
- Seed Pathology Research Department, Plant Pathology Research Institute, Agricultural Research Center (ID: 60019332), Giza 12112, Egypt
| | - Nehal A Salahuddin
- Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
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2
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Ayhan DH, Abbondante S, Martínez-Soto D, Milo S, Rickelton K, Sohrab V, Kotera S, Arie T, Marshall ME, Rocha MC, Haridas S, Grigoriev IV, Shlezinger N, Pearlman E, Ma LJ. The differential virulence of Fusarium strains causing corneal infections and plant diseases is associated with accessory chromosome composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595639. [PMID: 38826335 PMCID: PMC11142239 DOI: 10.1101/2024.05.23.595639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Fusarium oxysporum is a cross-kingdom pathogen. While some strains cause disseminated fusariosis and blinding corneal infections in humans, others are responsible for devastating vascular wilt diseases in plants. To better understand the distinct adaptations of F. oxysporum to animal or plant hosts, we conducted a comparative phenotypic and genetic analysis of two strains: MRL8996 (isolated from a keratitis patient) and Fol4287 (isolated from a wilted tomato [Solanum lycopersicum]). In vivo infection of mouse corneas and tomato plants revealed that, while both strains cause symptoms in both hosts, MRL8996 caused more severe corneal ulceration and perforation in mice, whereas Fol4287 induced more pronounced wilting symptoms in tomato. In vitro assays using abiotic stress treatments revealed that the human pathogen MRL8996 was better adapted to elevated temperatures, whereas the plant pathogen Fol4287 was more tolerant of osmotic and cell wall stresses. Both strains displayed broad resistance to antifungal treatment, with MRL8996 exhibiting the paradoxical effect of increased tolerance to higher concentrations of the antifungal caspofungin. We identified a set of accessory chromosomes (ACs) and protein-encoding genes with distinct transposon profiles and functions, respectively, between MRL8996 and Fol4287. Interestingly, ACs from both genomes also encode proteins with shared functions, such as chromatin remodeling and post-translational protein modifications. Our phenotypic assays and comparative genomics analyses lay the foundation for future studies correlating genotype with phenotype and for developing targeted antifungals for agricultural and clinical uses.
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Affiliation(s)
- Dilay Hazal Ayhan
- Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Serena Abbondante
- Physiology and Biophysics and Ophthalmology, University of California, Irvine, USA University of Massachusetts Amherst, Amherst, MA, USA
| | - Domingo Martínez-Soto
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Shira Milo
- Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Katherine Rickelton
- Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Vista Sohrab
- Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Shunsuke Kotera
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Michaela Ellen Marshall
- Physiology and Biophysics and Ophthalmology, University of California, Irvine, USA University of Massachusetts Amherst, Amherst, MA, USA
| | - Marina Campos Rocha
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Neta Shlezinger
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eric Pearlman
- Physiology and Biophysics and Ophthalmology, University of California, Irvine, USA University of Massachusetts Amherst, Amherst, MA, USA
| | - Li-Jun Ma
- Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA
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3
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Liang D, Jiang Y, Zhang Y, Mao C, Ma T, Zhang C. The Comparative Genomics of Botryosphaeriaceae Suggests Gene Families of Botryosphaeria dothidea Related to Pathogenicity on Chinese Hickory Tree. J Fungi (Basel) 2024; 10:299. [PMID: 38667970 PMCID: PMC11051394 DOI: 10.3390/jof10040299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Trunk canker poses a major threat to the production of Chinese hickory tree (Carya cathayensis Sarg.), which is primarily determined by Botryosphaeriaceae. In our previous work, we identified Botryosphaeria dothidea as the predominant pathogen of this disease. However, it is still unclear about corresponding gene families and mechanisms associated with B. dothidea's pathogenicity on Chinese hickory tree. Here, we present a comparative analysis of high-quality genome assemblies of Botryosphaeria dothidea and other isolated pathogens, showing highly syntenic relationships between B. dothidea and its closely related species and the conservative evolution of the Botryosphaeriaceae family. Higher GC contents were found in the genomes of B. dothidea and three other isolated pathogens (Botryshaeria cortices, Botryshaeria fabicerciana, and Botryshaeria qingyuanensis) compared to Macrophomina phaseolina, Neofusicoccum parvum, Diplodia corticola, and Lasiodiplodia theobromae. An investigation of genes specific to or expanded in B. dothidea revealed that one secreted glucanase, one orsellinic acid biosynthesis enzyme, and two MFS transporters positively regulated B. dothidea's pathogenicity. We also observed an overrepresentation of viral integrase like gene and heterokaryon incompatibility proteins in the B. dothidea's genome. In addition, we observed one LRR-domain-containing protein and two Sec-domain-containing proteins (Sec_1 and Sec_7) that underwent positive selection. This study will help to understand B. dothidea's pathogenicity and potential influence on the infection of Chinese hickory, which will help in the development of disease control and ensure the security of Chinese hickory production.
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Affiliation(s)
| | | | | | | | - Tianlin Ma
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
| | - Chuanqing Zhang
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
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4
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Kumakura N, Singkaravanit-Ogawa S, Gan P, Tsushima A, Ishihama N, Watanabe S, Seo M, Iwasaki S, Narusaka M, Narusaka Y, Takano Y, Shirasu K. Guanosine-specific single-stranded ribonuclease effectors of a phytopathogenic fungus potentiate host immune responses. THE NEW PHYTOLOGIST 2024; 242:170-191. [PMID: 38348532 DOI: 10.1111/nph.19582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/06/2024] [Indexed: 03/08/2024]
Abstract
Plants activate immunity upon recognition of pathogen-associated molecular patterns. Although phytopathogens have evolved a set of effector proteins to counteract plant immunity, some effectors are perceived by hosts and induce immune responses. Here, we show that two secreted ribonuclease effectors, SRN1 and SRN2, encoded in a phytopathogenic fungus, Colletotrichum orbiculare, induce cell death in a signal peptide- and catalytic residue-dependent manner, when transiently expressed in Nicotiana benthamiana. The pervasive presence of SRN genes across Colletotrichum species suggested the conserved roles. Using a transient gene expression system in cucumber (Cucumis sativus), an original host of C. orbiculare, we show that SRN1 and SRN2 potentiate host pattern-triggered immunity responses. Consistent with this, C. orbiculare SRN1 and SRN2 deletion mutants exhibited increased virulence on the host. In vitro analysis revealed that SRN1 specifically cleaves single-stranded RNAs at guanosine, leaving a 3'-end phosphate. Importantly, the potentiation of C. sativus responses by SRN1 and SRN2, present in the apoplast, depends on ribonuclease catalytic residues. We propose that the pathogen-derived apoplastic guanosine-specific single-stranded endoribonucleases lead to immunity potentiation in plants.
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Affiliation(s)
- Naoyoshi Kumakura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Pamela Gan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Ayako Tsushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Nobuaki Ishihama
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shunsuke Watanabe
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nakagami, Okinawa, 903-0213, Japan
| | - Shintaro Iwasaki
- RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mari Narusaka
- Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Research Institute for Biological Sciences, Kaga, Okayama, 716-1241, Japan
| | - Yoshihiro Narusaka
- Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Research Institute for Biological Sciences, Kaga, Okayama, 716-1241, Japan
| | - Yoshitaka Takano
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
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5
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Yu DS, Outram MA, Smith A, McCombe CL, Khambalkar PB, Rima SA, Sun X, Ma L, Ericsson DJ, Jones DA, Williams SJ. The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies. eLife 2024; 12:RP89280. [PMID: 38411527 PMCID: PMC10942635 DOI: 10.7554/elife.89280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein X-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire of Fol and show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate that Fol secretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding of Fol-tomato, and by extension plant-fungal interactions, which will assist in the development of novel control and engineering strategies to combat plant pathogens.
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Affiliation(s)
- Daniel S Yu
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Megan A Outram
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Ashley Smith
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Carl L McCombe
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Pravin B Khambalkar
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Sharmin A Rima
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Xizhe Sun
- Research School of Biology, The Australian National UniversityCanberraAustralia
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agriculture UniversityBaodingChina
| | - Lisong Ma
- Research School of Biology, The Australian National UniversityCanberraAustralia
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural UniversityBaodingChina
| | - Daniel J Ericsson
- Research School of Biology, The Australian National UniversityCanberraAustralia
- The Australian Nuclear Science and Technology Organisation, Australian SynchrotronClaytonAustralia
| | - David A Jones
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Simon J Williams
- Research School of Biology, The Australian National UniversityCanberraAustralia
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6
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Li J, Zhang D, Du Y, Song J, Li R, Dai X, Chen J, Li G, Liu Z. Genome Sequence Resource of Cladosporium velox Strain C4 Causing Cotton Boll Disease in Xinjiang, China. PLANT DISEASE 2023; 107:4010-4015. [PMID: 37368501 DOI: 10.1094/pdis-11-22-2694-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Cladosporium spp., as one of the largest and most heterogeneous genera of hyphomycetes, are widely distributed worldwide. This genus is usually adaptable to a wide variety of extreme environments. However, only 11 genomes of Cladosporium genus have been publicly released. From 2017, we found for the first time that Cladosporium velox could cause cotton boll disease and lead to stiffness and cracking boll in Xinjiang, China. Herein, we provide a high-quality reference genome for the C. velox strain C4 isolated from cotton boll in Xinjiang, China. The genome size and encoding gene number of the C. velox strain C4 and C. cucumerinum strain CCNX2, which was recently released and caused the cucumber scab, showed minor differences. This resource will contribute to future research that aims to elucidate the genetic basis of C. velox pathogenicity and could expand our knowledge of Cladosporium spp. genomic characteristics that will be valuable for the development of Cladosporium disease control measures.
