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Sahu S, Rao AR, Saxena S, Gupta P, Gaikwad K. Systematic profiling and analysis of growth and development responsive DE-lncRNAs in cluster bean (Cyamopsis tetragonoloba). Int J Biol Macromol 2024; 280:135821. [PMID: 39306152 DOI: 10.1016/j.ijbiomac.2024.135821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 09/07/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024]
Abstract
Long non-coding RNAs (lncRNAs) play crucial role in regulating genes involved in various processes including growth & development, flowering, and stress response in plants. The study aims to identify and characterize tissue-specific, growth & development and floral responsive differentially expressed lncRNAs (DE-lncRNAs) in cluster bean from a high-throughput RNA sequencing data. We have identified 3309 DE-lncRNAs, with an average length of 818 bp. Merely, around 4 % of DE-lncRNAs across the tissues were found to be conserved as rate of evolution of lncRNAs is high. Among the identified DE-lncRNAs, 204 were common in leaf vs. shoot, leaf vs. flower and flower vs. shoot. A total of 60 DE-lncRNAs targeted 10 protein-coding genes involved in flower development and initiation processes. We investigated 179 tissue-specific DE-lncRNAs based on tissue specificity index. Three DE-lncRNAs: Cb_lnc_0820, Cb_lnc_0430, Cb_lnc_0260 and their target genes show their involvement in floral development and stress mechanisms, which were validated by Quantitative real-time PCR (qRT-PCR). The identified DE-lncRNAs were expressed higher in flower bud than in leaf and similar expression pattern was observed in both RNA-seq data and qRT-PCR analyses. Notably, 362 DE-lncRNAs were predicted as eTM-lncRNAs with the participation of 84 miRNAs. Whereas 46 DE-lncRNAs were predicted to possess the internal ribosomal entry sites (IRES) and can encode for small peptides. The regulatory networks established between DE-lncRNAs, mRNAs and miRNAs have provided an insight into their association with plant growth & development, flowering, and stress mechanisms. Comprehensively, the characterization of DE-lncRNAs in various tissues of cluster bean shed a light on interactions among lncRNAs, miRNAs and mRNAs and help understand their involvement in growth & development and floral initiation processes. The information retrieved from the analyses was shared in the public domain in the form of a database: Cb-DElncRNAdb, and made available at http://backlin.cabgrid.res.in/Cb-DElncRNA/index.php, which may be useful for the scientific community engaged cluster bean research.
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Affiliation(s)
- Sarika Sahu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | | | - Swati Saxena
- ICAR - National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Palak Gupta
- ICAR - National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kishor Gaikwad
- ICAR - National Institute for Plant Biotechnology, New Delhi 110012, India
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2
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Fernández-Melero B, Del Moral L, Todesco M, Rieseberg LH, Owens GL, Carrère S, Chabaud M, Muños S, Velasco L, Pérez-Vich B. Development and characterization of a new sunflower source of resistance to race G of Orobanche cumana Wallr. derived from Helianthus anomalus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:56. [PMID: 38386181 PMCID: PMC10884359 DOI: 10.1007/s00122-024-04558-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/20/2024] [Indexed: 02/23/2024]
Abstract
KEY MESSAGE A new OrAnom1 gene introgressed in cultivated sunflower from wild Helianthus anomalus confers late post-attachment resistance to Orobanche cumana race G and maps to a target interval in Chromosome 4 where two receptor-like kinases (RLKs) have been identified in the H. anomalus genome as putative candidates. Sunflower broomrape is a parasitic weed that infects sunflower (Helianthus annuus L.) roots causing severe yield losses. Breeding for resistance is the most effective and sustainable control method. In this study, we report the identification, introgression, and genetic and physiological characterization of a new sunflower source of resistance to race G of broomrape developed from the wild annual sunflower H. anomalus (accession PI 468642). Crosses between PI 468642 and the susceptible line P21 were carried out, and the genetic study was conducted in BC1F1, BC1F2, and its derived BC1F3 populations. A BC1F5 germplasm named ANOM1 was developed through selection for race G resistance and resemblance to cultivated sunflower. The resistant trait showed monogenic and dominant inheritance. The gene, named OrAnom1, was mapped to Chromosome 4 within a 1.2 cM interval and co-segregated with 7 SNP markers. This interval corresponds to a 1.32 Mb region in the sunflower reference genome, housing a cluster of receptor-like kinase and receptor-like protein (RLK-RLP) genes. Notably, the analysis of the H. anomalus genome revealed the absence of RLPs in the OrAnom1 target region but featured two RLKs as possible OrAnom1 candidates. Rhizotron and histological studies showed that OrAnom1 determines a late post-attachment resistance mechanism. Broomrape can establish a vascular connection with the host, but parasite growth is stopped before tubercle development, showing phenolic compounds accumulation and tubercle necrosis. ANOM1 will contribute to broadening the genetic basis of broomrape resistance in the cultivated sunflower pool and to a better understanding of the molecular basis of the sunflower-broomrape interaction.
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Affiliation(s)
- Belén Fernández-Melero
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo S/N, 14004, Córdoba, Spain
| | - Lidia Del Moral
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo S/N, 14004, Córdoba, Spain
| | - Marco Todesco
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Sébastien Carrère
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Mireille Chabaud
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Leonardo Velasco
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo S/N, 14004, Córdoba, Spain
| | - Begoña Pérez-Vich
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo S/N, 14004, Córdoba, Spain.
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3
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Li R, Yao J, Ming Y, Guo J, Deng J, Liu D, Li Z, Cheng Y. Integrated proteomic analysis reveals interactions between phosphorylation and ubiquitination in rose response to Botrytis infection. HORTICULTURE RESEARCH 2024; 11:uhad238. [PMID: 38222823 PMCID: PMC10782497 DOI: 10.1093/hr/uhad238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/06/2023] [Indexed: 01/16/2024]
Abstract
As two of the most abundant post-translational modifications, phosphorylation and ubiquitination play a significant role in modulating plant-pathogen interactions and increasing evidence indicates their crosstalk in plant immunity. Rose (Rosa sp.) is one of the most important ornamental plants and can be seriously infected by Botrytis cinerea. Here, integrated proteomics analysis was performed to detect global proteome, phosphorylation, and ubiquitination changes in rose upon B. cinerea infection and investigate the possible phosphorylation and ubiquitination crosstalk. A total of 6165 proteins, 11 774 phosphorylation and 10 582 ubiquitination sites, and 77 phosphorylation and 13 ubiquitination motifs were identified. Botrytis cinerea infection resulted in 169 up-regulated and 122 down-regulated proteins, 291 up-regulated and 404 down-regulated phosphorylation sites, and 250 up-regulated and 634 down-regulated ubiquitination sites. There were 12 up-regulated PR10 proteins and half of them also showed reduced ubiquitination. A lot of kinases probably involved in plant pattern-triggered immunity signaling were up-regulated phosphoproteins. Noticeably, numerous kinases and ubiquitination-related proteins also showed a significant change in ubiquitination and phosphorylation, respectively. A cross-comparison of phosphoproteome and ubiquitylome indicated that both of two post-translational modifications of 104 proteins were dynamically regulated, and many putative pattern-triggered immunity signaling components in the plant plasma membrane were co-regulated. Moreover, five selected proteins, including four PR10 proteins and a plasma membrane aquaporin, were proven to be involved in rose resistance to B. cinerea. Our study provides insights into the molecular mechanisms underlying rose resistance to B. cinerea and also increases the database of phosphorylation and ubiquitination sites in plants.
