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Liu C, Wang Y, Du Y, Kang Z, Guo J, Guo J. Glycine-serine-rich effector PstGSRE4 in Puccinia striiformis f. sp. tritici targets and stabilizes TaGAPDH2 that promotes stripe rust disease. PLANT, CELL & ENVIRONMENT 2024; 47:947-960. [PMID: 38105492 DOI: 10.1111/pce.14786] [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: 09/14/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Puccinia striiformis f. sp. tritici (Pst) secretes effector proteins that enter plant cells and manipulate host processes. In a previous study, we identified a glycine-serine-rich effector PstGSRE4, which was proven to regulate the reactive oxygen species (ROS) pathway by interacting with TaCZSOD2. In this study, we further demonstrated that PstGSRE4 interacts with wheat glyceraldehyde-3-phosphate dehydrogenase TaGAPDH2, which is related to ROS signalling. In wheat, silencing of TaGAPDH2 by virus-induced gene silencing increased the accumulation of ROS induced by the Pst virulent race CYR31. Overexpression of TaGAPDH2 decreased the accumulation of ROS induced by the avirulent Pst race CYR23. In addition, TaGAPDH2 suppressed Pst candidate elicitor Pst322-triggered cell death by decreasing ROS accumulation in Nicotiana benthamiana. Knocking down TaGAPDH2 expression attenuated Pst infection, whereas overexpression of TaGAPDH2 promoted Pst infection, indicating that TaGAPDH2 is a negative regulator of plant defence. In N. benthamiana, PstGSRE4 stabilized TaGAPDH2 through inhibition of the 26S proteasome-mediated destabilization. Overall, these results suggest that TaGAPDH2 is hijacked by the Pst effector as a negative regulator of plant immunity to promote Pst infection in wheat.
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Affiliation(s)
- Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanyuan Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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2
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Zhang D, Lin R, Yamamoto N, Wang Z, Lin H, Okada K, Liu Y, Xiang X, Zheng T, Zheng H, Yi X, Noutoshi Y, Zheng A. Mitochondrial-targeting effector RsIA_CtaG/Cox11 in Rhizoctonia solani AG-1 IA has two functions: plant immunity suppression and cell death induction mediated by a rice cytochrome c oxidase subunit. MOLECULAR PLANT PATHOLOGY 2024; 25:e13397. [PMID: 37902589 PMCID: PMC10799210 DOI: 10.1111/mpp.13397] [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: 04/23/2023] [Revised: 09/24/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023]
Abstract
Rhizoctonia solani AG-1 IA causes a necrotrophic rice disease and is a serious threat to rice production. To date, only a few effectors have been characterized in AG-1 IA. We previously identified RsIA_CtaG/Cox11 and showed that infiltration of the recombinant protein into rice leaves caused disease-like symptoms. In the present study, we further characterized the functionality of RsIA_CtaG/Cox11. RsIA_CtaG/Cox11 is an alternative transcript of cytochrome c oxidase copper chaperone Cox11 that starts from the second AUG codon, but contains a functional secretion signal peptide. RNA interference with RsIA_CtaG/Cox11 reduced the pathogenicity of AG-1 IA towards rice and Nicotiana benthamiana without affecting its fitness or mycelial morphology. Transient expression of the RsIA_CtaG/Cox11-GFP fusion protein demonstrated the localization of RsIA_CtaG/Cox11 to mitochondria. Agro-infiltration of RsIA_CtaG/Cox11 into N. benthamiana leaves inhibited cell death by BAX and INF1. In contrast to rice, agro-infiltration of RsIA_CtaG/Cox11 did not induce cell death in N. benthamiana. However, cell death was observed when it was coinfiltrated with Os_CoxVIIa, which encodes a subunit of cytochrome c oxidase. Os_CoxVIIa appeared to interact with RsIA_CtaG/Cox11. The cell death triggered by coexpression of RsIA_CtaG/Cox11 and Os_CoxVIIa is independent of the leucine-rich repeat receptor kinases BAK1/SOBIR1 and enhanced the susceptibility of N. benthamiana to AG-1 IA. Two of the three evolutionarily conserved cysteine residues at positions 25 and 126 of RsIA_CtaG/Cox11 were essential for its immunosuppressive activity, but not for cell death induction. This report suggests that RsIA_CtaG/Cox11 appears to have a dual role in immunosuppression and cell death induction during pathogenesis.
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Affiliation(s)
- Danhua Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Runmao Lin
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests Ministry of EducationHainan UniversityHaikouChina
| | - Naoki Yamamoto
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Zhaoyilin Wang
- Rice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Hui Lin
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Kazunori Okada
- Agro‐Biotechnology Research CenterThe University of TokyoTokyoJapan
| | - Yao Liu
- Key Laboratory of Sichuan Province, Crop Research InstituteSichuan Academy of Agricultural SciencesChengduChina
| | - Xing Xiang
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Tengda Zheng
- School of AgronomySichuan Agricultural UniversityChengduChina
| | | | - Xiaoqun Yi
- School of AgronomySichuan Agricultural UniversityChengduChina
| | - Yoshiteru Noutoshi
- Graduate School of Environmental, Life, and Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Aiping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- School of AgronomySichuan Agricultural UniversityChengduChina
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McCombe CL, Catanzariti AM, Greenwood JR, Desai AM, Outram MA, Yu DS, Ericsson DJ, Brenner SE, Dodds PN, Kobe B, Jones DA, Williams SJ. A rust-fungus Nudix hydrolase effector decaps mRNA in vitro and interferes with plant immune pathways. THE NEW PHYTOLOGIST 2023; 239:222-239. [PMID: 36631975 DOI: 10.1111/nph.18727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/02/2023] [Indexed: 06/02/2023]
Abstract
To infect plants, pathogenic fungi secrete small proteins called effectors. Here, we describe the catalytic activity and potential virulence function of the Nudix hydrolase effector AvrM14 from the flax rust fungus (Melampsora lini). We completed extensive in vitro assays to characterise the enzymatic activity of the AvrM14 effector. Additionally, we used in planta transient expression of wild-type and catalytically dead AvrM14 versions followed by biochemical assays, phenotypic analysis and RNA sequencing to unravel how the catalytic activity of AvrM14 impacts plant immunity. AvrM14 is an extremely selective enzyme capable of removing the protective 5' cap from mRNA transcripts in vitro. Homodimerisation of AvrM14 promoted biologically relevant mRNA cap cleavage in vitro and this activity was conserved in related effectors from other Melampsora spp. In planta expression of wild-type AvrM14, but not the catalytically dead version, suppressed immune-related reactive oxygen species production, altered the abundance of some circadian-rhythm-associated mRNA transcripts and reduced the hypersensitive cell-death response triggered by the flax disease resistance protein M1. To date, the decapping of host mRNA as a virulence strategy has not been described beyond viruses. Our results indicate that some fungal pathogens produce Nudix hydrolase effectors with in vitro mRNA-decapping activity capable of interfering with plant immunity.