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Affiliation(s)
- Jingwen Li
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Dandan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Yejuan Du
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jian Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Xiaofeng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jieyin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Guoying Li
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zheng Liu
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
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7
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Andika IB, Cao X, Kondo H, Sun L. The intriguing phenomenon of cross-kingdom infections of plant and insect viruses to fungi: Can other animal viruses also cross-infect fungi? PLoS Pathog 2023; 19:e1011726. [PMID: 37883353 PMCID: PMC10602238 DOI: 10.1371/journal.ppat.1011726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
Fungi are highly widespread and commonly colonize multicellular organisms that live in natural environments. Notably, studies on viruses infecting plant-associated fungi have revealed the interesting phenomenon of the cross-kingdom transmission of viruses and viroids from plants to fungi. This implies that fungi, in addition to absorbing water, nutrients, and other molecules from the host, can acquire intracellular parasites that reside in the host. These findings further suggest that fungi can serve as suitable alternative hosts for certain plant viruses and viroids. Given the frequent coinfection of fungi and viruses in humans/animals, the question of whether fungi can also acquire animal viruses and serve as their hosts is very intriguing. In fact, the transmission of viruses from insects to fungi has been observed. Furthermore, the common release of animal viruses into the extracellular space (viral shedding) could potentially facilitate their acquisition by fungi. Investigations of the cross-infection of animal viruses in fungi may provide new insights into the epidemiology of viral diseases in humans and animals.
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Affiliation(s)
- Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Agricultural University, Tai’an, China
- Shouguang International Vegetable Sci-tech Fair Management Service Center, Shouguang, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xianyang, China
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8
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Wu H, Wang L, Wang W, Shao Z, Jia X, Xiao H, Chen J. The secretory Candida effector Sce1 licenses fungal virulence by masking the immunogenic β-1,3-glucan and promoting apoptosis of the host cells. MLIFE 2023; 2:159-177. [PMID: 38817625 PMCID: PMC10989805 DOI: 10.1002/mlf2.12066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 06/01/2024]
Abstract
Candida albicans deploys a variety of mechanisms such as morphological switch and elicitor release to promote virulence. However, the intricate interactions between the fungus and the host remain poorly understood, and a comprehensive inventory of fungal virulence factors has yet to be established. In this study, we identified a C. albicans secretory effector protein Sce1, whose induction and secretion are associated with vagina-simulative conditions and chlamydospore formation. Sequence alignment showed that Sce1 belongs to a Pir family in C. albicans, which is conserved across several fungi and primarily characterized as a β-glucan binding protein in the Saccharomyces cerevisiae. Mechanically, Sce1 is primarily localized to the cell wall in a cleaved form as an alkali-labile β-1,3-glucan binding protein and plays a role in masking β-glucan in acidic environments and chlamydospores, a feature that might underline C. albicans' ability to evade host immunity. Further, a cleaved short form of Sce1 protein could be released into extracellular compartments and presented in bone marrow-derived macrophages infected with chlamydospores. This cleaved short form of Sce1 also demonstrated a unique ability to trigger the caspases-8/9-dependent apoptosis in various host cells. Correspondingly, genetic deletion of SCE1 led to dampened vaginal colonization of C. albicans and diminished fungal virulence during systemic infection. The discovery of Sce1 as a versatile virulence effector that executes at various compartments sheds light on the fungus-host interactions and C. albicans pathogenesis.
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Affiliation(s)
- Hongyu Wu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Li Wang
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Wenjuan Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Zhugui Shao
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Biomedical SciencesShandong UniversityJinanChina
| | - Xin‐Ming Jia
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Hui Xiao
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Jiangye Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
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9
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Ahmad A, Akram W, Wang R, Shahzadi I, Umer M, Yasin NA, Wu T. Pathogenicity factors of Phytophthora melonis revealed by comparative proteomics. JOURNAL OF PLANT INTERACTIONS 2022; 17:183-197. [DOI: 10.1080/17429145.2021.2014581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 06/16/2023]
Affiliation(s)
- Aqeel Ahmad
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
| | - Waheed Akram
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Rui Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
| | - Iqra Shahzadi
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Engineering Center of Natural Polymers-based Medical Materials, School of Resource and Environmental Science, Wuhan University, Wuhan, People’s Republic of China
| | - Muhammad Umer
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, People’s Republic of China
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
| | | | - Tingquan Wu
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
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10
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Transcription Factor VdCf2 Regulates Growth, Pathogenicity, and the Expression of a Putative Secondary Metabolism Gene Cluster in Verticillium dahliae. Appl Environ Microbiol 2022; 88:e0138522. [PMID: 36342142 PMCID: PMC9680623 DOI: 10.1128/aem.01385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Verticillium dahliae
is an important soilborne phytopathogen which can ruinously attack numerous host plants and cause significant economic losses. Transcription factors (TFs) were reported to be involved in various biological processes, such as hyphal growth and virulence of pathogenic fungi.
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11
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Ma Z, Huang Y, Zhang Z, Liu X, Xuan Y, Liu B, Gao Z. Comparative genomic analysis reveals cellulase plays an important role in the pathogenicity of Setosphaeria turcica f. sp. zeae. Front Microbiol 2022; 13:925355. [PMID: 35935234 PMCID: PMC9355644 DOI: 10.3389/fmicb.2022.925355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Setosphaeria turcica f. sp. zeae and S. turcica f. sp. sorghi, the two formae speciales of S. turcica, cause northern leaf blight disease of corn and sorghum, respectively, and often cause serious economic losses. They have obvious physiological differentiation and show complete host specificity. Host specificity is often closely related to pathogen virulence factors, including secreted protein effectors and secondary metabolites. Genomic sequencing can provide more information for understanding the virulence mechanisms of pathogens. However, the complete genomic sequence of S. turcica f. sp. sorghi has not yet been reported, and no comparative genomic information is available for the two formae speciales. In this study, S. turcica f. sp. zeae was predicted to have fewer secreted proteins, pathogen-host interaction (PHI) genes and carbohydrate-active enzymes (CAZys) than S. turcica f. sp. sorghi. Fifteen and 20 polyketide synthase (PKS) genes were identified in S. turcica f. sp. zeae and S. turcica f. sp. sorghi, respectively, which maintained high homology. There were eight functionally annotated effector protein-encoding genes specifically in S. turcica f. sp. zeae, among which the encoding gene StCEL2 of endo-1, 4-β-D-glucanase, an important component of cellulase, was significantly up-regulated during the interaction process. Finally, gluconolactone inhibited cellulase activity and decreased infection rate and pathogenicity, which indicates that cellulase is essential for maintaining virulence. These findings demonstrate that cellulase plays an important role in the pathogenicity of S. turcica f. sp. zeae. Our results also provide a theoretical basis for future research on the molecular mechanisms underlying the pathogenicity of the two formae speciales and for identifying any associated genes.
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Affiliation(s)
- Zhoujie Ma
- Institute of Plant Immunology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yufei Huang
- Institute of Plant Immunology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Zhaoran Zhang
- Institute of Plant Immunology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xiaodi Liu
- Institute of Plant Immunology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuanhu Xuan
- Institute of Plant Immunology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Bo Liu
- College of Life Sciences, Yan’an University, Yan’an, China
- *Correspondence: Bo Liu,
| | - Zenggui Gao
- Institute of Plant Immunology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- Zenggui Gao,
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Afordoanyi DM, Diabankana RGC, Akosah YA, Validov SZ. Are formae speciales pathogens really host specific? A broadened host specificity in Fusarium oxysporum f.sp. radicis-cucumerinum. Braz J Microbiol 2022; 53:1745-1759. [PMID: 35841534 PMCID: PMC9679123 DOI: 10.1007/s42770-022-00793-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023] Open
Abstract
Phytopathogenic strains of Fusarium oxysporum Schlecht exhibit clear host specificity, which appears to be a persistent characteristic and a dependable base for the forma specialis system of these pathogens. Here, we report an altered host specificity of the F. oxysporum f.sp. radicis-cucumerinum strain V03-2 g (Forc V03-2 g) - a causative agent of cucumber root-rot, the clonal derivates of which acquired the ability to infect tomato plants. Since the clonal derivates of Forc V03-2 g with transformed host specificity preserved their ability to parasitize on cucumber plants, the changes that occurred can be classified as broadening of host specificity. To our knowledge, this is the first observation of pathogenicity changes in formae speciales of F. oxysporum. The clonal derivates acquired could be used to trace genetic determinants of the host specificity of phytopathogenic strains of F. oxysporum.
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Affiliation(s)
- Daniel Mawuena Afordoanyi
- Laboratory of Molecular Genetics and Microbiological Methods, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia ,Department of Animal Husbandry and Veterinary Medicine, Tatar Scientific Research Institute of Agrochemistry and Soil Science, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | | | - Yaw Abayie Akosah
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York City, USA
| | - Shamil Zavdatovich Validov
- Laboratory of Molecular Genetics and Microbiological Methods, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
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Comparative genomic analysis reveals cellulase plays an important role in the pathogenicity of Setosphaeria turcica f. sp. zeae. Fungal Biol 2022. [DOI: 10.1016/j.funbio.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Jeon J, Kim KT, Choi J, Cheong K, Ko J, Choi G, Lee H, Lee GW, Park SY, Kim S, Kim ST, Min CW, Kang S, Lee YH. Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection. RNA Biol 2022; 19:373-385. [PMID: 35311472 PMCID: PMC8942408 DOI: 10.1080/15476286.2022.2043040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae, a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host infection stages. We identified 4,270 AS isoforms derived from 2,413 genes, including 499 genes presumably regulated by infection-specific AS. AS appears to increase during infection, with 32.7% of the AS isoforms being produced during infection but absent in mycelia. Analysis of the isoforms observed at each infection stage showed that 636 AS isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant isoforms were predicted to encode regulatory proteins such as transcription factors and phospho-transferases. We also identified the genes encoding distinct proteins via AS and confirmed the translation of some isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice-M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice infection.