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Affiliation(s)
- Rui Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Juanni Yao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yue Ming
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jia Guo
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jingjing Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Daofeng Liu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
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4
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Langin G, González-Fuente M, Üstün S. The Plant Ubiquitin-Proteasome System as a Target for Microbial Manipulation. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:351-375. [PMID: 37253695 DOI: 10.1146/annurev-phyto-021622-110443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The plant immune system perceives pathogens to trigger defense responses. In turn, pathogens secrete effector molecules to subvert these defense responses. The initiation and maintenance of defense responses involve not only de novo synthesis of regulatory proteins and enzymes but also their regulated degradation. The latter is achieved through protein degradation pathways such as the ubiquitin-proteasome system (UPS). The UPS regulates all stages of immunity, from the perception of the pathogen to the execution of the response, and, therefore, constitutes an ideal candidate for microbial manipulation of the host. Pathogen effector molecules interfere with the plant UPS through several mechanisms. This includes hijacking general UPS functions or perturbing its ability to degrade specific targets. In this review, we describe how the UPS regulates different immunity-related processes and how pathogens subvert this to promote disease.
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Affiliation(s)
- Gautier Langin
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany;
- Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | | | - Suayib Üstün
- Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
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5
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Shi W, Stolze SC, Nakagami H, Misas Villamil JC, Saur IML, Doehlemann G. Combination of in vivo proximity labeling and co-immunoprecipitation identifies the host target network of a tumor-inducing effector in the fungal maize pathogen Ustilago maydis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4736-4750. [PMID: 37225161 PMCID: PMC10433927 DOI: 10.1093/jxb/erad188] [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: 01/05/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
Plant pathogens secrete effectors, which target host proteins to facilitate infection. The Ustilago maydis effector UmSee1 is required for tumor formation in the leaf during infection of maize. UmSee1 interacts with maize SGT1 (suppressor of G2 allele of skp1) and blocks its phosphorylation in vivo. In the absence of UmSee1, U. maydis cannot trigger tumor formation in the bundle sheath. However, it remains unclear which host processes are manipulated by UmSee1 and the UmSee1-SGT1 interaction to cause the observed phenotype. Proximity-dependent protein labeling involving the turbo biotin ligase tag (TurboID) for proximal labeling of proteins is a powerful tool for identifying the protein interactome. We have generated transgenic U. maydis that secretes biotin ligase-fused See1 effector (UmSee1-TurboID-3HA) directly into maize cells. This approach, in combination with conventional co-immunoprecipitation, allowed the identification of additional UmSee1 interactors in maize cells. Collectively, our data identified three ubiquitin-proteasome pathway-related proteins (ZmSIP1, ZmSIP2, and ZmSIP3) that either interact with or are close to UmSee1 during host infection of maize with U. maydis. ZmSIP3 represents a cell cycle regulator whose degradation appears to be promoted in the presence of UmSee1. Our data provide a possible explanation of the requirement for UmSee1 in tumor formation during U. maydis-Zea mays interaction.
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Affiliation(s)
- Wei Shi
- Institute for Plant Sciences University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
| | - Sara C Stolze
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Johana C Misas Villamil
- Institute for Plant Sciences University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
| | - Isabel M L Saur
- Institute for Plant Sciences University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
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6
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Ellur V, Wei W, Ghogare R, Solanki S, Vandemark G, Brueggeman R, Chen W. Unraveling the genomic reorganization of polygalacturonase-inhibiting proteins in chickpea. Front Genet 2023; 14:1189329. [PMID: 37342773 PMCID: PMC10278945 DOI: 10.3389/fgene.2023.1189329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Polygalacturonase-inhibiting proteins (PGIPs) are cell wall proteins that inhibit pathogen polygalacturonases (PGs). PGIPs, like other defense-related proteins, contain extracellular leucine-rich repeats (eLRRs), which are required for pathogen PG recognition. The importance of these PGIPs in plant defense has been well documented. This study focuses on chickpea (Cicer arietinum) PGIPs (CaPGIPs) owing to the limited information available on this important crop. This study identified two novel CaPGIPs (CaPGIP3 and CaPGIP4) and computationally characterized all four CaPGIPs in the gene family, including the previously reported CaPGIP1 and CaPGIP2. The findings suggest that CaPGIP1, CaPGIP3, and CaPGIP4 proteins possess N-terminal signal peptides, ten LRRs, theoretical molecular mass, and isoelectric points comparable to other legume PGIPs. Phylogenetic analysis and multiple sequence alignment revealed that the CaPGIP1, CaPGIP3, and CaPGIP4 amino acid sequences are similar to the other PGIPs reported in legumes. In addition, several cis-acting elements that are typical of pathogen response, tissue-specific activity, hormone response, and abiotic stress-related are present in the promoters of CaPGIP1, CaPGIP3, and CaPGIP4 genes. Localization experiments showed that CaPGIP1, CaPGIP3, and CaPGIP4 are located in the cell wall or membrane. Transcript levels of CaPGIP1, CaPGIP3, and CaPGIP4 genes analyzed at untreated conditions show varied expression patterns analogous to other defense-related gene families. Interestingly, CaPGIP2 lacked a signal peptide, more than half of the LRRs, and other characteristics of a typical PGIP and subcellular localization indicated it is not located in the cell wall or membrane. The study's findings demonstrate CaPGIP1, CaPGIP3, and CaPGIP4's similarity to other legume PGIPs and suggest they might possess the potential to combat chickpea pathogens.