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Affiliation(s)
- Carl L McCombe
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ann-Maree Catanzariti
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Julian R Greenwood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Anna M Desai
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Megan A Outram
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel S Yu
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3168, Australia
| | - Steven E Brenner
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, 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
| | - David A Jones
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Hilário S, Gonçalves MFM, Fidalgo C, Tacão M, Alves A. Genome Analyses of Two Blueberry Pathogens: Diaporthe amygdali CAA958 and Diaporthe eres CBS 160.32. J Fungi (Basel) 2022; 8:jof8080804. [PMID: 36012791 PMCID: PMC9409727 DOI: 10.3390/jof8080804] [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: 07/13/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/04/2023] Open
Abstract
The genus Diaporthe includes pathogenic species distributed worldwide and affecting a wide variety of hosts. Diaporthe amygdali and Diaporthe eres have been found to cause cankers, dieback, or twig blights on economically important crops such as soybean, almond, grapevine, and blueberry. Despite their importance as plant pathogens, the strategies of species of Diaporthe to infect host plants are poorly explored. To provide a genomic basis of pathogenicity, the genomes of D. amygdali CAA958 and D. eres CBS 160.32 were sequenced and analyzed. Cellular transporters involved in the transport of toxins, ions, sugars, effectors, and genes implicated in pathogenicity were detected in both genomes. Hydrolases and oxidoreductases were the most prevalent carbohydrate-active enzymes (CAZymes). However, analyses of the secreted proteins revealed that the secretome of D. eres CBS 160.32 is represented by 5.4% of CAZymes, whereas the secreted CAZymes repertoire of D. amygdali CAA958 represents 29.1% of all secretomes. Biosynthetic gene clusters (BGCs) encoding compounds related to phytotoxins and mycotoxins were detected in D. eres and D. amygdali genomes. The core gene clusters of the phytotoxin Fusicoccin A in D. amygdali are reported here through a genome-scale assembly. Comparative analyses of the genomes from 11 Diaporthe species revealed an average of 874 CAZymes, 101 secondary metabolite BGCs, 1640 secreted proteins per species, and genome sizes ranging from 51.5 to 63.6 Mbp. This study offers insights into the overall features and characteristics of Diaporthe genomes. Our findings enrich the knowledge about D. eres and D. amygdali, which will facilitate further research into the pathogenicity mechanisms of these species.
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Ludwig-Müller J. What Can We Learn from -Omics Approaches to Understand Clubroot Disease? Int J Mol Sci 2022; 23:ijms23116293. [PMID: 35682976 PMCID: PMC9180986 DOI: 10.3390/ijms23116293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
Clubroot is one of the most economically significant diseases worldwide. As a result, many investigations focus on both curing the disease and in-depth molecular studies. Although the first transcriptome dataset for the clubroot disease describing the clubroot disease was published in 2006, many different pathogen-host plant combinations have only recently been investigated and published. Articles presenting -omics data and the clubroot pathogen Plasmodiophora brassicae as well as different host plants were analyzed to summarize the findings in the richness of these datasets. Although genome data for the protist have only recently become available, many effector candidates have been identified, but their functional characterization is incomplete. A better understanding of the life cycle is clearly required to comprehend its function. While only a few proteome studies and metabolome analyses were performed, the majority of studies used microarrays and RNAseq approaches to study transcriptomes. Metabolites, comprising chemical groups like hormones were generally studied in a more targeted manner. Furthermore, functional approaches based on such datasets have been carried out employing mutants, transgenic lines, or ecotypes/cultivars of either Arabidopsis thaliana or other economically important host plants of the Brassica family. This has led to new discoveries of potential genes involved in disease development or in (partial) resistance or tolerance to P. brassicae. The overall contribution of individual experimental setups to a larger picture will be discussed in this review.
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Lu X, Miao J, Shen D, Dou D. Proteinaceous Effector Discovery and Characterization in Plant Pathogenic Colletotrichum Fungi. Front Microbiol 2022; 13:914035. [PMID: 35694285 PMCID: PMC9184758 DOI: 10.3389/fmicb.2022.914035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 02/05/2023] Open
Abstract
Anthracnose caused by plant pathogenic Colletotrichum fungi results in large economic losses in field crop production worldwide. To aid the establishment of plant host infection, Colletotrichum pathogens secrete numerous effector proteins either in apoplastic space or inside of host cells for effective colonization. Understanding these effector repertoires is critical for developing new strategies for resistance breeding and disease management. With the advance of genomics and bioinformatics tools, a large repertoire of putative effectors has been identified in Colletotrichum genomes, and the biological functions and molecular mechanisms of some studied effectors have been summarized. Here, we review recent advances in genomic identification, understanding of evolutional characteristics, transcriptional profiling, and functional characterization of Colletotrichum effectors. We also offer a perspective on future research.
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Affiliation(s)
| | | | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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7
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Severn-Ellis AA, Schoeman MH, Bayer PE, Hane JK, Rees DJG, Edwards D, Batley J. Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. FRONTIERS IN PLANT SCIENCE 2022; 13:811152. [PMID: 35283890 PMCID: PMC8914235 DOI: 10.3389/fpls.2022.811152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Guava wilt disease is caused by the fungus Nalanthamala psidii. The wilt disease results in large-scale destruction of orchards in South Africa, Taiwan, and several Southeast Asian countries. De novo assembly, annotation, and in-depth analysis of the N. psidii genome were carried out to facilitate the identification of characteristics associated with pathogenicity and pathogen evolution. The predicted secretome revealed a range of CAZymes, proteases, lipases and peroxidases associated with plant cell wall degradation, nutrient acquisition, and disease development. Further analysis of the N. psidii carbohydrate-active enzyme profile exposed the broad-spectrum necrotrophic lifestyle of the pathogen, which was corroborated by the identification of putative effectors and secondary metabolites with the potential to induce tissue necrosis and cell surface-dependent immune responses. Putative regulatory proteins including transcription factors and kinases were identified in addition to transporters potentially involved in the secretion of secondary metabolites. Transporters identified included important ABC and MFS transporters involved in the efflux of fungicides. Analysis of the repetitive landscape and the detection of mechanisms linked to reproduction such as het and mating genes rendered insights into the biological complexity and evolutionary potential of N. psidii as guava pathogen. Hence, the assembly and annotation of the N. psidii genome provided a valuable platform to explore the pathogenic potential and necrotrophic lifestyle of the guava wilt pathogen.