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Affiliation(s)
- Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, Korea
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
| | - Jaeho Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
| | - Hyunjun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | | | - Sook-Young Park
- Department of Agricultural Life Science, Sunchon National University, Suncheon, Korea
| | - Seongbeom Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
- Life and Energy Convergence Research Institute, Pusan National University, Miryang, Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA USA
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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15
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Verticillium dahliae CFEM proteins manipulate host immunity and differentially contribute to virulence. BMC Biol 2022; 20:55. [PMID: 35197059 PMCID: PMC8867779 DOI: 10.1186/s12915-022-01254-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/15/2022] [Indexed: 02/06/2023] Open
Abstract
Background Verticillium dahliae is a fungal pathogen that causes a vascular wilt on many economically important crops. Common fungal extracellular membrane (CFEM) domain proteins including secreted types have been implicated in virulence, but their roles in this pathogen are still unknown. Results Nine secreted small cysteine-rich proteins (VdSCPs) with CFEM domains were identified by bioinformatic analyses and their differential suppression of host immune responses were evaluated. Two of these proteins, VdSCP76 and VdSCP77, localized to the plant plasma membrane owing to their signal peptides and mediated broad-spectrum suppression of all immune responses induced by typical effectors. Deletion of either VdSCP76 or VdSCP77 significantly reduced the virulence of V. dahliae on cotton. Furthermore, VdSCP76 and VdSCP77 suppressed host immunity through the potential iron binding site conserved in CFEM family members, characterized by an aspartic acid residue in seven VdSCPs (Asp-type) in contrast with an asparagine residue (Asn-type) in VdSCP76 and VdSCP77. V. dahliae isolates carrying the Asn-type CFEM members were more virulent on cotton than those carrying the Asp-type. Conclusions In the iron-insufficient xylem, V. dahliae is likely to employ the Asp-type CFEM members to chelate iron, and Asn-type CFEM members to suppress immunity, for successful colonization and propagation in host plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01254-x.
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Zhu W, Yu M, Xu R, Bi K, Yu S, Xiong C, Liu Z, Sharon A, Jiang D, Wu M, Gu Q, Gong L, Chen W, Wei W. Botrytis cinerea BcSSP2 protein is a late infection phase, cytotoxic effector. Environ Microbiol 2022; 24:3420-3435. [PMID: 35170184 DOI: 10.1111/1462-2920.15919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 01/14/2023]
Abstract
Botrytis cinerea is a broad-host-range necrotrophic phytopathogen responsible for serious diseases in leading crops. To facilitate infection, B. cinerea secretes a large number of effectors that induce plant cell death. In screening secretome data of B. cinerea during infection stage, we identified a phytotoxic protein (BcSSP2) that can also induce immune resistance in plants. BcSSP2 is a small, cysteine-rich protein without any known domains. Transient expression of BcSSP2 in leaves caused chlorosis that intensifies with time and eventually leads to death. Point mutations in eight of 10 cysteine residues abolished phytotoxicity, but residual toxic activity remained after heating treatment, suggesting contribution of unknown epitopes to protein phytotoxicity. The expression of bcssp2 was low during the first 36 h after inoculation and increased sharply upon transition to late infection stage. Deletion of bcssp2 did not cause statistically significant changes in lesions size on bean and tobacco leaves. Further analyses indicated that the phytotoxicity of BcSSP2 is negatively regulated by the receptor-like kinases BAK1 and SOBIR1. Collectively, our findings show that BcSSP2 is an effector protein that toxifies the host cells, but is also recognized by the plant immune system.
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Affiliation(s)
- Wenjun Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
| | - Mengxue Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
| | - Ran Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
| | - Kai Bi
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
| | - Shuang Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
| | - Chao Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
| | - Zhiguo Liu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
| | - Amir Sharon
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mingde Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiongnan Gu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Ling Gong
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan, Hubei, 430065, China
| | - Weidong Chen
- Department of Plant Pathology/United States Department of Agriculture-Agricultural Research Service, Washington State University, Pullman, WA, 99164, USA
| | - Wei Wei
- Department of Plant Pathology/United States Department of Agriculture-Agricultural Research Service, Washington State University, Pullman, WA, 99164, USA
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Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt W(S, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia‐Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021; 89:1647-1672. [PMID: 34561912 PMCID: PMC8616854 DOI: 10.1002/prot.26247] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022]
Abstract
The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.
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Affiliation(s)
- Leila T. Alexander
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | | | - Athanassios Adamopoulos
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Markus Alahuhta
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Ann M. Arvin
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Yannick J. Bomble
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | - Valerio Chiarini
- Program in Structural Biology and BiophysicsInstitute of Biotechnology, University of HelsinkiHelsinkiFinland
| | - Naga babu Chinnam
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
| | - Wah Chiu
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
- BioengineeringStanford University School of MedicineStanfordCaliforniaUSA
- Division of Cryo‐EM and Bioimaging SSRLSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Rhys Grinter
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Gagan D. Gupta
- Radiation Biology & Health Sciences DivisionBhabha Atomic Research CentreMumbaiIndia
| | - Marcus D. Hartmann
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental BiologyUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
- Biomolecular Science and Engineering ProgramUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Tatjana Heidebrecht
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of the National Research Council of Italy (CNR)RomeItaly
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Romain Linares
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | | | - Vladimir V. Lunin
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Andrei N. Lupas
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Cihan Makbul
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John Moult
- Department of Cell Biology and Molecular GeneticsInstitute for Bioscience and Biotechnology Research, University of MarylandRockvilleMarylandUSA
| | - Prasun K. Mukherjee
- Nuclear Agriculture & Biotechnology DivisionBhabha Atomic Research CentreMumbaiIndia
| | - William (Sam) Nutt
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Stefan L. Oliver
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
| | - Anastassis Perrakis
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lucy Stols
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John A. Tainer
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
- Department of Cancer BiologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College LondonLondonUK
- Centre for Structural Systems Biology, Leibniz‐Institut für Experimentelle VirologieHamburgGermany
| | - Susan E. Tsutakawa
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | | | - Torsten Schwede
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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18
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Insights of the Neofusicoccum parvum- Liquidambar styraciflua Interaction and Identification of New Cysteine-Rich Proteins in Both Species. J Fungi (Basel) 2021; 7:jof7121027. [PMID: 34947009 PMCID: PMC8707630 DOI: 10.3390/jof7121027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
Neofusicoccum parvum belongs to the Botryosphaeriaceae family, which contains endophytes and pathogens of woody plants. In this study, we isolated 11 strains from diseased tissue of Liquidambar styraciflua. Testing with Koch's postulates-followed by a molecular approach-revealed that N. parvum was the most pathogenic strain. We established an in vitro pathosystem (L. styraciflua foliar tissue-N. parvum) in order to characterize the infection process during the first 16 days. New CysRPs were identified for both organisms using public transcriptomic and genomic databases, while mRNA expression of CysRPs was analyzed by RT-qPCR. The results showed that N. parvum caused disease symptoms after 24 h that intensified over time. Through in silico analysis, 5 CysRPs were identified for each organism, revealing that all of the proteins are potentially secreted and novel, including two of N. parvum proteins containing the CFEM domain. Interestingly, the levels of the CysRPs mRNAs change during the interaction. This study reports N. parvum as a pathogen of L. styraciflua for the first time and highlights the potential involvement of CysRPs in both organisms during this interaction.
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19
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Oberti H, Spangenberg G, Cogan N, Reyno R, Feijoo M, Murchio S, Dalla-Rizza M. Genome-wide analysis of Claviceps paspali: insights into the secretome of the main species causing ergot disease in Paspalum spp. BMC Genomics 2021; 22:766. [PMID: 34702162 PMCID: PMC8549174 DOI: 10.1186/s12864-021-08077-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The phytopatogen Claviceps paspali is the causal agent of Ergot disease in Paspalum spp., which includes highly productive forage grasses such as P. dilatatum. This disease impacts dairy and beef production by affecting seed quality and producing mycotoxins that can affect performance in feeding animals. The molecular basis of pathogenicity of C. paspali remains unknown, which makes it more difficult to find solutions for this problem. Secreted proteins are related to fungi virulence and can manipulate plant immunity acting on different subcellular localizations. Therefore, identifying and characterizing secreted proteins in phytopathogenic fungi will provide a better understanding of how they overcome host defense and cause disease. The aim of this work is to analyze the whole genome sequences of three C. paspali isolates to obtain a comparative genome characterization based on possible secreted proteins and pathogenicity factors present in their genome. In planta RNA-seq analysis at an early stage of the interaction of C. paspali with P. dilatatum stigmas was also conducted in order to determine possible secreted proteins expressed in the infection process. RESULTS C. paspali isolates had compact genomes and secretome which accounted for 4.6-4.9% of the predicted proteomes. More than 50% of the predicted secretome had no homology to known proteins. RNA-Seq revealed that three protein-coding genes predicted as secreted have mayor expression changes during 1 dpi vs 4 dpi. Also, three of the first 10 highly expressed genes in both time points were predicted as effector-like. CAZyme-like proteins were found in the predicted secretome and the most abundant family could be associated to pectine degradation. Based on this, pectine could be a main component affected by the cell wall degrading enzymes of C. paspali. CONCLUSIONS Based on predictions from DNA sequence and RNA-seq, unique probable secreted proteins and probable pathogenicity factors were identified in C. paspali isolates. This information opens new avenues in the study of the biology of this fungus and how it modulates the interaction with its host. Knowledge of the diversity of the secretome and putative pathogenicity genes should facilitate future research in disease management of Claviceps spp.