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Affiliation(s)
- Vishnutej Ellur
- Molecular Plant Science, Washington State University, Pullman, WA, United States
| | - Wei Wei
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Rishikesh Ghogare
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Shyam Solanki
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - George Vandemark
- Grain Legume Genetics Physiology Research, Pullman, WA, United States
| | - Robert Brueggeman
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Weidong Chen
- Grain Legume Genetics Physiology Research, Pullman, WA, United States
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7
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Zhang X, Kuang T, Dong W, Qian Z, Zhang H, Landis JB, Feng T, Li L, Sun Y, Huang J, Deng T, Wang H, Sun H. Genomic convergence underlying high-altitude adaptation in alpine plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36960823 DOI: 10.1111/jipb.13485] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive "greenhouse" morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Tianhui Kuang
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Wenlin Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihao Qian
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, New York, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Tao Feng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jinling Huang
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Tao Deng
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Hang Sun
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
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8
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Fragoso RR, Arraes FBM, Lourenço-Tessutti IT, Miranda VJ, Basso MF, Ferreira AVJ, Viana AAB, Lins CBJ, Lins PC, Moura SM, Batista JAN, Silva MCM, Engler G, Morgante CV, Lisei-de-Sa ME, Vasques RM, de Almeida-Engler J, Grossi-de-Sa MF. Functional characterization of the pUceS8.3 promoter and its potential use for ectopic gene overexpression. PLANTA 2022; 256:69. [PMID: 36066773 DOI: 10.1007/s00425-022-03980-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
The pUceS8.3 is a constitutive gene promoter with potential for ectopic and strong genes overexpression or active biomolecules in plant tissues attacked by pests, including nematode-induced giant cells or galls. Soybean (Glycine max) is one of the most important agricultural commodities worldwide and a major protein and oil source. Herein, we identified the soybean ubiquitin-conjugating (E2) enzyme gene (GmUBC4; Glyma.18G216000), which is significantly upregulated in response to Anticarsia gemmatalis attack and Meloidogyne incognita-induced galls during plant parasitism by plant nematode. The GmUBC4 promoter sequence and its different modules were functionally characterized in silico and in planta using transgenic Arabidopsis thaliana and G. max lines. Its full-length transcriptional regulatory region (promoter and 5´-UTR sequences, named pUceS8.3 promoter) was able to drive higher levels of uidA (β-glucuronidase) gene expression in different tissues of transgenic A. thaliana lines compared to its three shortened modules and the p35SdAMV promoter. Notably, higher β-glucuronidase (GUS) enzymatic activity was shown in M. incognita-induced giant cells when the full pUceS8.3 promoter drove the expression of this reporter gene. Furthermore, nematode-specific dsRNA molecules were successfully overexpressed under the control of the pUceS8.3 promoter in transgenic soybean lines. The RNAi gene construct used here was designed to post-transcriptionally downregulate the previously characterized pre-mRNA splicing factor genes from Heterodera glycines and M. incognita. A total of six transgenic soybean lines containing RNAi gene construct were selected for molecular characterization after infection with M. incognita pre-parasitic second-stage (ppJ2) nematodes. A strong reduction in the egg number produced by M. incognita after parasitism was observed in those transgenic soybean lines, ranging from 71 to 92% compared to wild-type control plants. The present data demonstrated that pUceS8.3 is a gene promoter capable of effectively driving dsRNA overexpression in nematode-induced giant cells of transgenic soybean lines and can be successfully applied as an important biotechnological asset to generate transgenic crops with improved resistance to root-knot nematodes as well as other pests.
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Affiliation(s)
- Rodrigo Rocha Fragoso
- Embrapa Savannah, Planaltina, DF, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Fabricio Barbosa Monteiro Arraes
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Isabela Tristan Lourenço-Tessutti
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Vívian Jesus Miranda
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Marcos Fernando Basso
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | | | | | - Camila Barrozo Jesus Lins
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Philippe Castro Lins
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Stéfanie Menezes Moura
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - João Aguiar Nogueira Batista
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Federal University of Minas Gerais, Belo Horizonte-MG, Brazil
| | - Maria Cristina Mattar Silva
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Gilbert Engler
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- INRAE, Université Côte d'Azur, CNRS, Sophia-Antipolis, France
| | - Carolina Vianna Morgante
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Embrapa Semiarid, Petrolina-PE, Brazil
| | - Maria Eugênia Lisei-de-Sa
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Minas Gerais Agricultural Research Company (EPAMIG), Uberaba-MG, Brazil
| | - Raquel Medeiros Vasques
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Janice de Almeida-Engler
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- INRAE, Université Côte d'Azur, CNRS, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil.
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil.
- Catholic University of Brasilia, Brasília-DF, Brazil.
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9
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E2 ubiquitin-conjugating enzymes (UBCs): drivers of ubiquitin signalling in plants. Essays Biochem 2022; 66:99-110. [PMID: 35766526 DOI: 10.1042/ebc20210093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/22/2022]
Abstract
Most research in the field of ubiquitination has focused on E3 ubiquitin ligases because they are the specificity determinants of the ubiquitination process. Nevertheless, E2s are responsible for the catalysis during ubiquitin transfer, and are therefore, at the heart of the ubiquitination process. Arabidopsis has 37 ubiquitin E2s with additional ones mediating the attachment of ubiquitin-like proteins (e.g. SUMO, Nedd8 and ATG8). Importantly, E2s largely determine the type of ubiquitin chain built, and therefore, the type of signal that decides over the fate of the modified protein, such as degradation by the proteasome (Lys48-linked ubiquitin chains) or relocalization (Lys63-linked ubiquitin chains). Moreover, new regulatory layers impinging on E2s activity, including post-translational modifications or cofactors, are emerging that highlight the importance of E2s.
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10
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Mano S, Hayashi Y, Hikino K, Otomo M, Kanai M, Nishimura M. Ubiquitin-conjugating activity by PEX4 is required for efficient protein transport to peroxisomes in Arabidopsis thaliana. J Biol Chem 2022; 298:102038. [PMID: 35595097 PMCID: PMC9190015 DOI: 10.1016/j.jbc.2022.102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022] Open
Abstract
Protein transport to peroxisomes requires various proteins, such as receptors in the cytosol and components of the transport machinery on peroxisomal membranes. The Arabidopsis apem (aberrant peroxisome morphology) mutant apem7 shows decreased efficiency of peroxisome targeting signal 1–dependent protein transport to peroxisomes. In apem7 mutants, peroxisome targeting signal 2–dependent protein transport is also disturbed, and plant growth is repressed. The APEM7 gene encodes a protein homologous to peroxin 4 (PEX4), which belongs to the ubiquitin-conjugating (UBC) protein family; however, the UBC activity of Arabidopsis PEX4 remains to be investigated. Here, we show using electron microscopy and immunoblot analysis using specific PEX4 antibodies and in vitro transcription/translation assay that PEX4 localizes to peroxisomal membranes and possesses UBC activity. We found that the substitution of proline with leucine by apem7 mutation alters ubiquitination of PEX4. Furthermore, substitution of the active-site cysteine residue at position 90 in PEX4, which was predicted to be a ubiquitin-conjugation site, with alanine did not restore the apem7 phenotype. Taken together, these findings indicate that abnormal ubiquitination in the apem7 mutant alters ubiquitin signaling during the process of protein transport, suggesting that the UBC activity of PEX4 is indispensable for efficient protein transport to peroxisomes.