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Affiliation(s)
- Anita A. Severn-Ellis
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- Aquaculture Research and Development, Department of Primary Industries and Regional Development, Indian Ocean Marine Research Centre, Watermans Bay, WA, Australia
| | - Maritha H. Schoeman
- Institute for Tropical and Subtropical Crops, Agricultural Research Council, Nelspruit, South Africa
| | - Philipp E. Bayer
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - D. Jasper G. Rees
- Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
- Botswana University of Agriculture and Natural Resources, Gaborone, Botswana
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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He H, Zhang Y, Wen B, Meng X, Wang N, Sun M, Zhang R, Zhao X, Tan Q, Xiao W, Li D, Fu X, Chen X, Li L. PpNUDX8, a Peach NUDIX Hydrolase, Plays a Negative Regulator in Response to Drought Stress. FRONTIERS IN PLANT SCIENCE 2022; 12:831883. [PMID: 35251068 PMCID: PMC8888663 DOI: 10.3389/fpls.2021.831883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Drought stress is a serious abiotic stress source that affects the growth and fruit quality of peach trees. However, the molecular mechanism of the NUDIX hydrolase family in peaches in response to drought stress is still unclear. Here, we isolated and identified the PpNUDX8 (Prupe.5G062300.1) gene from the peach NUDIX hydrolase family, and found that PpNUDX8 has a typical NUDIX hydrolase domain. In this study, we performed 15% PEG6000 drought treatment on peach seedlings, and qRT-PCR analysis showed that 15% PEG6000 induced the transcription level of PpNUDX8. Overexpression of PpNUDX8 reduced the tolerance of calli to 4% PEG6000 treatment. Compared with wild-type apple calli, PpNUDX8 transgenic apple calli had a lower fresh weight and higher MDA content. After 15% PEG6000 drought treatment, PpNUDX8 transgenic tobacco had a greater degree of wilting and shorter primary roots than Under control conditions. The chlorophyll, soluble protein, and proline contents in the transgenic tobacco decreased, and the MDA content and relative conductivity increased. At the same time, PpNUDX8 negatively regulated ABA signal transduction and reduced the transcriptional expression of stress response genes. In addition, PpNUDX8 was not sensitive to ABA, overexpression of PpNUDX8 reduced the expression of the ABA synthesis-related gene NCED6 and increases the expression of the ABA decomposition-related gene CYP1 in tobacco, which in turn leads to a decrease in the ABA content in tobacco. In addition, Under control conditions, overexpression of PpNUDX8 destroyed the homeostasis of NAD and reduced nicotinamide adenine dinucleotide (NADH) in tobacco. After 15% PEG6000 drought treatment, the changes in NAD and NADH in PpNUDX8 transgenic tobacco were more severe than those in WT tobacco. In addition, PpNUDX8 also interacted with PpSnRk1γ (Prupe.6G323700.1).
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Affiliation(s)
- HuaJie He
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - YuZheng Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - BinBin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - XiangGuang Meng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - Ning Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - MingYun Sun
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - Rui Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - XueHui Zhao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - QiuPing Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
- College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Wei Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - DongMei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - XiLing Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - XiuDe Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- Shandong Province Collaborative Innovation Center for High-Quality and High-Efficiency Vegetable Production, Taian, China
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Villalobos Solis MI, Engle NL, Spangler MK, Cottaz S, Fort S, Maeda J, Ané JM, Tschaplinski TJ, Labbé JL, Hettich RL, Abraham PE, Rush TA. Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:808578. [PMID: 37746234 PMCID: PMC10512320 DOI: 10.3389/ffunb.2022.808578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 09/26/2023]
Abstract
The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor, the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO4), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor. Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.
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Affiliation(s)
| | - Nancy L. Engle
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Margaret K. Spangler
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sylvain Cottaz
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Sébastien Fort
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Jesse L. Labbé
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Paul E. Abraham
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Tomás A. Rush
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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10
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Galindo-González L, Hwang SF, Strelkov SE. Candidate Effectors of Plasmodiophora brassicae Pathotype 5X During Infection of Two Brassica napus Genotypes. Front Microbiol 2021; 12:742268. [PMID: 34803960 PMCID: PMC8595600 DOI: 10.3389/fmicb.2021.742268] [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: 07/15/2021] [Accepted: 10/11/2021] [Indexed: 01/28/2023] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is one of the most important diseases of canola (Brassica napus) in Canada. Disease management relies heavily on planting clubroot resistant (CR) cultivars, but in recent years, new resistance-breaking pathotypes of P. brassicae have emerged. Current efforts against the disease are concentrated in developing host resistance using traditional genetic breeding, omics and molecular biology. However, because of its obligate biotrophic nature, limited resources have been dedicated to investigating molecular mechanisms of pathogenic infection. We previously performed a transcriptomic study with the cultivar resistance-breaking pathotype 5X on two B. napus hosts presenting contrasting resistance/susceptibility, where we evaluated the mechanisms of host response. Since cultivar-pathotype interactions are very specific, and pathotype 5X is one of the most relevant resistance-breaking pathotypes in Canada, in this study, we analyze the expression of genes encoding putative secreted proteins from this pathotype, predicted using a bioinformatics pipeline, protein modeling and orthologous comparisons with effectors from other pathosystems. While host responses were found to differ markedly in our previous study, many common effectors are found in the pathogen while infecting both hosts, and the gene response among biological pathogen replicates seems more consistent in the effectors associated with the susceptible interaction, especially at 21 days after inoculation. The predicted effectors indicate the predominance of proteins with interacting domains (e.g., ankyrin), and genes bearing kinase and NUDIX domains, but also proteins with protective action against reactive oxygen species from the host. Many of these genes confirm previous predictions from other clubroot studies. A benzoic acid/SA methyltransferase (BSMT), which methylates SA to render it inactive, showed high levels of expression in the interactions with both hosts. Interestingly, our data indicate that E3 ubiquitin proteasome elements are also potentially involved in pathogenesis. Finally, a gene with similarity to indole-3-acetaldehyde dehydrogenase is a promising candidate effector because of its involvement in indole acetic acid synthesis, since auxin is one of the major players in clubroot development.
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Affiliation(s)
| | | | - Stephen E. Strelkov
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada
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11
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Brouwer SM, Brus-Szkalej M, Saripella GV, Liang D, Liljeroth E, Grenville-Briggs LJ. Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani. PLANTS (BASEL, SWITZERLAND) 2021; 10:2212. [PMID: 34686023 PMCID: PMC8539873 DOI: 10.3390/plants10102212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022]
Abstract
Potato early blight is caused by the necrotrophic fungus Alternaria solani and can result in yield losses of up to 50% if left uncontrolled. At present, the disease is controlled by chemical fungicides, yet rapid development of fungicide resistance renders current control strategies unsustainable. On top of that, a lack of understanding of potato defences and the quantitative nature of resistance mechanisms against early blight hinders the development of more sustainable control methods. Necrotrophic pathogens, compared to biotrophs, pose an extra challenge to the plant, since common defence strategies to biotic stresses such as the hypersensitive response and programmed cell death are often beneficial for necrotrophs. With the aim of unravelling plant responses to both the early infection stages (i.e., before necrosis), such as appressorium formation and penetration, as well as to later responses to the onset of necrosis, we present here a transcriptome analysis of potato interactions with A. solani from 1 h after inoculation when the conidia have just commenced germination, to 48 h post inoculation when multiple cell necrosis has begun. Potato transcripts with putative functions related to biotic stress tolerance and defence against pathogens were upregulated, including a putative Nudix hydrolase that may play a role in defence against oxidative stress. A. solani transcripts encoding putative pathogenicity factors, such as cell wall degrading enzymes and metabolic processes that may be important for infection. We therefore identified the differential expression of several potato and A. solani transcripts that present a group of valuable candidates for further studies into their roles in immunity or disease development.
