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Wang P, Guo L, Morgan J, Dudareva N, Chapple C. Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2828-2846. [PMID: 35880844 PMCID: PMC9706439 DOI: 10.1093/plphys/kiac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.
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Affiliation(s)
- Peng Wang
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - John Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
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Duan S, Long Y, Cheng S, Li J, Ouyang Z, Wang N. Rapid Evaluation of the Resistance of Citrus Germplasms Against Xanthomonas citri subsp. citri. PHYTOPATHOLOGY 2022; 112:765-774. [PMID: 34495678 DOI: 10.1094/phyto-04-21-0175-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas citri subsp. citri (Xcc) is the causal agent of citrus bacterial canker (CBC), one of the most devastating citrus diseases. Most commercial citrus varieties are susceptible to CBC. However, some citrus varieties and wild citrus germplasms are CBC resistant and are promising in genetic increases in citrus resistance against CBC. We aimed to evaluate citrus germplasms for resistance against CBC. First, we developed a rapid evaluation method based on enhanced yellow fluorescent protein (eYFP)-labeled Xcc. The results demonstrated that eYFP does not affect the growth and virulence of Xcc. Xcc-eYFP allows measurement of bacterial titers but is more efficient and rapid than the plate colony counting method. Next, we evaluated citrus germplasms collected in China. Based on symptoms and bacterial titers, we identified that two citrus germplasms ('Ichang' papeda and 'Huapi' kumquat) are resistant, whereas eight citrus germplasms ('Chongyi' wild mandarin, 'Mangshan' wild mandarin, 'Ledong' kumquat, 'Dali' citron, 'Yiliang' citron, 'Longyan' kumquat, 'Bawang' kumquat, and 'Daoxian' wild mandarin) are tolerant. In summary, we have developed a rapid evaluation method to test the resistance of citrus plants against CBC. This method was successfully used to identify two highly canker-resistant citrus germplasms and eight citrus germplasms with canker tolerance. These results could be leveraged in traditional breeding contexts or be used to identify canker resistance genes to increase the disease resistance of commercial citrus varieties via biotechnological approaches.
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Affiliation(s)
- Shuo Duan
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Yunfei Long
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Shuyuan Cheng
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL 33850, U.S.A
| | - Zhigang Ouyang
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL 33850, U.S.A
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Jia H, Omar AA, Orbović V, Wang N. Biallelic Editing of the LOB1 Promoter via CRISPR/Cas9 Creates Canker-Resistant 'Duncan' Grapefruit. PHYTOPATHOLOGY 2022; 112:308-314. [PMID: 34213958 DOI: 10.1094/phyto-04-21-0144-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri is one of the most devastating citrus diseases worldwide. Generating disease-resistant citrus varieties is considered one of the most efficient and environmentally friendly measures for controlling canker. X. citri subsp. citri causes canker symptoms by inducing the expression of canker susceptibility gene LOB1 via PthA4, a transcription activator-like (TAL) effector, by binding to the effector binding element (EBE) in the promoter region. In previous studies, canker-resistant plants were generated by mutating the coding region or the EBE of LOB1. However, homozygous or biallelic canker-resistant plants have not been generated for commercial citrus varieties, such as grapefruit (Citrus paradisi), which usually contain two alleles of LOB1 and thus, have two types of LOB1 promoter sequences: TI LOBP and TII LOBP. Two different sgRNAs were used to target both EBE types. Both 35S promoter and Yao promoter were used to drive the expression of SpCas9p to modify EBEPthA4-LOBP in grapefruit. Using 'Duncan' grapefruit epicotyls as explants, 19 genome-edited grapefruit plants were generated with one biallelic mutant line (#DunYao7). X. citri subsp. citri caused canker symptoms on wild-type and nonbiallelic mutant plants but not on #DunYao7. XccPthA4 mutant containing the designer TAL effector dLOB1.5, which recognizes a conserved sequence in both wild-type and #DunYao7, caused canker symptoms on both wild-type and #DunYao7. No off-target mutations were detected in #DunYao7. This study represents the first time that CRISPR-mediated genome editing has been successfully used to generate disease-resistant plants for 'Duncan' grapefruit, paving the way for using disease-resistant varieties to control canker.