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Affiliation(s)
- Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, Japan.
| | - Yasuko Hayashi
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Kazumi Hikino
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Masayoshi Otomo
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
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11
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Wang P, Guo K, Su Q, Deng J, Zhang X, Tu L. Histone ubiquitination controls organ size in cotton (Gossypium hirsutum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1005-1020. [PMID: 35218092 DOI: 10.1111/tpj.15716] [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] [Received: 10/22/2020] [Revised: 01/21/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitination plays a vital role in modifying protein activity and destiny. Ub-conjugating enzyme E2 is one of the enzymes that participates in this precise process. There are at least 169 E2 proteins in the allotetraploid cotton (Gossypium hirsutum), but their function remains unknown. Here we identify an E2 gene GhUBC2L and show its positive role in cell proliferation and expansion. Complete knock-down of GhUBC2L in cotton resulted in retarded growth and reduced organ size. Conversely, overexpression of GhUBC2L promoted cotton growth, generating enlarged organs in size. Monoubiquitination of H2A and H2B was strongly impaired in GhUBC2L-suppressed cotton but slightly enhanced in GhUBC2L-overexpressed plant. GhUbox8, a U-box type E3 ligase protein, was found to interact with GhUBC2L both in vivo and in vitro, indicating their synergistical function in protein ubiquitination. Furthermore, GhUbox8 was shown to interact with a series of histone proteins, including histone H2A and H2B, indicating its potential monoubiquitination on H2A and H2B. Expression of genes relating to cell cycle and organ development were altered when the expression of GhUBC2L was changed. Our results show that GhUBC2L modulates histone monoubiquitination synergistically with GhUbox8 to regulate the expression of genes involved in organ development and cell cycle, thus controlling organ size in cotton. This research provides new insights into the role of protein ubiquitination in organ size control. Histone monoubiquitination plays an important role in plant development. Here, we identified an E2 enzyme GhUBC2L that modulates histone monoubiquitination synergistically with an E3 ligase GhUbox8 to mediate organ size control in cotton.
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Affiliation(s)
- Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qian Su
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jinwu Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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12
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Li M, Wang L, Liu Y, Lin Y, Zhang Y, Long Y, Luo C, Zhang Y, Chen Q, Chen P, Wang Y, Wang X, Tang H, Luo Y. Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening. BMC PLANT BIOLOGY 2022; 22:39. [PMID: 35045827 PMCID: PMC8767729 DOI: 10.1186/s12870-021-03421-8] [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] [Received: 10/20/2021] [Accepted: 12/24/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND E2 ubiquitin-conjugating (UBC) enzymes are an integral component of the ubiquitin proteasome system that play an important role in plant development, growth, and external stress responses. Several UBC genes have been identified in various plants. However, no studies exploring the functions of UBC genes in regulating fruit of strawberry have been reported. In the present study, a systematic analysis of the entire UBC family members were conducted in the genome of strawberry (Fragaria ×ananassa) based on bioinformatics method, and the gene functioning in strawberry ripening was explored. RESULTS A total of 191 UBC genes were identified in the genome of cultivated strawberry. These genes were unevenly distributed across the 28 chromosomes from the 4 subgenomes of cultivated strawberry, ranging from 3 to 11 genes per chromosome. Moreover, the expansion of FaUBC genes in strawberry was mainly driven by WGD. All the FaUBC genes were clarified into 13 groups and most of them were included in the group VI. The gene structure analysis showed that the number of exons varied from 1 to 23, and the structure of genes had few differences within the same groups but a distinction in different groups. Identification of the cis-acting elements of the promoter revealed multiple regulatory elements that responded to plant growth and development, phytohormone responsive, and abiotic and biotic stress. Data from functional annotation indicated that FaUBC genes play a role in a variety of biological processes. The RNA-seq data showed that FaUBC genes displayed different expression pattern during the fruit ripening process and clarified into 6 clusters. In particular, cluster 3 exhibiting a sudden expression increase in the turning red stage were speculated to be involved in fruit ripening. Hence, two FaUBC genes (FaUBC76 and FaUBC78) were selected for gene function analysis by transient over-expression method. The results indicated that FaUBC76 has a positive effect on the fruit development and ripening in strawberry by up-regulating accumulation of anthocyanins. Moreover, expression of some maturity-related genes were also significantly increased, further supporting a role for FaUBC76 in the regulation of fruit ripening or softening. On the contrary, the overexpression of FaUBC78 significantly increased the firmness of strawberry fruit, indicating that FaUBC78 had a positive role in inhibiting the decrease of strawberry fruit firmness. CONCLUSION Our study not only provide comprehensive information on system evolution and function on UBC genes, but also give a new insight into explore the roles of FaUBC genes in the regulation of strawberry ripening.
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Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liangxin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yiting Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Long
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chuanying Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pinwen Chen
- Departmental and Municipal Co-construction of Crops Genetic Improvement of Hill Land Key Laboratory of Sichuan, Nanchong, 637000, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
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Liu X, Song L, Zhang H, Lin Y, Shen X, Guo J, Su M, Shi G, Wang Z, Lu G. Rice ubiquitin-conjugating enzyme OsUBC26 is essential for immunity to the blast fungus Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2021; 22:1613-1623. [PMID: 34459564 PMCID: PMC8578843 DOI: 10.1111/mpp.13132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/17/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
The functions of ubiquitin-conjugating enzymes (E2) in plant immunity are not well understood. In this study, OsUBC26, a rice ubiquitin-conjugating enzyme, was characterized in the defence against Magnaporthe oryzae. The expression of OsUBC26 was induced by M. oryzae inoculation and methyl jasmonate treatment. Both RNA interference lines and CRISPR/Cas9 null mutants of OsUBC26 reduced rice resistance to M. oryzae. WRKY45 was down-regulated in OsUBC26 null mutants. In vitro E2 activity assay indicated that OsUBC26 is an active ubiquitin-conjugating enzyme. Yeast two-hybrid assays using OsUBC26 as bait identified the RING-type E3 ligase UCIP2 as an interacting protein. Coimmunoprecipitation assays confirmed the interaction between OsUBC26 and UCIP2. The CRISPR/Cas9 mutants of UCIP2 also showed compromised resistance to M. oryzae. Yeast two-hybrid screening using UCIP2 as bait revealed that APIP6 is a binding partner of UCIP2. Moreover, OsUBC26 working with APIP6 ubiquitinateds AvrPiz-t, an avirulence effector of M. oryzae, and OsUBC26 null mutation impaired the proteasome degradation of AvrPiz-t in rice cells. In summary, OsUBC26 plays important roles in rice disease resistance by regulating WRKY45 expression and working with E3 ligases such as APIP6 to counteract the effector protein AvrPiz-t from M. oryzae.