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Affiliation(s)
- Sophie M. Brouwer
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 7070, SE-750 07 Uppsala, Sweden; (M.B.-S.); (D.L.); (E.L.)
| | - Maja Brus-Szkalej
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 7070, SE-750 07 Uppsala, Sweden; (M.B.-S.); (D.L.); (E.L.)
| | - Ganapathi V. Saripella
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 7070, SE-750 07 Uppsala, Sweden;
| | - Dong Liang
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 7070, SE-750 07 Uppsala, Sweden; (M.B.-S.); (D.L.); (E.L.)
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Erland Liljeroth
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 7070, SE-750 07 Uppsala, Sweden; (M.B.-S.); (D.L.); (E.L.)
| | - Laura J. Grenville-Briggs
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 7070, SE-750 07 Uppsala, Sweden; (M.B.-S.); (D.L.); (E.L.)
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12
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Gazengel K, Aigu Y, Lariagon C, Humeau M, Gravot A, Manzanares-Dauleux MJ, Daval S. Nitrogen Supply and Host-Plant Genotype Modulate the Transcriptomic Profile of Plasmodiophora brassicae. Front Microbiol 2021; 12:701067. [PMID: 34305867 PMCID: PMC8298192 DOI: 10.3389/fmicb.2021.701067] [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: 04/27/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Nitrogen fertilization can affect the susceptibility of Brassica napus to the telluric pathogen Plasmodiophora brassicae. Our previous works highlighted that the influence of nitrogen can strongly vary regarding plant cultivar/pathogen strain combinations, but the underlying mechanisms are unknown. The present work aims to explore how nitrogen supply can affect the molecular physiology of P. brassicae through its life epidemiological cycle. A time-course transcriptome experiment was conducted to study the interaction, under two conditions of nitrogen supply, between isolate eH and two B. napus genotypes (Yudal and HD-018), harboring (or not harboring) low nitrogen-conditional resistance toward this isolate (respectively). P. brassicae transcriptional patterns were modulated by nitrogen supply, these modulations being dependent on both host-plant genotype and kinetic time. Functional analysis allowed the identification of P. brassicae genes expressed during the secondary phase of infection, which may play a role in the reduction of Yudal disease symptoms in low-nitrogen conditions. Candidate genes included pathogenicity-related genes ("NUDIX," "carboxypeptidase," and "NEP-proteins") and genes associated to obligate biotrophic functions of P. brassicae. This work illustrates the importance of considering pathogen's physiological responses to get a better understanding of the influence of abiotic factors on clubroot resistance/susceptibility.
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Affiliation(s)
| | | | | | | | | | | | - Stéphanie Daval
- IGEPP, INRAE, Institut Agro, Université Rennes 1, Le Rheu, France
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13
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Li D, Li S, Wei S, Sun W. Strategies to Manage Rice Sheath Blight: Lessons from Interactions between Rice and Rhizoctonia solani. RICE (NEW YORK, N.Y.) 2021; 14:21. [PMID: 33630178 PMCID: PMC7907341 DOI: 10.1186/s12284-021-00466-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Rhizoctonia solani is an important phytopathogenic fungus with a wide host range and worldwide distribution. The anastomosis group AG1 IA of R. solani has been identified as the predominant causal agent of rice sheath blight, one of the most devastating diseases of crop plants. As a necrotrophic pathogen, R. solani exhibits many characteristics different from biotrophic and hemi-biotrophic pathogens during co-evolutionary interaction with host plants. Various types of secondary metabolites, carbohydrate-active enzymes, secreted proteins and effectors have been revealed to be essential pathogenicity factors in R. solani. Meanwhile, reactive oxygen species, phytohormone signaling, transcription factors and many other defense-associated genes have been identified to contribute to sheath blight resistance in rice. Here, we summarize the recent advances in studies on molecular interactions between rice and R. solani. Based on knowledge of rice-R. solani interactions and sheath blight resistance QTLs, multiple effective strategies have been developed to generate rice cultivars with enhanced sheath blight resistance.
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Affiliation(s)
- Dayong Li
- College of Plant Protection, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Shuai Li
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China
| | - Songhong Wei
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, 110866, Shenyang, Liaoning, China
| | - Wenxian Sun
- College of Plant Protection, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China.
- Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, 100193, Beijing, China.
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14
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Daval S, Gazengel K, Belcour A, Linglin J, Guillerm‐Erckelboudt A, Sarniguet A, Manzanares‐Dauleux MJ, Lebreton L, Mougel C. Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes. Microb Biotechnol 2020; 13:1648-1672. [PMID: 32686326 PMCID: PMC7415369 DOI: 10.1111/1751-7915.13634] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
The contribution of surrounding plant microbiota to disease development has led to the 'pathobiome' concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time-course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defence-related genes (glucosinolate metabolism) in B. napus.
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Affiliation(s)
- Stéphanie Daval
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
| | - Kévin Gazengel
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
| | | | - Juliette Linglin
- INRAEAgrocampus OuestUniversité de RennesIGEPPPloudanielF‐29260France
| | | | - Alain Sarniguet
- INRAEAgrocampus OuestUniversité d'AngersIRHSBeaucouzéF‐49071France
| | | | - Lionel Lebreton
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
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15
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Sasseron GR, Benchimol-Reis LL, Perseguini JMKC, Paulino JFC, Bajay MM, Carbonell SAM, Chiorato AF. Fusarium oxysporum f. sp. phaseoli genetic variability assessed by new developed microsatellites. Genet Mol Biol 2020; 43:e20190267. [PMID: 32478796 PMCID: PMC7263423 DOI: 10.1590/1678-4685-gmb-2019-0267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 03/11/2020] [Indexed: 11/22/2022] Open
Abstract
Fusarium oxysporum f. sp. phaseoli (Fop) J.B. Kendrich & W.C. Snyder is the causal agent of Fusarium wilt of common bean (Phaseolus vulgaris L.). The objective of this study was to develop microsatellite markers (SSRs) to characterize the genetic diversity of Fop. Two libraries enriched with SSRs were developed and a total of 40 pairs of SSRs were characterized. Out of these, 15 SSRs were polymorphic for 42 Fop isolates. The number of alleles varied from two to ten, with an average of four alleles per locus and an average PIC (Polymorphic Information Content) of 0.38. The genetic diversity assessed by microsatellites for Fop was low, as expected for an asexual fungus, and not associated with geographic origin, but they were able to detect enough genetic variability among isolates in order to differentiate them. Microsatellites are a robust tool widely used for genetic fingerprinting and population structure analyses. SSRs for Fop may be an efficient tool for a better understanding of the ecology, epidemiology and evolution of this pathogen.