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Affiliation(s)
- H Oberti
- Instituto Nacional de Investigación Agropecuaria (INIA). Unidad de Biotecnología. Estación Experimental INIA Las Brujas, Ruta 48 km, 10, Canelones, Uruguay
| | - G Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - N Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - R Reyno
- Instituto Nacional de Investigación Agropecuaria (INIA). Programa Pasturas y Forrajes. Estación Experimental INIA Tacuarembó, Ruta 5 km, 386, Tacuarembó, Uruguay
| | - M Feijoo
- Centro Universitario Regional del Este (CURE), Polo de Desarrollo Universitario: Patogenicidad, toxicidad y genética en los ecosistemas pastoriles de la región Este de Uruguay, Ruta 8 km, 281, Treinta y Tres, Uruguay
| | - S Murchio
- Instituto Nacional de Investigación Agropecuaria (INIA). Unidad de Biotecnología. Estación Experimental INIA Las Brujas, Ruta 48 km, 10, Canelones, Uruguay
| | - M Dalla-Rizza
- Instituto Nacional de Investigación Agropecuaria (INIA). Unidad de Biotecnología. Estación Experimental INIA Las Brujas, Ruta 48 km, 10, Canelones, Uruguay.
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20
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Achari SR, Edwards J, Mann RC, Kaur JK, Sawbridge T, Summerell BA. Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles. BMC Genomics 2021; 22:734. [PMID: 34627148 PMCID: PMC8502283 DOI: 10.1186/s12864-021-08033-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 09/23/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The fungal pathogen Fusarium oxysporum f.sp. pisi (Fop) causes Fusarium wilt in peas. There are four races globally: 1, 2, 5 and 6 and all of these races are present in Australia. Molecular infection mechanisms have been studied in a few other F. oxysporum formae speciales; however, there has been no transcriptomic Fop-pea pathosystem study. RESULTS A transcriptomic study was carried out to understand the molecular pathogenicity differences between the races. Transcriptome analysis at 20 days post-inoculation revealed differences in the differentially expressed genes (DEGs) in the Fop races potentially involved in fungal pathogenicity variations. Most of the DEGs in all the races were engaged in transportation, metabolism, oxidation-reduction, translation, biosynthetic processes, signal transduction, proteolysis, among others. Race 5 expressed the most virulence-associated genes. Most genes encoding for plant cell wall degrading enzymes, CAZymes and effector-like proteins were expressed in race 2. Race 6 expressed the least number of genes at this time point. CONCLUSION Fop races deploy various factors and complex strategies to mitigate host defences to facilitate colonisation. This investigation provides an overview of the putative pathogenicity genes in different Fop races during the necrotrophic stage of infection. These genes need to be functionally characterised to confirm their pathogenicity/virulence roles and the race-specific genes can be further explored for molecular characterisation.
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Affiliation(s)
- Saidi R Achari
- AgriBio, Agriculture Victoria Research, DJPR, Bundoora, Victoria, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Jacqueline Edwards
- AgriBio, Agriculture Victoria Research, DJPR, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Ross C Mann
- AgriBio, Agriculture Victoria Research, DJPR, Bundoora, Victoria, Australia
| | - Jatinder K Kaur
- AgriBio, Agriculture Victoria Research, DJPR, Bundoora, Victoria, Australia
| | - Tim Sawbridge
- AgriBio, Agriculture Victoria Research, DJPR, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Brett A Summerell
- Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Sydney, NSW, Australia
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Becking T, Kiselev A, Rossi V, Street-Jones D, Grandjean F, Gaulin E. Pathogenicity of animal and plant parasitic Aphanomyces spp and their economic impact on aquaculture and agriculture. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Outram MA, Sung YC, Yu D, Dagvadorj B, Rima SA, Jones DA, Ericsson DJ, Sperschneider J, Solomon PS, Kobe B, Williams SJ. The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors. THE NEW PHYTOLOGIST 2021; 231:2282-2296. [PMID: 34053091 DOI: 10.1111/nph.17516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 05/22/2023]
Abstract
Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel Yu
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sharmin A Rima
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - David A Jones
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, VIC, 3168, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Outram MA, Sung YC, Yu D, Dagvadorj B, Rima SA, Jones DA, Ericsson DJ, Sperschneider J, Solomon PS, Kobe B, Williams SJ. The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors. THE NEW PHYTOLOGIST 2021; 231:2282-2296. [PMID: 34053091 DOI: 10.1101/2020.05.27.120113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 05/25/2023]
Abstract
Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel Yu
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sharmin A Rima
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - David A Jones
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, VIC, 3168, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Havenga M, Wingfield BD, Wingfield MJ, Dreyer LL, Roets F, Aylward J. Genetic response to nitrogen starvation in the aggressive Eucalyptus foliar pathogen Teratosphaeria destructans. Curr Genet 2021; 67:981-990. [PMID: 34432124 DOI: 10.1007/s00294-021-01208-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/20/2021] [Accepted: 08/21/2021] [Indexed: 12/13/2022]
Abstract
Teratosphaeria destructans is one of the most aggressive foliar pathogens of Eucalyptus. The biological factors underpinning T. destructans infections, which include shoot and leaf blight on young trees, have never been interrogated. Thus, the means by which the pathogen modifies its host environment to overcome host defences remain unknown. By applying transcriptome sequencing, the aim of this study was to compare gene expression in a South African isolate of T. destructans grown on nitrogen-deficient and complete media. This made it possible to identify upregulated genes in a nitrogen-starved environment, often linked to the pathogenicity of the fungus. The results support the hypothesis that nitrogen starvation in T. destructans likely mirrors an in planta genetic response. This is because 45% of genes that were highly upregulated under nitrogen starvation have previously been reported to be associated with infection in other pathogen systems. These included several CAZymes, fungal effector proteins, peptidases, kinases, toxins, lipases and proteins associated with detoxification of toxic compounds. Twenty-five secondary metabolites were identified and expressed in both nitrogen-deficient and complete conditions. Additionally, the most highly expressed genes in both growth conditions had pathogenicity-related functions. This study highlights the large number of expressed genes associated with pathogenicity and overcoming plant defences. As such, the generated baseline knowledge regarding pathogenicity and aggressiveness in T. destructans is a valuable reference for future in planta work.
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Affiliation(s)
- Minette Havenga
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. .,Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa.
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa
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25
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Kumar J, Ramlal A, Kumar K, Rani A, Mishra V. Signaling Pathways and Downstream Effectors of Host Innate Immunity in Plants. Int J Mol Sci 2021; 22:ijms22169022. [PMID: 34445728 PMCID: PMC8396522 DOI: 10.3390/ijms22169022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Phytopathogens, such as biotrophs, hemibiotrophs and necrotrophs, pose serious stress on the development of their host plants, compromising their yields. Plants are in constant interaction with such phytopathogens and hence are vulnerable to their attack. In order to counter these attacks, plants need to develop immunity against them. Consequently, plants have developed strategies of recognizing and countering pathogenesis through pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Pathogen perception and surveillance is mediated through receptor proteins that trigger signal transduction, initiated in the cytoplasm or at the plasma membrane (PM) surfaces. Plant hosts possess microbe-associated molecular patterns (P/MAMPs), which trigger a complex set of mechanisms through the pattern recognition receptors (PRRs) and resistance (R) genes. These interactions lead to the stimulation of cytoplasmic kinases by many phosphorylating proteins that may also be transcription factors. Furthermore, phytohormones, such as salicylic acid, jasmonic acid and ethylene, are also effective in triggering defense responses. Closure of stomata, limiting the transfer of nutrients through apoplast and symplastic movements, production of antimicrobial compounds, programmed cell death (PCD) are some of the primary defense-related mechanisms. The current article highlights the molecular processes involved in plant innate immunity (PII) and discusses the most recent and plausible scientific interventions that could be useful in augmenting PII.
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Affiliation(s)
- Jitendra Kumar
- Bangalore Bioinnovation Centre, Life Sciences Park, Electronics City Phase 1, Bengaluru 560100, India;
| | - Ayyagari Ramlal
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi 110012, India;
| | - Kamal Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110066, India;
| | - Anita Rani
- Department of Botany, Dyal Singh College, University of Delhi, Delhi 110003, India;
| | - Vachaspati Mishra
- Department of Botany, Dyal Singh College, University of Delhi, Delhi 110003, India;
- Correspondence:
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26
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Jangir P, Mehra N, Sharma K, Singh N, Rani M, Kapoor R. Secreted in Xylem Genes: Drivers of Host Adaptation in Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2021; 12:628611. [PMID: 33968096 PMCID: PMC8101498 DOI: 10.3389/fpls.2021.628611] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/01/2021] [Indexed: 05/17/2023]
Abstract
Fusarium oxysporum (Fo) is a notorious pathogen that significantly contributes to yield losses in crops of high economic status. It is responsible for vascular wilt characterized by the browning of conductive tissue, wilting, and plant death. Individual strains of Fo are host specific (formae speciales), and approximately, 150 forms have been documented so far. The pathogen secretes small effector proteins in the xylem, termed as Secreted in Xylem (Six), that contribute to its virulence. Most of these proteins contain cysteine residues in even numbers. These proteins are encoded by SIX genes that reside on mobile pathogenicity chromosomes. So far, 14 proteins have been reported. However, formae speciales vary in SIX protein profile and their respective gene sequence. Thus, SIX genes have been employed as ideal markers for pathogen identification. Acquisition of SIX-encoding mobile pathogenicity chromosomes by non-pathogenic lines, through horizontal transfer, results in the evolution of new virulent lines. Recently, some SIX genes present on these pathogenicity chromosomes have been shown to be involved in defining variation in host specificity among formae speciales. Along these lines, the review entails the variability (formae speciales, races, and vegetative compatibility groups) and evolutionary relationships among members of F. oxysporum species complex (FOSC). It provides updated information on the diversity, structure, regulation, and (a)virulence functions of SIX genes. The improved understanding of roles of SIX in variability and virulence of Fo has significant implication in establishment of molecular framework and techniques for disease management. Finally, the review identifies the gaps in current knowledge and provides insights into potential research landscapes that can be explored to strengthen the understanding of functions of SIX genes.