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Affiliation(s)
- Xin Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Linlin Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Heng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yijuan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaolei Shen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Meiling Su
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Gaosheng Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Guo‐Dong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
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14
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Ghimire S, Tang X, Liu W, Fu X, Zhang H, Zhang N, Si H. SUMO conjugating enzyme: a vital player of SUMO pathway in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2421-2431. [PMID: 34744375 PMCID: PMC8526628 DOI: 10.1007/s12298-021-01075-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plants face numerous challenges such as biotic and abiotic stresses during their whole lifecycle. As they are sessile in nature, they ought to develop multiple ways to act during stressed conditions to maintain cellular homeostasis. Among various defense mechanisms, the small ubiquitin-like modifiers (SUMO) pathway is considered as the most important because several nuclear proteins regulated by this pathway are involved in several cellular functions such as response to stress, transcription, translation, metabolism of RNA, energy metabolism, repairing damaged DNA, ensuring genome stability and nuclear trafficking. In general, the SUMO pathway has its own particular set of enzymes E1, E2, and E3. The SUMO conjugating enzyme [SCE (E2)] is a very crucial member of the pathway which can transfer SUMO to its target protein even without the involvement of E3. More than just a middle player, it has shown its involvement in effective triggered immunity in crops like tomato and various abiotic stresses like drought and salinity in maize, rice, and Arabidopsis. This review tries to explore the importance of the SUMOylation process, focusing on the E2 enzyme and its regulatory role in the abiotic stress response, plant immunity, and DNA damage repair.
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Affiliation(s)
- Shantwana Ghimire
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Weigang Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Xue Fu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Huanhuan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
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15
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Trujillo M. Ubiquitin signalling: controlling the message of surface immune receptors. THE NEW PHYTOLOGIST 2021; 231:47-53. [PMID: 33792068 DOI: 10.1111/nph.17360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/25/2021] [Indexed: 05/27/2023]
Abstract
Microbial attack is first detected by immune receptors located at the plasma membrane. Their activation triggers a plethora of signalling cascades that culminate in the immune response. Ubiquitin and ubiquitin-like protein modifiers play key roles in controlling signalling amplitude and intensity, as well as in buffering proteome imbalances caused by pathogen attack. Here I highlight some of the important advances in the field, which are starting to reveal an intertwined and complex signalling circuitry, which regulates cellular dynamics and protein degradation to maintain homeostasis.
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Affiliation(s)
- Marco Trujillo
- Faculty of Biology, Cell Biology, University of Freiburg, Freiburg, 79104, Germany
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16
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Dubiella U, Serrano I. The Ubiquitin Proteasome System as a Double Agent in Plant-Virus Interactions. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10050928. [PMID: 34066628 PMCID: PMC8148538 DOI: 10.3390/plants10050928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 05/03/2023]
Abstract
The ubiquitin proteasome is a rapid, adaptive mechanism for selective protein degradation, crucial for proper plant growth and development. The ubiquitin proteasome system (UPS) has also been shown to be an integral part of plant responses to stresses, including plant defence against pathogens. Recently, significant progress has been made in the understanding of the involvement of the UPS in the signalling and regulation of the interaction between plants and viruses. This review aims to discuss the current knowledge about the response of plant viral infection by the UPS and how the viruses counteract this system, or even use it for their own benefit.
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Affiliation(s)
- Ullrich Dubiella
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574 Einbeck, Germany;
| | - Irene Serrano
- Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, 37077 Göttingen, Germany
- Correspondence:
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17
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Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa. BMC Genomics 2021; 22:93. [PMID: 33516199 PMCID: PMC7847607 DOI: 10.1186/s12864-021-07406-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/25/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network. RESULTS In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development. CONCLUSIONS These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.
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18
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Hada A, Dutta TK, Singh N, Singh B, Rai V, Singh NK, Rao U. A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola. PLoS One 2020; 15:e0239085. [PMID: 32960916 PMCID: PMC7508375 DOI: 10.1371/journal.pone.0239085] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022] Open
Abstract
Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.
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Affiliation(s)
- Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Tushar K. Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Nisha Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Balwant Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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19
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Basso MF, Lourenço-Tessutti IT, Busanello C, Pinto CEM, de Oliveira Freitas E, Ribeiro TP, de Almeida Engler J, de Oliveira AC, Morgante CV, Alves-Ferreira M, Grossi-de-Sa MF. Insights obtained using different modules of the cotton uceA1.7 promoter. PLANTA 2020; 251:56. [PMID: 32006110 DOI: 10.1007/s00425-020-03348-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The structure of the cotton uceA1.7 promoter and its modules was analyzed; the potential of their key sequences has been confirmed in different tissues, proving to be a good candidate for the development of new biotechnological tools. Transcriptional promoters are among the primary genetic engineering elements used to control genes of interest (GOIs) associated with agronomic traits. Cotton uceA1.7 was previously characterized as a constitutive promoter with activity higher than that of the constitutive promoter from the Cauliflower mosaic virus (CaMV) 35S gene in various plant tissues. In this study, we generated Arabidopsis thaliana homozygous events stably overexpressing the gfp reporter gene driven by different modules of the uceA1.7 promoter. The expression level of the reporter gene in different plant tissues and the transcriptional stability of these modules was determined compared to its full-length promoter and the 35S promoter. The full-length uceA1.7 promoter exhibited higher activity in different plant tissues compared to the 35S promoter. Two modules of the promoter produced a low and unstable transcription level compared to the other promoters. The other two modules rich in cis-regulatory elements showed similar activity levels to full-length uceA1.7 and 35S promoters but were less stable. This result suggests the location of a minimal portion of the promoter that is required to initiate transcription properly (the core promoter). Additionally, the full-length uceA1.7 promoter containing the 5'-untranslated region (UTR) is essential for higher transcriptional stability in various plant tissues. These findings confirm the potential use of the full-length uceA1.7 promoter for the development of new biotechnological tools (NBTs) to achieve higher expression levels of GOIs in, for example, the root or flower bud for the efficient control of phytonematodes and pest-insects, respectively, in important crops.
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Affiliation(s)
- Marcos Fernando Basso
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil.
| | | | - Carlos Busanello
- Federal University of Pelotas, Capão Do Leão, RS, 96160-000, Brazil
| | - Clidia Eduarda Moreira Pinto
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Elínea de Oliveira Freitas
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Thuanne Pires Ribeiro
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
| | | | | | - Carolina Vianna Morgante
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Embrapa Semi Arid, Petrolina, PE, 56302-970, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil.
- Catholic University of Brasília, Brasília, DF, 71966-700, Brazil.
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Strohmayer A, Moser M, Si-Ammour A, Krczal G, Boonrod K. ' Candidatus Phytoplasma mali' Genome Encodes a Protein that Functions as an E3 Ubiquitin Ligase and Could Inhibit Plant Basal Defense. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1487-1495. [PMID: 31241412 DOI: 10.1094/mpmi-04-19-0107-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytoplasmas are the causative agent of numerous diseases of plant species all over the world, including important food crops. The mode by which phytoplasmas multiply and behave in their host is poorly understood and often based on genomic data. We used yeast two-hybrid screening to find new protein-protein interactions between the causal agent of apple proliferation 'Candidatus Phytoplasma mali' and its host plant. Here, we report that the 'Ca. P. mali' strain PM19 genome encodes a protein PM19_00185 that interacts with at least six different ubiquitin-conjugating enzymes (UBC; E2) of Arabidopsis thaliana. An in vitro ubiquitination assay showed that PM19_00185 is enzymatically active as E3 ligase with A. thaliana E2 UBC09 and Malus domestica E2 UBC10. We show that a nonhost bacteria (Pseudomonas syringae pv. tabaci) can grow in transgenic A. thaliana plant lines expressing PM19_00185. A connection of phytoplasma effector proteins with the proteasome proteolytic pathway has been reported before. However, this is, to our knowledge, the first time that a phytoplasma effector protein with E3 ligase activity has been reported.