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Affiliation(s)
- Graziéle R Sasseron
- Instituto Agrônomico (IAC), Centro de Pesquisa em Recursos Genéticos, Campinas, SP, Brazil
| | | | | | - Jean Fausto C Paulino
- Instituto Agrônomico (IAC), Centro de Pesquisa em Recursos Genéticos, Campinas, SP, Brazil
| | - Miklos M Bajay
- Universidade do Estado de Santa Catarina (UDESC), Centro de Educação Superior da Região Sul da (CERES), Departamento de Engenharia de Pesca e Ciências Biológicas (DEPB), Laguna, SC, Brazil
| | - Sérgio A M Carbonell
- Instituto Agrônomico (IAC), Centro de Análise e Pesquisa Tecnológica do Agronegócio dos Grãos e Fibras, Campinas, SP, Brazil
| | - Alisson F Chiorato
- Instituto Agrônomico (IAC), Centro de Análise e Pesquisa Tecnológica do Agronegócio dos Grãos e Fibras, Campinas, SP, Brazil
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16
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Bhaskar Rao T, Chopperla R, Prathi NB, Balakrishnan M, Prakasam V, Laha GS, Balachandran SM, Mangrauthia SK. A Comprehensive Gene Expression Profile of Pectin Degradation Enzymes Reveals the Molecular Events during Cell Wall Degradation and Pathogenesis of Rice Sheath Blight Pathogen Rhizoctonia solani AG1-IA. J Fungi (Basel) 2020; 6:E71. [PMID: 32466257 PMCID: PMC7345747 DOI: 10.3390/jof6020071] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 11/16/2022] Open
Abstract
Sheath blight disease of rice caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris) remains a global challenge due to the absence of reliable resistance genes and poor understanding of pathogen biology. Pectin, one of the most vital constituents of the plant cell wall, is targeted by pectin methylesterases, polygalacturonases, and few other enzymes of fungal pathogens. In this study, we catalogued the expressed genes of the fungal genome from RNAseq of R. solani infected four rice genotypes. Analysis of RNAseq revealed 3325 pathogen genes commonly expressed in all rice genotypes, in which 49, 490, and 83 genes were specific to BPT5204, Tetep, and Pankaj genotypes, respectively. To identify the early and late responding genes of R. solani during plant cell wall degradation, a real-time PCR analysis of 30 pectinolytic enzymes was done at six different time points after inoculation. The majority of these genes showed maximum induction at the 72 h time point, suggesting that it is the most crucial stage of infection. Pankaj showed lesser induction of these genes as compared to other genotypes. Leaf-blade tissue and 45 days old-growth stage are more favorable for the expression of pectin degradation genes of R. solani. Additionally, the expression analysis of these genes from four different strains of R. solani suggested differential regulation of genes but no distinct expression pattern between highly virulent and mild strains. The implications of the differential regulation of these genes in disease development have been discussed. This study provides the first such comprehensive analysis of R. solani genes encoding pectin degrading enzymes, which would help to decipher the pathogen biology and sheath blight disease development.
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Affiliation(s)
- Talluri Bhaskar Rao
- Indian Council of Agricultural Research-Indian Institute of Rice Research, Hyderabad 500030, India; (T.B.R.); (R.C.); (N.B.P.); (V.P.); (G.S.L.); (S.M.B.)
| | - Ramakrishna Chopperla
- Indian Council of Agricultural Research-Indian Institute of Rice Research, Hyderabad 500030, India; (T.B.R.); (R.C.); (N.B.P.); (V.P.); (G.S.L.); (S.M.B.)
| | - Naresh Babu Prathi
- Indian Council of Agricultural Research-Indian Institute of Rice Research, Hyderabad 500030, India; (T.B.R.); (R.C.); (N.B.P.); (V.P.); (G.S.L.); (S.M.B.)
| | - Marudamuthu Balakrishnan
- Bioinformatics Lab, ICAR- National Academy of Agricultural Research Management, Hyderabad 500030, India;
| | - Vellaisamy Prakasam
- Indian Council of Agricultural Research-Indian Institute of Rice Research, Hyderabad 500030, India; (T.B.R.); (R.C.); (N.B.P.); (V.P.); (G.S.L.); (S.M.B.)
| | - Gouri Sankar Laha
- Indian Council of Agricultural Research-Indian Institute of Rice Research, Hyderabad 500030, India; (T.B.R.); (R.C.); (N.B.P.); (V.P.); (G.S.L.); (S.M.B.)
| | - Sena Munuswamy Balachandran
- Indian Council of Agricultural Research-Indian Institute of Rice Research, Hyderabad 500030, India; (T.B.R.); (R.C.); (N.B.P.); (V.P.); (G.S.L.); (S.M.B.)
| | - Satendra K. Mangrauthia
- Indian Council of Agricultural Research-Indian Institute of Rice Research, Hyderabad 500030, India; (T.B.R.); (R.C.); (N.B.P.); (V.P.); (G.S.L.); (S.M.B.)
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17
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Pérez‐López E, Hossain MM, Tu J, Waldner M, Todd CD, Kusalik AJ, Wei Y, Bonham‐Smith PC. Transcriptome Analysis Identifies Plasmodiophora brassicae Secondary Infection Effector Candidates. J Eukaryot Microbiol 2020; 67:337-351. [PMID: 31925980 PMCID: PMC7317818 DOI: 10.1111/jeu.12784] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 12/15/2019] [Accepted: 01/04/2020] [Indexed: 12/17/2022]
Abstract
Plasmodiophora brassicae (Wor.) is an obligate intracellular plant pathogen affecting Brassicas worldwide. Identification of effector proteins is key to understanding the interaction between P. brassicae and its susceptible host plants. To date, there is very little information available on putative effector proteins secreted by P. brassicae during a secondary infection of susceptible host plants, resulting in root gall production. A bioinformatics pipeline approach to RNA-Seq data from Arabidopsis thaliana (L.) Heynh. root tissues at 17, 20, and 24 d postinoculation (dpi) identified 32 small secreted P. brassicae proteins (SSPbPs) that were highly expressed over this secondary infection time frame. Functional signal peptides were confirmed for 31 of the SSPbPs, supporting the accuracy of the pipeline designed to identify secreted proteins. Expression profiles at 0, 2, 5, 7, 14, 21, and 28 dpi verified the involvement of some of the SSPbPs in secondary infection. For seven of the SSPbPs, a functional domain was identified using Blast2GO and 3D structure analysis and domain functionality was confirmed for SSPbP22, a kinase localized to the cytoplasm and nucleus.