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Affiliation(s)
- Hongge Jia
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred 33850, U.S.A
| | - Ahmad A Omar
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred 33850, U.S.A
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt
| | - Vladimir Orbović
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred 33850, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred 33850, U.S.A
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Huang X, Wang Y, Wang N. Highly Efficient Generation of Canker-Resistant Sweet Orange Enabled by an Improved CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2022; 12:769907. [PMID: 35087548 PMCID: PMC8787272 DOI: 10.3389/fpls.2021.769907] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/09/2021] [Indexed: 06/02/2023]
Abstract
Sweet orange (Citrus sinensis) is the most economically important species for the citrus industry. However, it is susceptible to many diseases including citrus bacterial canker caused by Xanthomonas citri subsp. citri (Xcc) that triggers devastating effects on citrus production. Conventional breeding has not met the challenge to improve disease resistance of sweet orange due to the long juvenility and other limitations. CRISPR-mediated genome editing has shown promising potentials for genetic improvements of plants. Generation of biallelic/homozygous mutants remains difficult for sweet orange due to low transformation rate, existence of heterozygous alleles for target genes, and low biallelic editing efficacy using the CRISPR technology. Here, we report improvements in the CRISPR/Cas9 system for citrus gene editing. Based on the improvements we made previously [dicot codon optimized Cas9, tRNA for multiplexing, a modified sgRNA scaffold with high efficiency, citrus U6 (CsU6) to drive sgRNA expression], we further improved our CRISPR/Cas9 system by choosing superior promoters [Cestrum yellow leaf curling virus (CmYLCV) or Citrus sinensis ubiquitin (CsUbi) promoter] to drive Cas9 and optimizing culture temperature. This system was able to generate a biallelic mutation rate of up to 89% for Carrizo citrange and 79% for Hamlin sweet orange. Consequently, this system was used to generate canker-resistant Hamlin sweet orange by mutating the effector binding element (EBE) of canker susceptibility gene CsLOB1, which is required for causing canker symptoms by Xcc. Six biallelic Hamlin sweet orange mutant lines in the EBE were generated. The biallelic mutants are resistant to Xcc. Biallelic mutation of the EBE region abolishes the induction of CsLOB1 by Xcc. This study represents a significant improvement in sweet orange gene editing efficacy and generating disease-resistant varieties via CRISPR-mediated genome editing. This improvement in citrus genome editing makes genetic studies and manipulations of sweet orange more feasible.
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Zhang Y, Andrade MO, Wang W, Teper D, Romeo T, Wang N. Examination of the Global Regulon of CsrA in Xanthomonas citri subsp. citri Using Quantitative Proteomics and Other Approaches. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1236-1249. [PMID: 34282945 DOI: 10.1094/mpmi-05-21-0113-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The RNA-binding protein CsrA is a global posttranscriptional regulator and controls many physiological processes and virulence traits. Deletion of csrA caused loss of virulence, reduced motility and production of xanthan gum and substantial increase in glycogen accumulation, as well as enhanced bacterial aggregation and cell adhesion in Xanthomonas spp. How CsrA controls these traits is poorly understood. In this study, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis was conducted to compare the protein profile of wild-type strain Xanthomonas citri subsp. citri and the isogenic ΔcsrA strain. A total of 2,374 proteins were identified, and 284 were considered to be differentially expressed proteins (DEPS), among which 151 proteins were up-regulated and 133 were down-regulated in the ΔcsrA strain with respect to the wild-type strain. Enrichment analysis and a protein-protein interaction network analysis showed that CsrA regulates bacterial secretion systems, flagella, and xanthan gum biosynthesis. Several proteins encoded by the gumB operon were down-regulated, whereas proteins associated with flagellum assembly and the type IV secretion system were up-regulated in the ΔcsrA strain relative to the Xcc306 strain. These results were confirmed by β-glucuronidase assay or Western blot. RNA secondary structure prediction and a gel-shift assay indicated that CsrA binds to the Shine-Dalgarno sequence of virB5. In addition, the iTRAQ analysis identified 248 DEPs that were not previously identified in transcriptome analyses. Among them, CsrA regulates levels of eight regulatory proteins (ColR, GacA, GlpR, KdgR, MoxR, PilH, RecX, and YgiX), seven TonB-dependent receptors, four outer membrane proteins, and two ferric enterobactin receptors. Taken together, this study greatly expands understanding of the regulatory network of CsrA in X. citri subsp. citri.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yanan Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Maxuel O Andrade