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Affiliation(s)
| | | | | | | | | | - Rupam Kapoor
- Department of Botany, University of Delhi, New Delhi, India
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Comparative analysis of extracellular proteomes reveals putative effectors of the boxwood blight pathogens, Calonectria henricotiae and C. pseudonaviculata. Biosci Rep 2021; 41:227917. [PMID: 33619567 PMCID: PMC7937907 DOI: 10.1042/bsr20203544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 02/05/2021] [Indexed: 01/25/2023] Open
Abstract
Calonectria henricotiae (Che) and C. pseudonaviculata (Cps) are destructive fungal pathogens causing boxwood blight, a persistent threat to horticultural production, landscape industries, established gardens, and native ecosystems. Although extracellular proteins including effectors produced by fungal pathogens are known to play a fundamental role in pathogenesis, the composition of Che and Cps extracellular proteins has not been examined. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics prediction tools, 630 extracellular proteins and 251 cell membrane proteins of Che and Cps were identified in the classical secretion pathway in the present study. In the non-classical secretion pathway, 79 extracellular proteins were identified. The cohort of proteins belonged to 364 OrthoMCL clusters, with the majority (62%) present in both species, and a subset unique to Che (19%) and Cps (20%). These extracellular proteins were predicted to play important roles in cell structure, regulation, metabolism, and pathogenesis. A total of 124 proteins were identified as putative effectors. Many of them are orthologs of proteins with documented roles in suppressing host defense and facilitating infection processes in other pathosystems, such as SnodProt1-like proteins in the OrthoMCL cluster OG5_152723 and PhiA-like cell wall proteins in the cluster OG5_155754. This exploratory study provides a repository of secreted proteins and putative effectors that can provide insights into the virulence mechanisms of the boxwood blight pathogens.
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Mat Razali N, Hisham SN, Kumar IS, Shukla RN, Lee M, Abu Bakar MF, Nadarajah K. Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani. Int J Mol Sci 2021; 22:ijms22042183. [PMID: 33671736 PMCID: PMC7926851 DOI: 10.3390/ijms22042183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 12/17/2022] Open
Abstract
Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.
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Affiliation(s)
- Nurhani Mat Razali
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Siti Norvahida Hisham
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Ilakiya Sharanee Kumar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Rohit Nandan Shukla
- Bionivid Technology Pte Ltd., 209, 4th Cross Rd, B Channasandra, East of NGEF Layout, Kasturi Nagar, Bengaluru 560043, Karnataka, India;
| | - Melvin Lee
- Codon Genomics Sdn. Bhd., No 26, Jalan Dutamas 7 Taman Dutamas Balakong, Seri Kembangan 43200, Selangor, Malaysia;
| | | | - Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
- Correspondence:
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Batson AM, Fokkens L, Rep M, du Toit LJ. Putative Effector Genes Distinguish Two Pathogenicity Groups of Fusarium oxysporum f. sp. spinaciae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:141-156. [PMID: 33103963 DOI: 10.1094/mpmi-06-20-0145-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is an important disease during warm conditions in production regions with acid soils, yet little is known about what confers pathogenicity to spinach in F. oxysporum f. sp. spinaciae genetically. To identify candidate fungal genes that contribute to spinach Fusarium wilt, each of 69 geographically diverse F. oxysporum isolates was tested for pathogenicity on each of three spinach inbreds. Thirty-nine isolates identified as F. oxysporum f. sp. spinaciae caused quantitative differences in disease severity among the inbreds that revealed two distinct pathogenicity groups of F. oxysporum f. sp. spinaciae. Putative effector gene profiles, predicted from whole-genome sequences generated for nine F. oxysporum f. sp. spinaciae isolates and five nonpathogenic, spinach-associated F. oxysporum (NPS) isolates, distinguished the F. oxysporum f. sp. spinaciae isolates from the NPS isolates, and separated the F. oxysporum f. sp. spinaciae isolates into two groups. Five of the putative effector genes appeared to be unique to F. oxysporum f. sp. spinaciae, as they were not found in 222 other publicly available genome assemblies of F. oxysporum, implicating potential involvement of these genes in pathogenicity to spinach. In addition, two combinations of the 14 known Secreted in Xylem (SIX) genes that have been affiliated with host pathogenicity in other formae speciales of F. oxysporum were identified in genome assemblies of the nine F. oxysporum f. sp. spinaciae isolates, either SIX8 and SIX9 or SIX4, SIX8, and SIX14. Characterization of these putative effector genes should aid in understanding mechanisms of pathogenicity in F. oxysporum f. sp. spinaciae, developing molecular tools for rapid detection and quantification of F. oxysporum f. sp. spinaciae, and breeding for resistance to Fusarium wilt in spinach.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Alexander M Batson
- Washington State University Northwestern Washington Research and Extension Center Mount Vernon, Mount Vernon, WA 98273, U.S.A
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Lindsey J du Toit
- Washington State University Northwestern Washington Research and Extension Center Mount Vernon, Mount Vernon, WA 98273, U.S.A
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Abstract
Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen F. oxysporum, this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes.
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Adhikari TB, Gao A, Ingram T, Louws FJ. Pathogenomics Characterization of an Emerging Fungal Pathogen, Fusarium oxysporum f. sp. lycopersici in Greenhouse Tomato Production Systems. Front Microbiol 2020; 11:1995. [PMID: 32973719 PMCID: PMC7482420 DOI: 10.3389/fmicb.2020.01995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 01/19/2023] Open
Abstract
In recent years, greenhouse-grown tomato (Solanum lycopersicum) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type (MAT) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly (P < 0.001). Cultivar 'Happy Root' (I-1, I-2, and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (Fmk1, Fow1, Ftf1, Orx1, Pda1, PelA, PelD, Pep1, Pep2, eIF-3, Rho1, Scd1, Snf1, Ste12, and Sge1), and 14 Secreted In Xylem (SIX) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA, Rho1, Sge1, and Ste12 were present in all isolates while Fow1, Ftf1, Orx1, Peda1, Pep1, eIF-3, Scd1, and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD, were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12, and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type (MAT-1 or MAT-2) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3- and the translation elongation factor 1-α encoding genes SIX3 and tef1-α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on SIX3- and tef1-α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.
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Affiliation(s)
- Tika B Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Anne Gao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thomas Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States.,Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
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Wang CJ, Thanarut C, Sun PL, Chung WH. Colonization of human opportunistic Fusarium oxysporum (HOFo) isolates in tomato and cucumber tissues assessed by a specific molecular marker. PLoS One 2020; 15:e0234517. [PMID: 32530955 PMCID: PMC7292389 DOI: 10.1371/journal.pone.0234517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
Abstract
Fusarium oxysporum is a large complex cosmopolitan species composed of plant pathogens, human opportunistic pathogens, and nonpathogenic isolates. Many plant pathogenic strains are known based on host plant specificity and the large number of plant species attacked. F. oxysporum is an opportunistic pathogen in humans with a compromised immune system. The objectives of this study were: (1) to develop a specific marker to detect human opportunistic F. oxysporum (HOFo) isolates; (2) to determine whether or not HOFo isolates can colonize and cause disease symptoms in plants; and (3) to assess Taiwan isolates sensitivity to two agro-fungicides. The primer pair, Primer 5/ST33-R, specifically amplifying Taiwan and international reference HOFo isolates was developed and used to detect and assess the distribution of a Taiwan isolate in inoculated tomato plants and tomato and cucumber fruit. Taiwan HOFo isolate MCC2074 was shown to colonize tomato roots, hypocotyls, and cotyledons, but did not show any visible symptoms. Four days after surface inoculation of tomato and cucumber fruit with the same isolate, MCC2074 was detected in the pericarp and locular cavities of both tomato and cucumber fruit and in columella of tomato fruit. Three Taiwan HOFo isolates were found to be moderately sensitive to azoxystrobin and highly sensitive to difenconazole.
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Affiliation(s)
- Chao-Jen Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Chinnapan Thanarut
- Faculty of Agricultural Production, Division of Pomology Maejo University, Chiangmai, Thailand
| | - Pei-Lun Sun
- Department of Dermatology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
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Bansal R, Mistry HU, Mukherjee PK, Gupta GD. Expression, purification, crystallization and X-ray diffraction studies of a novel root-induced secreted protein from Trichoderma virens. Acta Crystallogr F Struct Biol Commun 2020; 76:257-262. [PMID: 32510466 PMCID: PMC7278501 DOI: 10.1107/s2053230x20007025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/25/2020] [Indexed: 11/10/2022] Open
Abstract
Small secreted cysteine-rich proteins (SSCPs) from fungi play an important role in fungi-host interactions. The plant-beneficial fungi Trichoderma spp. are in use worldwide as biocontrol agents and protect the host plant from soil-borne as well as foliar pathogens. Recently, a novel SSCP, Tsp1, has been identified in the secreted protein pool of T. virens and is overinduced upon its interaction with the roots of the maize plant. The protein was observed to be well conserved in the Ascomycota division of fungi, and its homologs are present in many plant-pathogenic fungi such as Fusarium oxysporum and Magnaporthe oryzae. However, none of these homologs have yet been characterized. Recombinant Tsp1 protein has been expressed and purified using an Escherichia coli expression system. The protein, with four conserved cysteines, forms a dimer in solution as observed by size-exclusion chromatography. The dimerization, however, does not involve disulfide bonds. Circular-dichroism data suggested that the protein has a β-strand-rich secondary structure that matched well with the secondary structure predicted using bioinformatics methods. The protein was crystallized using sodium malonate as a precipitant. The crystals diffracted X-rays to 1.7 Å resolution and belonged to the orthorhombic space group P212121 (Rmeas = 5.4%), with unit-cell parameters a = 46.3, b = 67.0, c = 173.2 Å. The Matthews coefficient (VM) of the crystal is 2.32 Å3 Da-1, which corresponds to nearly 47% solvent content with four subunits of Tsp1 protein in the asymmetric unit. This is the first report of the structural study of any homolog of the novel Tsp1 protein. These structural studies will help in understanding the classification and function of the protein.