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Affiliation(s)
- Edel Pérez‐López
- Department of BiologyUniversity of SaskatchewanSaskatoonSKS7N 5E2Canada
| | | | - Jiangying Tu
- Agriculture and Agri‐food CanadaSaskatoon Research CentreSaskatoonSKS7N 0X2Canada
| | - Matthew Waldner
- Department of Computer ScienceUniversity of SaskatchewanSaskatoonSKS7N 5C9Canada
| | | | - Anthony J. Kusalik
- Department of Computer ScienceUniversity of SaskatchewanSaskatoonSKS7N 5C9Canada
| | - Yangdou Wei
- Department of BiologyUniversity of SaskatchewanSaskatoonSKS7N 5E2Canada
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18
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McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux SJ, Browning KS, Chen ZJ, Ronald PC, Marcotte EM. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. Cell 2020; 181:460-474.e14. [PMID: 32191846 PMCID: PMC7297045 DOI: 10.1016/j.cell.2020.02.049] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/08/2020] [Accepted: 02/21/2020] [Indexed: 01/11/2023]
Abstract
Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.
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Affiliation(s)
- Claire D McWhite
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Kevin Drew
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Rachael M Cox
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Viviana June
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA; Joint Bioenergy Institute, Emeryville, CA 94608, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Cuihong Wan
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA; Hubei Key Lab of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, P.R. China
| | - Mari L Salmi
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Karen S Browning
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Pamela C Ronald
- Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA; Joint Bioenergy Institute, Emeryville, CA 94608, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA.
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19
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Zhang Y, Fletcher K, Han R, Michelmore R, Yang R. Genome-Wide Analysis of Cyclophilin Proteins in 21 Oomycetes. Pathogens 2019; 9:E24. [PMID: 31888032 PMCID: PMC7168621 DOI: 10.3390/pathogens9010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
Cyclophilins (CYPs), a highly-conserved family of proteins, belong to a subgroup of immunophilins. Ubiquitous in eukaryotes and prokaryotes, CYPs have peptidyl-prolyl cis-trans isomerase (PPIase) activity and have been implicated as virulence factors in plant pathogenesis by oomycetes. We identified 16 CYP orthogroups from 21 diverse oomycetes. Each species was found to encode 15 to 35 CYP genes. Three of these orthogroups contained proteins with signal peptides at the N-terminal end, suggesting a role in secretion. Multidomain analysis revealed five conserved motifs of the CYP domain of oomycetes shared with other eukaryotic PPIases. Expression analysis of CYP proteins in different asexual life stages of the hemibiotrophic Phytophthora infestans and the biotrophic Plasmopara halstedii demonstrated distinct expression profiles between life stages. In addition to providing detailed comparative information on the CYPs in multiple oomycetes, this study identified candidate CYP effectors that could be the foundation for future studies of virulence.
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Affiliation(s)
- Yan Zhang
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China;
- Genome Center, University of California, Davis, CA 95616, USA; (K.F.); (R.H.); (R.M.)
| | - Kyle Fletcher
- Genome Center, University of California, Davis, CA 95616, USA; (K.F.); (R.H.); (R.M.)
| | - Rongkui Han
- Genome Center, University of California, Davis, CA 95616, USA; (K.F.); (R.H.); (R.M.)
| | - Richard Michelmore
- Genome Center, University of California, Davis, CA 95616, USA; (K.F.); (R.H.); (R.M.)
| | - Ruiwu Yang
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China;
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20
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Gonçalves MFM, Nunes RB, Tilleman L, Van de Peer Y, Deforce D, Van Nieuwerburgh F, Esteves AC, Alves A. Dual RNA Sequencing of Vitis vinifera during Lasiodiplodia theobromae Infection Unveils Host-Pathogen Interactions. Int J Mol Sci 2019; 20:E6083. [PMID: 31816814 PMCID: PMC6928909 DOI: 10.3390/ijms20236083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 11/25/2022] Open
Abstract
Lasiodiplodia theobromae is one of the most aggressive agents of the grapevine trunk disease Botryosphaeria dieback. Through a dual RNA-sequencing approach, this study aimed to give a broader perspective on the infection strategy deployed by L. theobromae, while understanding grapevine response. Approximately 0.05% and 90% of the reads were mapped to the genomes of L. theobromae and Vitis vinifera, respectively. Over 2500 genes were significantly differentially expressed in infected plants after 10 dpi, many of which are involved in the inducible defense mechanisms of grapevines. Gene expression analysis showed changes in the fungal metabolism of phenolic compounds, carbohydrate metabolism, transmembrane transport, and toxin synthesis. These functions are related to the pathogenicity mechanisms involved in plant cell wall degradation and fungal defense against antimicrobial substances produced by the host. Genes encoding for the degradation of plant phenylpropanoid precursors were up-regulated, suggesting that the fungus could evade the host defense response using the phenylpropanoid pathway. The up-regulation of many distinct components of the phenylpropanoid pathway in plants supports this hypothesis. Moreover, genes related to phytoalexin biosynthesis, hormone metabolism, cell wall modification enzymes, and pathogenesis-related proteins seem to be involved in the host responses observed. This study provides additional insights into the molecular mechanisms of L. theobromae and V. vinifera interactions.
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Affiliation(s)
- Micael F. M. Gonçalves
- Department of Biology, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (R.B.N.)
| | - Rui B. Nunes
- Department of Biology, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (R.B.N.)
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium; (L.T.); (D.D.); (F.V.N.)
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium; (L.T.); (D.D.); (F.V.N.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium; (L.T.); (D.D.); (F.V.N.)
| | - Ana C. Esteves
- Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, Estrada da Circunvalação, 3504-505 Viseu, Portugal;
| | - Artur Alves
- Department of Biology, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (R.B.N.)
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21
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Frank AC. Molecular host mimicry and manipulation in bacterial symbionts. FEMS Microbiol Lett 2019; 366:5342066. [PMID: 30877310 DOI: 10.1093/femsle/fnz038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/18/2019] [Indexed: 12/17/2022] Open
Abstract
It is common among intracellular bacterial pathogens to use eukaryotic-like proteins that mimic and manipulate host cellular processes to promote colonization and intracellular survival. Eukaryotic-like proteins are bacterial proteins with domains that are rare in bacteria, and known to function in the context of a eukaryotic cell. Such proteins can originate through horizontal gene transfer from eukaryotes or, in the case of simple repeat proteins, through convergent evolution. Recent studies of microbiomes associated with several eukaryotic hosts suggest that similar molecular strategies are deployed by cooperative bacteria that interact closely with eukaryotic cells. Some mimics, like ankyrin repeats, leucine rich repeats and tetratricopeptide repeats are shared across diverse symbiotic systems ranging from amoebae to plants, and may have originated early, or evolved independently in multiple systems. Others, like plant-mimicking domains in members of the plant microbiome are likely to be more recent innovations resulting from horizontal gene transfer from the host, or from microbial eukaryotes occupying the same host. Host protein mimics have only been described in a limited set of symbiotic systems, but are likely to be more widespread. Systematic searches for eukaryote-like proteins in symbiont genomes could lead to the discovery of novel mechanisms underlying host-symbiont interactions.