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Wenting Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
- Department of Plant Pathology, University of Florida, Gainesville FL 32611, U.S.A
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
| | - Tony Romeo
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville FL 32611, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
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Ding Y, Sheng J, Cheng F. Assessment of the role of brassinosteroid in regulating the disease resistance of postharvest tomato fruit by proteomic analysis. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yang Ding
- School of Logistics/Key Laboratory of Logistics Systems and Technology Beijing Wuzi University Beijing China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology Chinese Academy of Agricultural Sciences Beijing China
| | - Jiping Sheng
- School of Agricultural Economics and Rural Development Renmin University of China Beijing China
| | - Fansheng Cheng
- College of Food Science and Engineering Qingdao Agricultural University Qingdao China
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Teper D, Xu J, Pandey SS, Wang N. PthAW1, a Transcription Activator-Like Effector of Xanthomonas citri subsp. citri, Promotes Host-Specific Immune Responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1033-1047. [PMID: 33970668 DOI: 10.1094/mpmi-01-21-0026-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Citrus canker disease caused by Xanthomonas citri subsp. citri is one of the most destructive diseases in citrus. X. citri subsp. citri pathotypes display different host ranges. X. citri subsp. citri strain A (XccA) causes canker disease in most commercial citrus varieties, whereas strain AW (XccAW), which is genetically similar to XccA, infects only lime and alemow. Understanding the mechanism that determines the host range of pathogens is critical to investigating and utilizing host resistance. We hypothesized that XccAW would undergo mutations in genes that restrict its host range when artificially inoculated into incompatible citrus varieties. To test this hypothesis, we used an experimental evolution approach to identify phenotypic traits and genetic loci associated with the adaptation of XccAW to incompatible sweet orange. Repeated inoculation and reisolation cycles improved the ability of three independent XccAW strains to colonize sweet orange. Adapted XccAW strains displayed increased expression of type III secretion system and effector genes. Genome sequencing analysis indicated that two of the adapted strains harbored mutations in pthAW1, a transcription activator-like effector (TALE) gene, that corresponded to the removal of one or two repeats from the central DNA-binding repeat region. Introduction of the original but not the adapted pthAW1 variants into XccA abolished its ability to cause canker symptoms in sweet orange, Meyer lemon, and clementine but not in other XccAW-resistant citrus varieties. The original pthAW1, when expressed in XccA, induced ion leakage and the expression of pathogenesis-related genes but had no effect on CsLOB1 expression in sweet orange. Our study has identified a novel host-specific avirulence TALE and demonstrated active adaptive rearrangements of the TALE repeat array during host adaptation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Sheo Shankar Pandey
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
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Liu X, Cui X, Ji D, Zhang Z, Li B, Xu Y, Chen T, Tian S. Luteolin-induced activation of the phenylpropanoid metabolic pathway contributes to quality maintenance and disease resistance of sweet cherry. Food Chem 2020; 342:128309. [PMID: 33051099 DOI: 10.1016/j.foodchem.2020.128309] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 01/05/2023]
Abstract
Redox imbalance and fungal infection are major causes for quality deterioration and postharvest decay of fruit. Therefore, it is crucial to activate intrinsic antioxidative capacity and disease responses for fruit quality maintenance. Although plant-derived flavonoids have been reported for health-promoting benefits, their roles in the maintenance of fruit quality remains largely unexplored. Here, we exogenously applied luteolin, a flavonoid substance, and further examined its efficacy in maintaining fruit quality and inhibiting fungal diseases in sweet cherry. The results showed that 100 or 200 mg/L luteolin maintained better organoleptic quality and decreased disease incidence during storage. Biochemical assays revealed that luteolin activated the phenylpropanoid metabolic pathway and improved antioxidative capacity, thereby elevating total anthocyanin and flavonoid contents. Notably, luteolin inhibited mycelial growth of fungal pathogens and reduced patulin yield by Penicillium expansum. Collectively, these results suggest that luteolin is a promising alternative for maintaining better fruit quality and ameliorating disease resistance.
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Affiliation(s)
- Xiaoyun Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Cui
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongchao Ji
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, Beijing 100093, China
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