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Affiliation(s)
- Ravindra Bansal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Hiral U. Mistry
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India
| | - Prasun K. Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Gagan D. Gupta
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India
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Carreón-Anguiano KG, Islas-Flores I, Vega-Arreguín J, Sáenz-Carbonell L, Canto-Canché B. EffHunter: A Tool for Prediction of Effector Protein Candidates in Fungal Proteomic Databases. Biomolecules 2020; 10:biom10050712. [PMID: 32375409 PMCID: PMC7277995 DOI: 10.3390/biom10050712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/17/2020] [Accepted: 03/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pathogens are able to deliver small-secreted, cysteine-rich proteins into plant cells to enable infection. The computational prediction of effector proteins remains one of the most challenging areas in the study of plant fungi interactions. At present, there are several bioinformatic programs that can help in the identification of these proteins; however, in most cases, these programs are managed independently. Here, we present EffHunter, an easy and fast bioinformatics tool for the identification of effectors. This predictor was used to identify putative effectors in 88 proteomes using characteristics such as size, cysteine residue content, secretion signal and transmembrane domains.
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Affiliation(s)
- Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Julio Vega-Arreguín
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores-UNAM, León, México
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
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Wang D, Tian L, Zhang D, Song J, Song S, Yin C, Zhou L, Liu Y, Wang B, Kong Z, Klosterman SJ, Li J, Wang J, Li T, Adamu S, Subbarao KV, Chen J, Dai X. Functional analyses of small secreted cysteine-rich proteins identified candidate effectors in Verticillium dahliae. MOLECULAR PLANT PATHOLOGY 2020; 21:667-685. [PMID: 32314529 PMCID: PMC7170778 DOI: 10.1111/mpp.12921] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 05/09/2023]
Abstract
Secreted small cysteine-rich proteins (SCPs) play a critical role in modulating host immunity in plant-pathogen interactions. Bioinformatic analyses showed that the fungal pathogen Verticillium dahliae encodes more than 100 VdSCPs, but their roles in host-pathogen interactions have not been fully characterized. Transient expression of 123 VdSCP-encoding genes in Nicotiana benthamiana identified three candidate genes involved in host-pathogen interactions. The expression of these three proteins, VdSCP27, VdSCP113, and VdSCP126, in N. benthamiana resulted in cell death accompanied by a reactive oxygen species burst, callose deposition, and induction of defence genes. The three VdSCPs mainly localized to the periphery of the cell. BAK1 and SOBIR1 (associated with receptor-like protein) were required for the immunity triggered by these three VdSCPs in N. benthamiana. Site-directed mutagenesis showed that cysteine residues that form disulphide bonds are essential for the functioning of VdSCP126, but not VdSCP27 and VdSCP113. VdSCP27, VdSCP113, and VdSCP126 individually are not essential for V. dahliae infection of N. benthamiana and Gossypium hirsutum, although there was a significant reduction of virulence on N. benthamiana and G. hirsutum when inoculated with the VdSCP27/VdSCP126 double deletion strain. These results illustrate that the SCPs play a critical role in the V. dahliae-plant interaction via an intrinsic virulence function and suppress immunity following infection.
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Affiliation(s)
- Dan Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Li Tian
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Dan‐Dan Zhang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
| | - Jian Song
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | | | - Chun‐Mei Yin
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Lei Zhou
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
| | - Yan Liu
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Bao‐Li Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Zhi‐Qiang Kong
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Steven J. Klosterman
- United States Department of AgricultureAgricultural Research ServiceSalinasCAUSA
| | - Jun‐Jiao Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Jie Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Ting‐Gang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Sabiu Adamu
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Krishna V. Subbarao
- Department of Plant PathologyUniversity of CaliforniaDavis, c/o United States Agricultural Research StationSalinasCAUSA
| | - Jie‐Yin Chen
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
| | - Xiao‐Feng Dai
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
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Seifbarghi S, Borhan MH, Wei Y, Ma L, Coutu C, Bekkaoui D, Hegedus DD. Receptor-Like Kinases BAK1 and SOBIR1 Are Required for Necrotizing Activity of a Novel Group of Sclerotinia sclerotiorum Necrosis-Inducing Effectors. FRONTIERS IN PLANT SCIENCE 2020; 11:1021. [PMID: 32754179 PMCID: PMC7367142 DOI: 10.3389/fpls.2020.01021] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/22/2020] [Indexed: 05/03/2023]
Abstract
Sclerotinia sclerotiorum is a characteristic necrotrophic plant pathogen and is dependent on the induction of host cell death for nutrient acquisition. To identify necrosis-inducing effectors, the genome of S. sclerotiorum was scanned for genes encoding small, secreted, cysteine-rich proteins. These potential effectors were tested for their ability to induce necrosis in Nicotiana benthamiana via Agrobacterium-mediated expression and for cellular localization in host cells. Six novel proteins were discovered, of which all but one required a signal peptide for export to the apoplast for necrotizing activity. Virus-induced gene silencing revealed that the five necrosis-inducing effectors with a requirement for secretion also required the plant co-receptor-like kinases Brassinosteroid Insensitive 1-Associated Receptor Kinase 1 (BAK1) and Suppressor of BAK1-Interacting Receptor-like Kinase 1 (SOBIR1) for the induction of necrosis. S. sclerotiorum necrosis-inducing effector 2 (SsNE2) represented a new class of necrosis-inducing proteins as orthologs were identified in several other phytopathogenic fungi that were also capable of inducing necrosis. Substitution of conserved cysteine residues with alanine reduced, but did not abolish, the necrotizing activity of SsNE2 and full-length protein was required for function as peptides spanning the entire protein were unable to induce necrosis. These results illustrate the importance of necrosis-inducing effectors for S. sclerotiorum virulence and the role of host extracellular receptor(s) in effector-triggered susceptibility to this pathogen.
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Affiliation(s)
- Shirin Seifbarghi
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lisong Ma
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | | | - Dwayne D. Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Dwayne D. Hegedus,
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37
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Taylor A, Armitage AD, Handy C, Jackson AC, Hulin MT, Harrison RJ, Clarkson JP. Basal Rot of Narcissus: Understanding Pathogenicity in Fusarium oxysporum f. sp. narcissi. Front Microbiol 2019; 10:2905. [PMID: 31921077 PMCID: PMC6930931 DOI: 10.3389/fmicb.2019.02905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Fusarium oxysporum is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic F. oxysporum isolates are highly host specific and are classified as formae speciales. Narcissus is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by F. oxysporum f. sp. narcissi (FON); 154 Fusarium isolates were obtained from different locations and Narcissus cultivars in the United Kingdom, representing a valuable resource. A subset of 30 F. oxysporum isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14 Secreted in Xylem (SIX) genes, previously shown to be associated with pathogenicity in other F. oxysporum f. spp., revealed different complements of SIX7, SIX9, SIX10, SIX12 and SIX13 within FON isolates which may suggest a race structure. SIX gene sequences were unique to FON and SIX10 was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the SIX genes. Real-time RT-PCR, showed that SIX genes and selected putative effectors were expressed in planta with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics.
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Affiliation(s)
- Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | - Claire Handy
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | | | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
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38
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Ali SS, Asman A, Shao J, Firmansyah AP, Susilo AW, Rosmana A, McMahon P, Junaid M, Guest D, Kheng TY, Meinhardt LW, Bailey BA. Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback in Theobroma cacao. Fungal Biol Biotechnol 2019; 6:14. [PMID: 31583107 PMCID: PMC6767637 DOI: 10.1186/s40694-019-0077-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022] Open
Abstract
Background Ceratobasidium theobromae, a member of the Ceratobasidiaceae family, is the causal agent of vascular-streak dieback (VSD) of cacao, a major threat to the chocolate industry in the South-East Asia. The fastidious pathogen is very hard to isolate and maintain in pure culture, which is a major bottleneck in the study of its genetic diversity and genome. Result This study describes for the first time, a 33.90 Mbp de novo assembled genome of a putative C. theobromae isolate from cacao. Ab initio gene prediction identified 9264 protein-coding genes, of which 800 are unique to C. theobromae when compared to Rhizoctonia spp., a closely related group. Transcriptome analysis using RNA isolated from 4 independent VSD symptomatic cacao stems identified 3550 transcriptionally active genes when compared to the assembled C. theobromae genome while transcripts for only 4 C. theobromae genes were detected in 2 asymptomatic stems. De novo assembly of the non-cacao associated reads from the VSD symptomatic stems uniformly produced genes with high identity to predicted genes in the C. theobromae genome as compared to Rhizoctonia spp. or genes found in Genbank. Further analysis of the predicted C. theobromae transcriptome was carried out identifying CAZy gene classes, KEGG-pathway associated genes, and 138 putative effector proteins. Conclusion These findings put forth, for the first time, a predicted genome for the fastidious basidiomycete C. theobromae causing VSD on cacao providing a model for testing and comparison in the future. The C. theobromae genome predicts a pathogenesis model involving secreted effector proteins to suppress plant defense mechanisms and plant cell wall degrading enzymes.