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Affiliation(s)
- A Carolin Frank
- Life and Environmental Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA.,Sierra Nevada Research Institute, School of Natural Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA
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22
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Félix C, Meneses R, Gonçalves MFM, Tilleman L, Duarte AS, Jorrín-Novo JV, Van de Peer Y, Deforce D, Van Nieuwerburgh F, Esteves AC, Alves A. A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes. Sci Rep 2019; 9:13144. [PMID: 31511626 PMCID: PMC6739476 DOI: 10.1038/s41598-019-49551-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022] Open
Abstract
Lasiodiplodia theobromae (Botryosphaeriaceae, Ascomycota) is a plant pathogen and human opportunist whose pathogenicity is modulated by temperature. The molecular effects of temperature on L. theobromae are mostly unknown, so we used a multi-omics approach to understand how temperature affects the molecular mechanisms of pathogenicity. The genome of L. theobromae LA-SOL3 was sequenced (Illumina MiSeq) and annotated. Furthermore, the transcriptome (Illumina TruSeq) and proteome (Orbitrap LC-MS/MS) of LA-SOL3 grown at 25 °C and 37 °C were analysed. Proteins related to pathogenicity (plant cell wall degradation, toxin synthesis, mitogen-activated kinases pathway and proteins involved in the velvet complex) were more abundant when the fungus grew at 25 °C. At 37 °C, proteins related to pathogenicity were less abundant than at 25 °C, while proteins related to cell wall organisation were more abundant. On the other hand, virulence factors involved in human pathogenesis, such as the SSD1 virulence protein, were expressed only at 37 °C. Taken together, our results showed that this species presents a typical phytopathogenic molecular profile that is compatible with a hemibiotrophic lifestyle. We showed that L. theobromae is equipped with the pathogenesis toolbox that enables it to infect not only plants but also animals.
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Affiliation(s)
- Carina Félix
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Rodrigo Meneses
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Micael F M Gonçalves
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Ana S Duarte
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
- Portuguese Catholic University, Health Science Institute-Viseu, Estrada da Circunvalação, 3504-505, Viseu, Portugal
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Córdoba, Spain
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Ana C Esteves
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
- Portuguese Catholic University, Health Science Institute-Viseu, Estrada da Circunvalação, 3504-505, Viseu, Portugal
| | - Artur Alves
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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23
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Cale JA, Klutsch JG, Dykstra CB, Peters B, Erbilgin N. Pathophysiological responses of pine defensive metabolites largely lack differences between pine species but vary with eliciting ophiostomatoid fungal species. TREE PHYSIOLOGY 2019; 39:1121-1135. [PMID: 30877758 DOI: 10.1093/treephys/tpz012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/18/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Phytopathogenic ophiostomatoid fungi are common associates of bark beetles and contribute to beetle-associated mortality of trees. Mountain pine beetle outbreaks in Canada are facilitating novel associations between its vectored fungi (Grosmannia clavigera, Leptographium longiclavatum and Ophiostoma montium) and jack pine. How the induced defense-related metabolite responses of jack and lodgepole pines vary in response to the fungi is unknown. Understanding this variation is important to clarifying pine susceptibility to and the physiological impacts of infection. We used a comparative metabolite profiling approach to investigate the defense-related signaling, carbon utilization/mobilization, and synthesis responses of both pines to the fungi. Both pine species largely exhibited similar metabolite responses to the fungi. The magnitude of pine metabolite responses positively reflected pathogen virulence. Our findings indicate that pines can recognize and metabolomically respond to novel pathogens, likely due to signals common between the novel fungi and fungi coevolved with the pine. Thus, jack pine is likely as susceptible as lodgepole pine to infections by each of the MPB-vectored fungi. Furthermore, the magnitude of the metabolite responses of both pines varied by the eliciting fungal species, with the most virulent pathogen causing the greatest reduction in carbohydrates and the highest accumulation of defensive terpenes.
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Affiliation(s)
- Jonathan A Cale
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Jennifer G Klutsch
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Christien B Dykstra
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Brosnon Peters
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
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24
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Sun Y, Li P, Shen D, Wei Q, He J, Lu Y. The Ralstonia solanacearum effector RipN suppresses plant PAMP-triggered immunity, localizes to the endoplasmic reticulum and nucleus, and alters the NADH/NAD + ratio in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2019; 20:533-546. [PMID: 30499216 PMCID: PMC6637912 DOI: 10.1111/mpp.12773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ralstonia solanacearum, one of the most destructive plant bacterial pathogens, delivers an array of effector proteins via its type III secretion system for pathogenesis. However, the biochemical functions of most of these proteins remain unclear. RipN is a type III effector with unknown function(s) from the pathogen R. solanacearum. Here, we demonstrate that RipN is a conserved type III effector found within the R. solanacearum species complex that contains a putative Nudix hydrolase domain and has ADP-ribose/NADH pyrophosphorylase activity in vitro. Further analysis shows that RipN localizes to the endoplasmic reticulum (ER) and nucleus in Nicotiana tabacum leaf cells and Arabidopsis protoplasts, and truncation of the C-terminus of RipN results in a loss of nuclear and ER targeting. Furthermore, the expression of RipN in Arabidopsis suppresses callose deposition and the transcription of pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) marker genes under flg22 treatment, and promotes bacterial growth in planta. In addition, the expression of RipN in plant cells alters NADH/NAD+ , but not GSH/GSSG, ratios, and its Nudix hydrolase activity is indispensable for such biochemical function. These results suggest that RipN acts as a Nudix hydrolase, alters the NADH/NAD+ ratio of the plant and contributes to R. solanacearum virulence by suppression of PTI of the host.
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Affiliation(s)
- Yunhao Sun
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- State Key Laboratory of BiocontrolSun Yat‐sen UniversityGuangzhou510275China
| | - Pai Li
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- State Key Laboratory of BiocontrolSun Yat‐sen UniversityGuangzhou510275China
| | - Dong Shen
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- State Key Laboratory of BiocontrolSun Yat‐sen UniversityGuangzhou510275China
| | - Qiaoling Wei
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- State Key Laboratory of BiocontrolSun Yat‐sen UniversityGuangzhou510275China
| | - Jianguo He
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- State Key Laboratory of BiocontrolSun Yat‐sen UniversityGuangzhou510275China
| | - Yongjun Lu
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- State Key Laboratory of BiocontrolSun Yat‐sen UniversityGuangzhou510275China
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25
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Liu L, Xu L, Jia Q, Pan R, Oelmüller R, Zhang W, Wu C. Arms race: diverse effector proteins with conserved motifs. PLANT SIGNALING & BEHAVIOR 2019; 14:1557008. [PMID: 30621489 PMCID: PMC6351098 DOI: 10.1080/15592324.2018.1557008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.