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Affiliation(s)
- Alisa Strohmayer
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
| | - Mirko Moser
- Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund March, San Michele All'Adige, Italy
| | - Azeddine Si-Ammour
- Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund March, San Michele All'Adige, Italy
| | - Gabi Krczal
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
| | - Kajohn Boonrod
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
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Time-dependent effects of Pochonia chlamydosporia endophytism on gene expression profiles of colonized tomato roots. Appl Microbiol Biotechnol 2019; 103:8511-8527. [PMID: 31392375 DOI: 10.1007/s00253-019-10058-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/26/2023]
Abstract
A transcriptome analysis was produced from tomato roots inoculated with the hyphomycete Pochonia chlamydosporia at three different times. Gene expression data were also yielded from fungus grown in vitro or endophytic. A next-generation sequencing (NGS) and network analysis approach were applied. We identified 3.676 differentially expressed tomato genes (DEG), highlighting a core of 93 transcripts commonly down- or upregulated at every time point, shedding light on endophytism process. Functional categories related to plant information-processing system, which recognizes, percepts, and transmits signals, were associated with gene upregulated early in time, with higher representations in processes such as plant defense regulation later in time. Network analysis of a DEG subset showed dominance of MAP kinase hubs in the uninoculated control samples, replaced by an increased centrality of WRKY transcription factor and ETR-ethylene response factor genes in the colonized roots. Fungus genes expressed during progression of plant colonization, therefore related to the host colonization process or endophytism persistence, were also identified. Data provided a high-resolution insight on tomato transcriptome changes as induced by endophytism, highlighting a specific modulation of stress-responsive transcripts, related to a selective activation of defense pathways, likely required by the fungus to establish a persistent endophytic lifestyle.
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Ahn E, Hu Z, Perumal R, Prom LK, Odvody G, Upadhyaya HD, Magill C. Genome wide association analysis of sorghum mini core lines regarding anthracnose, downy mildew, and head smut. PLoS One 2019; 14:e0216671. [PMID: 31086384 PMCID: PMC6516728 DOI: 10.1371/journal.pone.0216671] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/26/2019] [Indexed: 02/04/2023] Open
Abstract
In previous studies, a sorghum mini core collection was scored over several years for response to Colletotrichum sublineola, Peronosclerospora sorghi, and Sporisorium reilianum, the causal agents of the disease anthracnose, downy mildew, and head smut, respectively. The screening results were combined with over 290,000 Single nucleotide polymorphic (SNP) loci from an updated version of a publicly available genotype by sequencing (GBS) dataset available for the mini core collection. GAPIT (Genome Association and Prediction Integrated Tool) R package was used to identify chromosomal locations that differ in disease response. When the top scoring SNPs were mapped to the most recent version of the published sorghum genome, in each case, a nearby and most often the closest annotated gene has precedence for a role in host defense.
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Affiliation(s)
- Ezekiel Ahn
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Ramasamy Perumal
- Kansas State University, Agricultural Research Center, Hays, Kansas, United States of America
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, Texas, United States of America
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, Texas, United States of America
| | - Hari D. Upadhyaya
- ICRISAT, Patancheru, Telangana, India
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Clint Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
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Tunsagool P, Jutidamrongphan W, Phaonakrop N, Jaresitthikunchai J, Roytrakul S, Leelasuphakul W. Insights into stress responses in mandarins triggered by Bacillus subtilis cyclic lipopeptides and exogenous plant hormones upon Penicillium digitatum infection. PLANT CELL REPORTS 2019; 38:559-575. [PMID: 30715581 DOI: 10.1007/s00299-019-02386-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/25/2019] [Indexed: 05/11/2023]
Abstract
Bacillus subtilis CLP extract activates defense gene expression and increases the unique protein production involving in pathways of ISR, SAR, ubiquitin-proteasome system, and glycolysis for stress responses in flavedo tissues. Cyclic lipopeptides (CLPs) of Bacillus subtilis ABS-S14 had ability to activate plant defensive pathways, increase resistance and control green mold rot caused by Penicillium digitatum in mandarin fruit. The current study investigated transcriptional and proteomic data to highlight the unique induction effect of CLPs produced by B. subtilis ABS-S14 on the defense mechanism of mandarins in response to P. digitatum attack, and their differences from those following the exogenous plant hormone application. The proteomic patterns of the flavedo tissues as affected by Bacillus CLP extract, salicylic acid (SA), methyl jasmonate (MeJA), and ethephon (Et) were explored. qPCR analysis revealed the great effects of CLP extract in enhancing the transcription of PAL, ACS1, GLU, POD, and PR1. Tryptic peptides by LC-MS analysis between treatments with and without fungal infection were compared. B. subtilis CLP extract empowered the plant's immune response to wound stress by the significant production of calmodulin-binding receptor-like cytoplasmic kinase 2, molybdenum cofactor sulfurase, and NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase. Ubiquitin carrier protein abundance was developed only in the treated flavedo with CLP extract coupled with P. digitatum infection. The gene expression and overall proteome findings involving pathways of ubiquitin proteasome system, ISR, SAR, and energy production provide a new insight into the molecular mechanisms of the antagonist B. subtilis ABS-S14 inducing resistance against green mold in mandarins.