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Affiliation(s)
- Shahin S Ali
- 1Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705 USA.,2Department of Viticulture & Enology, University of California, Davis, CA 95616 USA
| | - Asman Asman
- 3Department of Plant Pests and Diseases, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia.,4Cocoa Research Group, Faculty of Agriculture, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia
| | | | - Amanda P Firmansyah
- 6Faculty of Agriculture, Muhammadiyah University of Makassar, Makassar, Sulawesi Selatan 90221 Indonesia
| | - Agung W Susilo
- 7Indonesian Coffee and Cocoa Research Institute, Jl. PB Sudirman 90, Jember, 68118 Indonesia
| | - Ade Rosmana
- 3Department of Plant Pests and Diseases, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia.,4Cocoa Research Group, Faculty of Agriculture, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia
| | - Peter McMahon
- 8Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Muhammad Junaid
- 3Department of Plant Pests and Diseases, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia.,4Cocoa Research Group, Faculty of Agriculture, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia
| | - David Guest
- 8Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Tee Yei Kheng
- 9Cocoa Upstream Technology Department, Malaysian Cocoa Board, P.O. Box 30, Sg. Dulang Road, Sg. Sumun, Perak Malaysia
| | - Lyndel W Meinhardt
- 1Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705 USA
| | - Bryan A Bailey
- 1Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705 USA
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Carvalhais LC, Henderson J, Rincon-Florez VA, O’Dwyer C, Czislowski E, Aitken EAB, Drenth A. Molecular Diagnostics of Banana Fusarium Wilt Targeting Secreted-in-Xylem Genes. FRONTIERS IN PLANT SCIENCE 2019; 10:547. [PMID: 31214206 PMCID: PMC6554419 DOI: 10.3389/fpls.2019.00547] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/10/2019] [Indexed: 06/01/2023]
Abstract
Fusarium wilt is currently spreading in banana growing regions around the world leading to substantial losses. The disease is caused by the fungus Fusarium oxysporum f. sp. cubense (Foc), which is further classified into distinct races according to the banana varieties that they infect. Cavendish banana is resistant to Foc race 1, to which the popular Gros Michel subgroup succumbed last century. Cavendish effectively saved the banana industry, and became the most cultivated commercial subgroup worldwide. However, Foc tropical race 4 (TR4) subsequently emerged in Southeast Asia, causing significant yield losses due to its high level of aggressiveness to cultivars of Cavendish, and other commonly grown cultivars. Preventing further spread is crucially important in the absence of effective control methods or resistant market-acceptable banana cultivars. Implementation of quarantine and containment measures depends on early detection of the pathogen through reliable diagnostics. In this study, we tested the hypothesis that secreted in xylem (SIX) genes, which currently comprise the only known family of effectors in F. oxysporum, contain polymorphisms to allow the design of molecular diagnostic assays that distinguish races and relevant VCGs of Foc. We present specific and reproducible diagnostic assays based on conventional PCR targeting SIX genes, using as templates DNA extracted from pure Foc cultures. Sets of primers specifically amplify regions of: SIX6 in Foc race 1, SIX1 gene in TR4, SIX8 in subtropical race 4, SIX9/SIX10 in Foc VCG 0121, and SIX13 in Foc VCG 0122. These assays include simplex and duplex PCRs, with additional restriction digestion steps applied to amplification products of genes SIX1 and SIX13. Assay validations were conducted to a high international standard including the use of 250 Fusarium spp. isolates representing 16 distinct Fusarium species, 59 isolates of F. oxysporum, and 21 different vegetative compatibility groups (VCGs). Tested parameters included inter and intraspecific analytical specificity, sensitivity, robustness, repeatability, and reproducibility. The resulting suite of assays is able to reliably and accurately detect R1, STR4, and TR4 as well as two VCGs (0121 and 0122) causing Fusarium wilt in bananas.
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Affiliation(s)
- Lilia C. Carvalhais
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, Ecosciences Precinct, The University of Queensland, Brisbane, QLD, Australia
| | - Juliane Henderson
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, Ecosciences Precinct, The University of Queensland, Brisbane, QLD, Australia
| | - Vivian A. Rincon-Florez
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, Ecosciences Precinct, The University of Queensland, Brisbane, QLD, Australia
| | - Cecilia O’Dwyer
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, Ecosciences Precinct, The University of Queensland, Brisbane, QLD, Australia
| | - Elizabeth Czislowski
- School of Agriculture and Food Sciences, The University of Queenslandxy3Saint Lucia, QLD, Australia
| | - Elizabeth A. B. Aitken
- School of Agriculture and Food Sciences, The University of Queenslandxy3Saint Lucia, QLD, Australia
| | - André Drenth
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, Ecosciences Precinct, The University of Queensland, Brisbane, QLD, Australia
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40
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Rahnama M, Maclean P, Fleetwood DJ, Johnson RD. The LaeA orthologue in Epichloë festucae is required for symbiotic interaction with Lolium perenne. Fungal Genet Biol 2019; 129:74-85. [PMID: 31071427 DOI: 10.1016/j.fgb.2019.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
LaeA is a conserved global regulator of secondary metabolism and development in fungi. It is often required for successful pathogenic interactions. In this study, the laeA homologue in the fungal grass endophyte E. festucae was deleted and functionally characterised in vitro and its role in the mutualistic E. festucae interaction with Lolium perenne (perennial ryegrass) was determined. We showed that laeA in E. festucae is required for normal hyphal morphology, resistance to oxidative stress, and conidiation under nutrient-limited in vitro conditions. In planta studies revealed that laeA is expressed in a tissue-specific manner and is required to form a compatible plant interaction, with the majority of seedlings inoculated with a laeA deletion mutant either dying or being uninfected. In mature infected plants no difference was observed in the number or morphology of endophytic hyphae. However, the number of epiphyllous hyphae were greatly increased. Comparative transcriptomics analyses suggested roles for plant cell wall degradation, fungal cell wall composition, secondary metabolism and small-secreted proteins in Epichloë foliar symbiosis.
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Affiliation(s)
- M Rahnama
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; School of Biological Sciences, University of Auckland, New Zealand
| | - P Maclean
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - D J Fleetwood
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; Biotelliga Ltd, Auckland, New Zealand.
| | - R D Johnson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.
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Nie J, Yin Z, Li Z, Wu Y, Huang L. A small cysteine-rich protein from two kingdoms of microbes is recognized as a novel pathogen-associated molecular pattern. THE NEW PHYTOLOGIST 2019; 222:995-1011. [PMID: 30537041 DOI: 10.1111/nph.15631] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/01/2018] [Indexed: 05/24/2023]
Abstract
Pathogen-associated molecular patterns (PAMPs) are conserved molecules that are crucial for normal life cycle of microorganisms. However, the diversity of microbial PAMPs is little known. During screening of cell-death-inducing factors from the necrotrophic fungus Valsa mali, we identified a novel PAMP VmE02 that is widely spread in oomycetes and fungi. Agrobacterium tumefaciens-mediated transient expression or infiltration of recombinant protein produced by Escherichia coli was performed to assay elicitor activity of the proteins tested. Virus-induced gene silencing in Nicotiana benthamiana was used to determine the components involved in VmE02-triggered cell death. The role of VmE02 in virulence and conidiation of V. mali were characterized by gene deletion and complementation. We found that VmE02, together with some of its homologues from both oomycete and fungal species, exhibited cell-death-inducing activity in N. benthamiana. VmE02-triggered cell death was shown to be dependent on BRI1-ASSOCIATED KINASE-1, SUPPRESSOR OF BIR1-1, HSP90 and SGT1 in N. benthamiana. Deletion of VmE02 in V. mali greatly attenuated pathogen conidiation but not virulence, and treatment of N. benthamiana with VmE02 enhances plant resistance to Sclerotinia sclerotiorum and Phytophthora capsici. We conclude that VmE02 is a novel cross-kingdom PAMP produced by several fungi and oomycetes.
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Affiliation(s)
- Jiajun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhiyuan Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhengpeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuxing Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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42
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Neu E, Debener T. Prediction of the Diplocarpon rosae secretome reveals candidate genes for effectors and virulence factors. Fungal Biol 2018; 123:231-239. [PMID: 30798878 DOI: 10.1016/j.funbio.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 01/01/2023]
Abstract
Rose black spot is one of the most severe diseases of field-grown roses. Though R-genes have been characterised, little information is known about the molecular details of the interaction between pathogen and host. Based on the recently published genome sequence of the black spot fungus, we analysed gene models with various bioinformatic tools utilising the expression data of infected host tissues, which led to the prediction of 827 secreted proteins. A significant proportion of the predicted secretome comprises enzymes for the degradation of cell wall components, several of which were highly expressed during the first infection stages. As the secretome comprises major factors determining the ability of the fungus to colonise its host, we focused our further analyses on predicted effector candidates. In total, 52 sequences of 251 effector candidates matched several bioinformatic criteria of effectors, contained a Y/F/WxC motif, and did not match annotated proteins from other fungi. Additional sequences were identified based on their high expression levels during the penetration/haustorium formation phase and/or by matching known effectors from other fungi. Several host genotypes that are resistant to the sequenced isolate but differ in the R-genes responsible for this resistance are available. The combination of these genotypes with functional studies of the identified candidate effectors will allow the mechanisms of the rose black spot interaction to be dissected.
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Affiliation(s)
- Enzo Neu
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhaeuser Str. 2, Hannover 30419, Germany
| | - Thomas Debener
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhaeuser Str. 2, Hannover 30419, Germany.
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Aylward J, Wingfield BD, Dreyer LL, Roets F, Wingfield MJ, Steenkamp ET. Genomic overview of closely related fungi with different Protea host ranges. Fungal Biol 2018; 122:1201-1214. [PMID: 30449358 DOI: 10.1016/j.funbio.2018.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/06/2018] [Accepted: 10/04/2018] [Indexed: 11/28/2022]
Abstract
Genome comparisons of species with distinctive ecological traits can elucidate genetic divergence that influenced their differentiation. The interaction of a microorganism with its biotic environment is largely regulated by secreted compounds, and these can be predicted from genome sequences. In this study, we considered Knoxdaviesia capensis and Knoxdaviesia proteae, two closely related saprotrophic fungi found exclusively in Protea plants. We investigated their genome structure to compare their potential inter-specific interactions based on gene content. Their genomes displayed macrosynteny and were approximately 10 % repetitive. Both species had fewer secreted proteins than pathogens and other saprotrophs, reflecting their specialized habitat. The bulk of the predicted species-specific and secreted proteins coded for carbohydrate metabolism, with a slightly higher number of unique carbohydrate-degrading proteins in the broad host-range K. capensis. These fungi have few secondary metabolite gene clusters, suggesting minimal competition with other microbes and symbiosis with antibiotic-producing bacteria common in this niche. Secreted proteins associated with detoxification and iron sequestration likely enable these Knoxdaviesia species to tolerate antifungal compounds and compete for resources, facilitating their unusual dominance. This study confirms the genetic cohesion between Protea-associated Knoxdaviesia species and reveals aspects of their ecology that have likely evolved in response to their specialist niche.