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Affiliation(s)
- Liping Liu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Qie Jia
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
- CONTACT Wenying Zhang Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou 434025, China; Chu Wu College of Horticulture & Gardening, Yangtze University, Jingzhou 434025, China
| | - Chu Wu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
- Institute of Plant Ecology and Environmental Restoration, Yangtze University, Jingzhou, China
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26
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Armitage AD, Lysøe E, Nellist CF, Lewis LA, Cano LM, Harrison RJ, Brurberg MB. Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum. PLoS One 2018; 13:e0202305. [PMID: 30278048 PMCID: PMC6168125 DOI: 10.1371/journal.pone.0202305] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022] Open
Abstract
The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.
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Affiliation(s)
| | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway
| | | | | | - Liliana M. Cano
- University of Florida, UF/IFAS Indian River Research and Education Center, Fort Pierce, Florida, United States of America
- The Sainsbury Laboratory, Norwich, United Kingdom
| | | | - May B. Brurberg
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway
- Norwegian University of Life Sciences (NMBU), Department of Plant Sciences, Ås, Norway
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27
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Plaumann PL, Schmidpeter J, Dahl M, Taher L, Koch C. A Dispensable Chromosome Is Required for Virulence in the Hemibiotrophic Plant Pathogen Colletotrichum higginsianum. Front Microbiol 2018; 9:1005. [PMID: 29867895 PMCID: PMC5968395 DOI: 10.3389/fmicb.2018.01005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/30/2018] [Indexed: 01/01/2023] Open
Abstract
The hemibiotrophic plant pathogen Colletotrichum higginsianum infects Brassicaceae and in combination with Arabidopsis thaliana, represents an important model system to investigate various ecologically important fungal pathogens and their infection strategies. After penetration of plant cells by appressoria, C. higginsianum establishes large biotrophic primary hyphae in the first infected cell. Shortly thereafter, a switch to necrotrophic growth occurs leading to the invasion of neighboring cells by secondary hyphae. In a forward genetic screen for virulence mutants by insertional mutagenesis, we identified mutants that penetrate the plant but show a defect in the passage from biotrophy to necrotrophy. Genome sequencing and pulsed-field gel electrophoresis revealed that two mutants were lacking chromosome 11, encoding potential pathogenicity genes. We established a chromosome loss assay to verify that strains lacking this small chromosome abort infection during biotrophy, while their ability to grow on artificial media was not affected. C. higginsianum harbors a second small chromosome, which can be lost without effects on virulence or growth on agar plates. Furthermore, we found that chromosome 11 is required to suppress Arabidopsis thaliana plant defense mechanisms dependent on tryptophan derived secondary metabolites.
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Affiliation(s)
- Peter-Louis Plaumann
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schmidpeter
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marlis Dahl
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Leila Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Koch
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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28
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Rao S, Nandineni MR. Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum. PLoS One 2017; 12:e0183567. [PMID: 28846714 PMCID: PMC5573122 DOI: 10.1371/journal.pone.0183567] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/07/2017] [Indexed: 12/16/2022] Open
Abstract
Colletotrichum truncatum, a major fungal phytopathogen, causes the anthracnose disease on an economically important spice crop chilli (Capsicum annuum), resulting in huge economic losses in tropical and sub-tropical countries. It follows a subcuticular intramural infection strategy on chilli with a short, asymptomatic, endophytic phase, which contrasts with the intracellular hemibiotrophic lifestyle adopted by most of the Colletotrichum species. However, little is known about the molecular determinants and the mechanism of pathogenicity in this fungus. A high quality whole genome sequence and gene annotation based on transcriptome data of an Indian isolate of C. truncatum from chilli has been obtained. Analysis of the genome sequence revealed a rich repertoire of pathogenicity genes in C. truncatum encoding secreted proteins, effectors, plant cell wall degrading enzymes, secondary metabolism associated proteins, with potential roles in the host-specific infection strategy, placing it next only to the Fusarium species. The size of genome assembly, number of predicted genes and some of the functional categories were similar to other sequenced Colletotrichum species. The comparative genomic analyses with other species and related fungi identified some unique genes and certain highly expanded gene families of CAZymes, proteases and secondary metabolism associated genes in the genome of C. truncatum. The draft genome assembly and functional annotation of potential pathogenicity genes of C. truncatum provide an important genomic resource for understanding the biology and lifestyle of this important phytopathogen and will pave the way for designing efficient disease control regimens.
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Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, India
- Graduate studies, Manipal University, Manipal, Karnataka, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, India
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29
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Srouji JR, Xu A, Park A, Kirsch JF, Brenner SE. The evolution of function within the Nudix homology clan. Proteins 2017; 85:775-811. [PMID: 27936487 PMCID: PMC5389931 DOI: 10.1002/prot.25223] [Citation(s) in RCA: 42] [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: 06/21/2016] [Revised: 10/15/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
The Nudix homology clan encompasses over 80,000 protein domains from all three domains of life, defined by homology to each other. Proteins with a domain from this clan fall into four general functional classes: pyrophosphohydrolases, isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), and nonenzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed a structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 "select" Nudix homology domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix homology clan revealed general monophyly with regard to function and a few instances of probable homoplasy. Proteins 2017; 85:775-811. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John R. Srouji
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Present address: Molecular and Cellular Biology DepartmentHarvard UniversityCambridgeMassachusetts02138
| | - Anting Xu
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Annsea Park
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
| | - Jack F. Kirsch
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Steven E. Brenner
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
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30
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Buiate EAS, Xavier KV, Moore N, Torres MF, Farman ML, Schardl CL, Vaillancourt LJ. A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genomics 2017; 18:67. [PMID: 28073340 PMCID: PMC5225507 DOI: 10.1186/s12864-016-3457-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/22/2016] [Indexed: 01/10/2023] Open
Abstract
Background Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains. Results Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another. Conclusions Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3457-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E A S Buiate
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Monsanto Company Brazil, Uberlândia, Minas Gerais, Brazil
| | - K V Xavier
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - N Moore
- Department of Computer Science, University of Kentucky, Davis Marksbury Building, 328 Rose Street, Lexington, KY, 40504-0633, USA
| | - M F Torres
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Functional Genomics Laboratory, Weill Cornell Medicine, Doha, Qatar
| | - M L Farman
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - C L Schardl
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - L J Vaillancourt
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.
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