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Affiliation(s)
- Paiboon Tunsagool
- Department of Biochemistry, Prince of Songkla University, Songkhla, 90112, Thailand
| | | | - Narumon Phaonakrop
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park (TSP), Pathum Thani, 12120, Thailand
| | - Janthima Jaresitthikunchai
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park (TSP), Pathum Thani, 12120, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park (TSP), Pathum Thani, 12120, Thailand
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Kud J, Wang W, Gross R, Fan Y, Huang L, Yuan Y, Gray A, Duarte A, Kuhl JC, Caplan A, Goverse A, Liu Y, Dandurand LM, Xiao F. The potato cyst nematode effector RHA1B is a ubiquitin ligase and uses two distinct mechanisms to suppress plant immune signaling. PLoS Pathog 2019; 15:e1007720. [PMID: 30978251 PMCID: PMC6461251 DOI: 10.1371/journal.ppat.1007720] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
Plant pathogens, such as bacteria, fungi, oomycetes and nematodes, rely on wide range of virulent effectors delivered into host cells to suppress plant immunity. Although phytobacterial effectors have been intensively investigated, little is known about the function of effectors of plant-parasitic nematodes, such as Globodera pallida, a cyst nematode responsible for vast losses in the potato and tomato industries. Here, we demonstrate using in vivo and in vitro ubiquitination assays the potato cyst nematode (Globodera pallida) effector RHA1B is an E3 ubiquitin ligase that employs multiple host plant E2 ubiquitin conjugation enzymes to catalyze ubiquitination. RHA1B was able to suppress effector-triggered immunity (ETI), as manifested by suppression of hypersensitive response (HR) mediated by a broad range of nucleotide-binding leucine-rich repeat (NB-LRR) immune receptors, presumably via E3-dependent degradation of the NB-LRR receptors. RHA1B also blocked the flg22-triggered expression of Acre31 and WRKY22, marker genes of pathogen‐associated molecular pattern (PAMP)‐triggered immunity (PTI), but this did not require the E3 activity of RHA1B. Moreover, transgenic potato overexpressing the RHA1B transgene exhibited enhanced susceptibility to G. pallida. Thus, our data suggest RHA1B facilitates nematode parasitism not only by triggering degradation of NB-LRR immune receptors to block ETI signaling but also by suppressing PTI signaling via an as yet unknown E3-independent mechanism. Globodera pallida is a plant-parasitic cyst nematode that causes vast losses in economically important crops such as potato and tomato. To successfully parasitize host plants, G. pallida produces proteins called effectors to overcome plant defenses. Here, we report identification of a novel G. pallida effector RHA1B as an E3 ubiquitin ligase, which is responsible for ubiquitin-proteasome-mediated protein degradation in general. We found that RHA1B can suppress plant defense signaling via both E3-dependent and -independent manners. In particular, it promotes degradation of a broad range of NB-LRR immune receptors. In addition, expression of RHA1B in potato plants made the plants more susceptible to G. pallida infection, indicating that RHA1B acts as an effector that aids parasitism. Overall, we found RHA1B as the first effector with ubiquitin ligase activity identified from eukaryotic pathogen infecting plants or animals. Our data suggest nematode uses RHA1B as a powerful weapon to manipulate host cellular signaling pathways, thereby interfering with plant immunity for successful parasitism.
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Affiliation(s)
- Joanna Kud
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
| | - Wenjie Wang
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
- School of Food Science, Hefei University of Technology, Hefei, China
| | - Rachel Gross
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
| | - Youhong Fan
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
- School of Food Science, Hefei University of Technology, Hefei, China
| | - Li Huang
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
| | - Yulin Yuan
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
| | - Amanda Gray
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States of America
| | - Aida Duarte
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States of America
| | - Joseph C. Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
| | - Allan Caplan
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Yongsheng Liu
- School of Food Science, Hefei University of Technology, Hefei, China
- School of Horticulture, Anhui Agricultural University, Hefei, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Louise-Marie Dandurand
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States of America
- * E-mail: (LMD); (FX)
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States of America
- * E-mail: (LMD); (FX)
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25
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Qin T, Liu S, Zhang Z, Sun L, He X, Lindsey K, Zhu L, Zhang X. GhCyP3 improves the resistance of cotton to Verticillium dahliae by inhibiting the E3 ubiquitin ligase activity of GhPUB17. PLANT MOLECULAR BIOLOGY 2019; 99:379-393. [PMID: 30671725 DOI: 10.1007/s11103-019-00824-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 01/12/2019] [Indexed: 05/02/2023]
Abstract
A U-box E3 ubiquitin ligase GhPUB17 is inhibited by GhCyP3 with antifungal activity and acts as a negative regulator involved in cotton resistance to Verticillium dahliae. E3 ubiquitin ligases, the key component enzymes of the ubiquitin-proteasome system, which contains the most diverse structural and functional members involved in the determination of target specificity and the regulation of metabolism, have been well documented in previous studies. Here, we identify GhPUB17, a U-box E3 ligase in cotton that has ubiquitination activity and is involved in the cotton immune response to Verticillium dahliae. The expression level of GhPUB17 is downregulated in the ssn mutant with a constitutively activated immune response (Sun et al., Nat Commun 5:5372, 2014). Infection with V. dahliae or exogenous hormone treatment, including jasmonic acid and salicylic acid, significantly upregulated GhPUB17 in cotton roots, which suggested a possible role for this E3 ligase in the plant immune response to pathogens. Moreover, GhPUB17-knockdown cotton plants are more resistant to V. dahliae, whereas GhPUB17-overexpressing plants are more susceptible to the pathogen, which indicated that GhPUB17 is a negative regulator of cotton resistance to V. dahliae. A yeast two-hybrid (Y2H) assay identified GhCyP3 as a protein that interacts with GhPUB17, and this finding was confirmed by further protein interaction assays. The downregulation of GhCyP3 in cotton seedlings attenuated the plants' resistance to V. dahliae. In addition, GhCyP3 showed antifungal activity against V. dahliae, and the E3 ligase activity of GhPUB17 was repressed by GhCyP3 in vitro. These results suggest that GhPUB17 negatively regulates cotton immunity to V. dahliae and that the antifungal protein GhCyP3 likely interacts with and inhibits the ligase activity of GhPUB17 and plays an important role in the cotton-Verticillium interaction.
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Affiliation(s)
- Tao Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shiming Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhennan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Longqing Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Jia L, Zhao Q, Chen S. Evolution and expression analysis of the sorghum ubiquitin-conjugating enzyme family. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:236-247. [PMID: 32172767 DOI: 10.1071/fp18184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/02/2018] [Indexed: 06/10/2023]
Abstract
Ubiquitin-conjugating enzymes (UBCs), which catalyse the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. Current knowledge regarding the sorghum (Sorghum bicolor (L.) Moench) ubiquitin-conjugating enzyme (SbUBC) family remains very limited. We identified 53 UBC-encoding genes in the sorghum genome and divided these into 18 groups according to their phylogenetic relationship with Arabidopsis thaliana (L.) Heynh., which was further supported by conserved motif and gene structure analyses. Different expression levels under a variety of abiotic stresses suggested that these might participate in distinct signalling pathways and that they underwent functional divergence during evolution. Furthermore, several SbUBC genes responded to single treatments, and individual SbUBC genes responded to multiple treatments, suggesting that sorghum UBCs may mediate crosstalk among different signalling pathways. Overall, the results provide valuable information for better understanding the classification and putative functions of sorghum UBC-encoding genes.
