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Zhou X, Wen K, Huang SX, Lu Y, Liu Y, Jin JH, Kale SD, Chen XR. Time-Course Transcriptome Profiling Reveals Differential Resistance Responses of Tomato to a Phytotoxic Effector of the Pathogenic Oomycete Phytophthora cactorum. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040883. [PMID: 36840230 PMCID: PMC9964705 DOI: 10.3390/plants12040883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 05/22/2023]
Abstract
Blight caused by Phytophthora pathogens has a devastating impact on crop production. Phytophthora species secrete an array of effectors, such as Phytophthora cactorum-Fragaria (PcF)/small cysteine-rich (SCR) phytotoxic proteins, to facilitate their infections. Understanding host responses to such proteins is essential to developing next-generation crop resistance. Our previous work identified a small, 8.1 kDa protein, SCR96, as an important virulence factor in Phytophthora cactorum. Host responses to SCR96 remain obscure. Here, we analyzed the effect of SCR96 on the resistance of tomato treated with this recombinant protein purified from yeast cells. A temporal transcriptome analysis of tomato leaves infiltrated with 500 nM SCR96 for 0, 3, 6, and 12 h was performed using RNA-Seq. In total, 36,779 genes, including 2704 novel ones, were detected, of which 32,640 (88.7%) were annotated. As a whole, 5929 non-redundant genes were found to be significantly co-upregulated in SCR96-treated leaves (3, 6, 12 h) compared to the control (0 h). The combination of annotation, enrichment, and clustering analyses showed significant changes in expression beginning at 3 h after treatment in genes associated with defense and metabolism pathways, as well as temporal transcriptional accumulation patterns. Noticeably, the expression levels of resistance-related genes encoding receptor-like kinases/proteins, resistance proteins, mitogen-activated protein kinases (MAPKs), transcription factors, pathogenesis-related proteins, and transport proteins were significantly affected by SCR96. Quantitative reverse transcription PCR (qRT-PCR) validated the transcript changes in the 12 selected genes. Our analysis provides novel information that can help delineate the molecular mechanism and components of plant responses to effectors, which will be useful for the development of resistant crops.
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Affiliation(s)
- Xue Zhou
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Ke Wen
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Shen-Xin Huang
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Yi Lu
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Yang Liu
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Jing-Hao Jin
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Shiv D. Kale
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24060, USA
| | - Xiao-Ren Chen
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Correspondence:
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Doni F, Suhaimi NSM, Mispan MS, Fathurrahman F, Marzuki BM, Kusmoro J, Uphoff N. Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies. Int J Mol Sci 2022; 23:737. [PMID: 35054923 PMCID: PMC8775878 DOI: 10.3390/ijms23020737] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/03/2022] [Accepted: 01/08/2022] [Indexed: 12/26/2022] Open
Abstract
Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.
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Affiliation(s)
- Febri Doni
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Nurul Shamsinah Mohd Suhaimi
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (N.S.M.S.); (M.S.M.)
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (N.S.M.S.); (M.S.M.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur 50603, Malaysia
| | - F Fathurrahman
- Department of Agrotechnology, Faculty of Agriculture, Universitas Islam Riau, Pekanbaru 28284, Indonesia;
| | - Betty Mayawatie Marzuki
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Joko Kusmoro
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Norman Uphoff
- SRI International Network and Resources Center, Cornell University, Ithaca, NY 14853, USA;
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dos Santos KCG, Pelletier G, Séguin A, Guillemette F, Hawkes J, Desgagné-Penix I, Germain H. Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions. Microorganisms 2021; 9:microorganisms9050996. [PMID: 34063040 PMCID: PMC8148019 DOI: 10.3390/microorganisms9050996] [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: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/30/2021] [Indexed: 11/21/2022] Open
Abstract
Rust fungi cause epidemics that threaten the production of important plant species, such as wheat and soy. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1184 candidate effectors (CEs) whose functions are poorly known. In this study, we sequenced the transcriptome and used mass spectrometry to analyze the metabolome of Arabidopsis plants constitutively expressing 14 Mlp CEs and of a control line to discover alterations leading to plant susceptibility. We found 2299 deregulated genes across the experiment. Genes involved in pattern-triggered immunity, such as FRK1, PR1, RBOHD, and WRKY33, as well as AUX/IAA genes were down-regulated. We further observed that 680 metabolites were deregulated in at least one CE-expressing transgenic line, with “highly unsaturated and phenolic compounds” and “peptides” enriched among down- and up-regulated metabolites. Interestingly, transgenic lines expressing unrelated CEs had correlated patterns of gene and metabolite deregulation, while expression of CEs belonging to the same family deregulated different genes and metabolites. Thus, our results uncouple effector sequence similarity and function. This supports that effector functional investigation in the context of their virulence activity and effect on plant susceptibility requires the investigation of the individual effector and precludes generalization based on sequence similarity.
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Affiliation(s)
- Karen Cristine Goncalves dos Santos
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
| | - Gervais Pelletier
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC G1V 4C7, Canada; (G.P.); (A.S.)
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC G1V 4C7, Canada; (G.P.); (A.S.)
| | - François Guillemette
- Centre for Research on Aquatic Ecosystem Interactions (RIVE), Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada;
| | - Jeffrey Hawkes
- Department of Chemistry—BMC, Analytical Chemistry, Uppsala University, VJ2J+92 Uppsala, Sweden;
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
- Correspondence:
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Meng Q, Gupta R, Min CW, Kwon SW, Wang Y, Je BI, Kim YJ, Jeon JS, Agrawal GK, Rakwal R, Kim ST. Proteomics of Rice- Magnaporthe oryzae Interaction: What Have We Learned So Far? FRONTIERS IN PLANT SCIENCE 2019; 10:1383. [PMID: 31737011 PMCID: PMC6828948 DOI: 10.3389/fpls.2019.01383] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/07/2019] [Indexed: 05/21/2023]
Abstract
Rice blast disease, caused by Magnaporthe oryzae, is one of the major constraints to rice production, which feeds half of the world's population. Proteomic technologies have been used as effective tools in plant-pathogen interactions to study the biological pathways involved in pathogen infection, plant response, and disease progression. Advancements in mass spectrometry (MS) and apoplastic and plasma membrane protein isolation methods facilitated the identification and quantification of subcellular proteomes during plant-pathogen interaction. Proteomic studies conducted during rice-M. oryzae interaction have led to the identification of several proteins eminently involved in pathogen perception, signal transduction, and the adjustment of metabolism to prevent plant disease. Some of these proteins include receptor-like kinases (RLKs), mitogen-activated protein kinases (MAPKs), and proteins related to reactive oxygen species (ROS) signaling and scavenging, hormone signaling, photosynthesis, secondary metabolism, protein degradation, and other defense responses. Moreover, post-translational modifications (PTMs), such as phosphoproteomics and ubiquitin proteomics, during rice-M. oryzae interaction are also summarized in this review. In essence, proteomic studies carried out to date delineated the molecular mechanisms underlying rice-M. oryzae interactions and provided candidate proteins for the breeding of rice blast resistant cultivars.
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Affiliation(s)
- Qingfeng Meng
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
- Department of Botany, School of Chemical and Life Science, Jamia Hamdard, New Delhi, India
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Soon Wook Kwon
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Byoung Il Je
- Department of Horticultural Bioscience, Pusan National University, Miryang, South Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
- *Correspondence: Sun Tae Kim,
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