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Affiliation(s)
- Janneke Aylward
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
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Widinugraheni S, Niño-Sánchez J, van der Does HC, van Dam P, García-Bastidas FA, Subandiyah S, Meijer HJG, Kistler HC, Kema GHJ, Rep M. A SIX1 homolog in Fusarium oxysporum f.sp. cubense tropical race 4 contributes to virulence towards Cavendish banana. PLoS One 2018; 13:e0205896. [PMID: 30346962 PMCID: PMC6197647 DOI: 10.1371/journal.pone.0205896] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 10/03/2018] [Indexed: 11/28/2022] Open
Abstract
The fungus Fusarium oxysporum f.sp. cubense (Focub) causes Fusarium wilt of banana. Focub strains are divided into races according to their host specificity, but which virulence factors underlie these interactions is currently unknown. In the F. oxysporum f.sp. lycopersici (Fol)-tomato system, small secreted fungal proteins, called Six proteins, were identified in the xylem sap of infected plants. The Fol Six1 protein contributes to virulence and has an avirulence function by activating the I-3 immune receptor of tomato. The Focub tropical race 4 (TR4) genome harbors three SIX1 homologs: SIX1a, b and c. In this study, the role of Focub-SIX1a in pathogenicity was evaluated since this homolog is present in not only TR4 but also in other races. A deletion mutant of the SIX1a gene from Focub TR4 strain II5 was generated (FocubΔSIX1a) and tested in planta. Mutants were found to be severely compromised in their virulence. Ectopic integration of the Focub-SIX1a gene in the FocubΔSIX1a strain restored virulence to wild type levels. We conclude that Focub-SIX1a is required for full virulence of Focub TR4 towards Cavendish banana.
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Affiliation(s)
- S. Widinugraheni
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Faculty of Agriculture, Nusa Cendana University, Kupang, Indonesia
| | - J. Niño-Sánchez
- ARS-USDA Cereal Disease Laboratory, University of Minnesota, St. Paul, Minnesota, United States of America
| | - H. C. van der Does
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - P. van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - F. A. García-Bastidas
- Wageningen University and Research, Wageningen Plant Research, Wageningen, the Netherlands
| | - S. Subandiyah
- Dept. Plant Protection, Fac. Agriculture, Gadjah Mada University, Yogyakarta, Indonesia
- Research Center for Biotechnology, Gadjah Mada University, Yogyakarta, Indonesia
| | - H. J. G. Meijer
- Wageningen University and Research, Wageningen Plant Research, Wageningen, the Netherlands
| | - H. C. Kistler
- ARS-USDA Cereal Disease Laboratory, University of Minnesota, St. Paul, Minnesota, United States of America
| | - G. H. J. Kema
- Wageningen University and Research, Wageningen Plant Research, Wageningen, the Netherlands
| | - M. Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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45
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Simbaqueba J, Catanzariti A, González C, Jones DA. Evidence for horizontal gene transfer and separation of effector recognition from effector function revealed by analysis of effector genes shared between cape gooseberry- and tomato-infecting formae speciales of Fusarium oxysporum. MOLECULAR PLANT PATHOLOGY 2018; 19:2302-2318. [PMID: 29786161 PMCID: PMC6638030 DOI: 10.1111/mpp.12700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNA sequencing (RNAseq) reads from cape gooseberry plants (Physalis peruviana) infected with Fusarium oxysporumf. sp. physali (Foph) were mapped against the lineage-specific transcriptome of Fusarium oxysporumf. sp. lycopersici (Fol) to look for putative effector genes. Homologues of Fol SIX1(designated SIX1a and SIX1b), SIX7, SIX10, SIX12, SIX15 and Ave1were identified. The near identity of the Foph and Fol SIX7, SIX10 and SIX12genes and their intergenic regions suggest that this gene cluster may have undergone recent lateral transfer. Foph SIX1a and SIX1bwere tested for their ability to complement a SIX1 knockout mutant of Fol. This mutant shows reduced pathogenicity on susceptible tomato plants, but is able to infect otherwise resistant tomato plants carrying the I-3 gene for Fusarium wilt resistance (SIX1 corresponds to Avr3). Neither SIX1a nor SIX1b could restore full pathogenicity on susceptible tomato plants, suggesting that any role they may play in pathogenicity is likely to be specific to cape gooseberry. SIX1b, but not SIX1a, was able to restore avirulence on tomato plants carrying I-3.These findings separate the recognition of SIX1 from its role as an effector and suggest direct recognition by I-3. A hypervariable region of SIX1undergoing diversifying selection within the F. oxysporum species complex is likely to play an important role in SIX1 recognition. These findings also indicate that I-3could potentially be deployed as a transgene in cape gooseberry to protect this emerging crop from Foph.Alternatively, cape gooseberry germplasm could be explored for I-3homologues capable of providing resistance to Foph.
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Affiliation(s)
- Jaime Simbaqueba
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityActonACT2601Australia
| | - Ann‐Maree Catanzariti
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityActonACT2601Australia
| | | | - David A. Jones
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityActonACT2601Australia
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46
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Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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47
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Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A, Fior S. Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization. Mol Ecol 2018; 27:3070-3086. [PMID: 29633410 DOI: 10.1111/mec.14585] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022]
Abstract
Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp. typhina and clarkii. The life cycle of these fungi entails unrestricted dispersal of gametes and sexual reproduction before infection of a new host, implying that the host imposes a selective barrier on viability of the progeny. We aimed to detect genes under divergent selection between subspecies, experiencing restricted gene flow due to adaptation to different hosts. Using pooled whole-genome sequencing data, we combined FST and DXY population statistics in genome scans and detected 57 outlier genes showing strong differentiation between the two subspecies. Genomewide analyses of nucleotide diversity (π), Tajima's D and dN/dS ratios indicated that these genes have evolved under positive selection. Genes encoding secreted proteins were enriched among the genes showing evidence of positive selection, suggesting that molecular plant-fungus interactions are strong drivers of endophyte divergence. We focused on five genes encoding secreted proteins, which were further sequenced in 28 additional isolates collected across Europe to assess genetic variation in a larger sample size. Signature of positive selection in these isolates and putative identification of pathogenic function supports our findings that these genes represent strong candidates for host specialization determinants in Epichloë endophytes. Our results highlight the role of secreted proteins as key determinants of host specialization.
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Affiliation(s)
- Melanie K Schirrmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.,Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Adrian Leuchtmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
| | - Simone Fior
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
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48
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Hartmann FE, Croll D. Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen. Mol Biol Evol 2018; 34:2808-2822. [PMID: 28981698 PMCID: PMC5850472 DOI: 10.1093/molbev/msx208] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence–absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence–absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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49
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Oh Y, Robertson SL, Parker J, Muddiman DC, Dean RA. Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae. Proteome Sci 2017; 15:20. [PMID: 29158724 PMCID: PMC5684745 DOI: 10.1186/s12953-017-0128-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/02/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen Magnaporthe oryzae copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed. METHODS M. oryzae strain 70-15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source. Proteins were isolated and subjected to unfractionated gel-free based liquid chromatography-tandem mass spectrometry (LC-MS/MS). The subcellular localization and function of the identified proteins were predicted using bioinformatics tools. RESULTS A total of 5498 M. oryzae proteins were identified. Comparative analysis of protein expression showed 363 proteins and 266 proteins significantly induced or uniquely expressed under nitrogen starved or nitrogen supplemented conditions, respectively. A functional analysis of differentially expressed proteins revealed that during nitrogen starvation nitrogen catabolite repression, melanin biosynthesis, protein degradation and protein translation pathways underwent extensive alterations. In addition, nitrogen starvation induced accumulation of various extracellular proteins including small extracellular proteins consistent with observations of a link between nitrogen starvation and the development of pathogenicity in M. oryzae. CONCLUSION The results from this study provide a comprehensive understanding of fungal responses to nitrogen availability.
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Affiliation(s)
- Yeonyee Oh
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | - Suzanne L. Robertson
- W. M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695 USA
| | - Jennifer Parker
- W. M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695 USA
| | - David C. Muddiman
- W. M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695 USA
| | - Ralph A. Dean
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
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50
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Zhang Y, Ma LJ. Deciphering Pathogenicity of Fusarium oxysporum From a Phylogenomics Perspective. ADVANCES IN GENETICS 2017; 100:179-209. [PMID: 29153400 DOI: 10.1016/bs.adgen.2017.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC. The existence of a diverse array of SP chromosomes determines the broad host range of this species complex, while the conserved core genome maintains essential house-keeping functions. Recognition of these SP chromosomes enables the functional and structural compartmentalization of F. oxysporum genomes. In this review, we examine the impact of this group of cross-kingdom pathogens on agricultural productivity and human health. Focusing on the pathogenicity of F. oxysporum in the phylogenomic framework of the genus Fusarium, we elucidate the evolution of pathogenicity within the FOSC. We conclude that a population genomics approach within a clearly defined phylogenomic framework is essential not only for understanding the evolution of the pathogenicity mechanism but also for identifying informative candidates associated with pathogenicity that can be developed as targets in disease management programs.
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Affiliation(s)
- Yong Zhang
- University of Massachusetts Amherst, Amherst, MA, United States
| | - Li-Jun Ma
- University of Massachusetts Amherst, Amherst, MA, United States.
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