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Affiliation(s)
- Liqiang Jia
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - QiuFang Zhao
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Shu Chen
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
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Li D, Zhang T, Wang M, Liu Y, Brestic M, Chen THH, Yang X. Genetic Engineering of the Biosynthesis of Glycine Betaine Modulates Phosphate Homeostasis by Regulating Phosphate Acquisition in Tomato. FRONTIERS IN PLANT SCIENCE 2019; 9:1995. [PMID: 30687378 PMCID: PMC6335352 DOI: 10.3389/fpls.2018.01995] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/21/2018] [Indexed: 05/03/2023]
Abstract
Glycine betaine (GB), as a putative compatible substance, protects plants against the damaging effects of abiotic stresses. Phosphorus deficiency is one type of abiotic stress that is detrimental to plant growth. Maintenance of phosphate (Pi) homeostasis is crucial. This study demonstrates GB-regulated phosphate homeostasis in the tomato (Solanum lycopersicum cv. 'Moneymaker') transformed with the choline oxidase gene codA from Arthrobacter globiformis. The codA-transgenic lines displayed more resistance to low-phosphate stress. The data revealed that the wild-type plants were stunted and consistently retained less Pi than transgenic lines, especially when grown under low-phosphate conditions. This difference in Pi retention was attributable to the enhanced Pi uptake ability in the transgenic lines. The transgenic plants translocated more Pi into the plant cell due to the enhanced enzymatic activity of plasma membrane H+-ATPase and increased Pi/H+ co-transport, which improved Pi uptake. The differential expression of 'PHO regulon' genes further maintained intracellular Pi homeostasis. Furthermore, GB maintained a higher photosynthesis rate, thus increasing the production and translocation of sucrose via phloem loading to enhance plant response to low-phosphate stress. We conclude that GB mediates Pi uptake and translocation by regulating physiological and biochemical processes that promote adaptation to environmental changes in Pi availability. These processes eventually lead to better growth and development of the codA-transgenic lines. This finding will help to further elucidate the signaling mechanism of how GB perceives and transmits low-phosphate signals to alleviate Pi nutritional stress.
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Affiliation(s)
- Daxing Li
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Tianpeng Zhang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Mengwei Wang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Yang Liu
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia
| | - Tony H. H. Chen
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Xinghong Yang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
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28
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Regulation of Plant Immunity by the Proteasome. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 343:37-63. [DOI: 10.1016/bs.ircmb.2018.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Furniss JJ, Grey H, Wang Z, Nomoto M, Jackson L, Tada Y, Spoel SH. Proteasome-associated HECT-type ubiquitin ligase activity is required for plant immunity. PLoS Pathog 2018; 14:e1007447. [PMID: 30458055 PMCID: PMC6286022 DOI: 10.1371/journal.ppat.1007447] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/07/2018] [Accepted: 10/31/2018] [Indexed: 11/19/2022] Open
Abstract
Regulated degradation of proteins by the 26S proteasome plays important roles in maintenance and signalling in eukaryotic cells. Proteins are marked for degradation by the action of E3 ligases that site-specifically modify their substrates by adding chains of ubiquitin. Innate immune signalling in plants is deeply reliant on the ubiquitin-26S proteasome system. While progress has been made in understanding substrate ubiquitination during plant immunity, how these substrates are processed upon arrival at the proteasome remains unclear. Here we show that specific members of the HECT domain-containing family of ubiquitin protein ligases (UPL) play important roles in proteasomal substrate processing during plant immunity. Mutations in UPL1, UPL3 and UPL5 significantly diminished immune responses activated by the immune hormone salicylic acid (SA). In depth analyses of upl3 mutants indicated that these plants were impaired in reprogramming of nearly the entire SA-induced transcriptome and failed to establish immunity against a hemi-biotrophic pathogen. UPL3 was found to physically interact with the regulatory particle of the proteasome and with other ubiquitin-26S proteasome pathway components. In agreement, we demonstrate that UPL3 enabled proteasomes to form polyubiquitin chains, thereby regulating total cellular polyubiquitination levels. Taken together, our findings suggest that proteasome-associated ubiquitin ligase activity of UPL3 promotes proteasomal processivity and is indispensable for development of plant immunity.
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Affiliation(s)
- James J. Furniss
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Heather Grey
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Zhishuo Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mika Nomoto
- The Center for Gene Research, Division of Biological Science, Nagoya University, Nagoya, Japan
| | - Lorna Jackson
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yasuomi Tada
- The Center for Gene Research, Division of Biological Science, Nagoya University, Nagoya, Japan
| | - Steven H. Spoel
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Zhang C, Song L, Choudhary MK, Zhou B, Sun G, Broderick K, Giesler L, Zeng L. Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode. BMC PLANT BIOLOGY 2018; 18:149. [PMID: 30021519 PMCID: PMC6052599 DOI: 10.1186/s12870-018-1365-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/09/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Ubiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes. The ubiquitination process typically involves three distinct classes of enzymes, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). To date, a comprehensive identification and analysis of core components comprising of the whole soybean (Glycine max) ubiquitin system (UBS) has not been reported. RESULTS We performed a systematic, genome-wide analysis of genes that encode core members of the soybean UBS in this study. A total of 1431 genes were identified with high confidence to encode putative soybean UBS components, including 4 genes encoding E1s, 71 genes that encode the E2s, and 1356 genes encoding the E3-related components. Among the E3-encoding genes, 760 encode RING-type E3s, 124 encode U-box domain-containing E3s, and 472 encode F-box proteins. To find out whether the identified soybean UBS genes encode active enzymes, a set of genes were randomly selected and the enzymatic activities of their recombinant proteins were tested. Thioester assays indicated proteins encoded by the soybean E1 gene GmUBA1 and the majority of selected E2 genes are active E1 or E2 enzymes, respectively. Meanwhile, most of the purified RING and U-box domain-containing proteins displayed E3 activity in the in vitro ubiquitination assay. In addition, 1034 of the identified soybean UBS genes were found to express in at least one of 14 soybean tissues examined and the transcript level of 338 soybean USB genes were significantly changed after abiotic or biotic (Fusarium oxysporum and Rhizobium strains) stress treatment. Finally, the expression level of a large number of the identified soybean UBS-related genes was found significantly altered after soybean cyst nematode (SCN) treatment, suggesting the soybean UBS potentially plays an important role in soybean immunity against SCN. CONCLUSIONS Our findings indicate the presence of a large and diverse number of core UBS proteins in the soybean genome, which suggests that target-specific modification by ubiquitin is a complex and important part of cellular and physiological regulation in soybean. We also revealed certain members of the soybean UBS may be involved in immunity against soybean cyst nematode (SCN). This study sets up an essential foundation for further functional characterization of the soybean UBS in various physiological processes, such as host immunity against SCN.
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Affiliation(s)
- Chunyu Zhang
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588 USA
| | - Li Song
- Department of Information Science, University of Arkansas, Little Rock, AR 72204 USA
| | - Mani Kant Choudhary
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588 USA
| | - Bangjun Zhou
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588 USA
| | - Guangchao Sun
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588 USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583 USA
| | - Kyle Broderick
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
| | - Loren Giesler
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
| | - Lirong Zeng
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588 USA
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The rice blast resistance gene Ptr encodes an atypical protein required for broad-spectrum disease resistance. Nat Commun 2018; 9:2039. [PMID: 29795191 PMCID: PMC5966436 DOI: 10.1038/s41467-018-04369-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/16/2018] [Indexed: 11/08/2022] Open
Abstract
Plant resistance genes typically encode proteins with nucleotide binding site-leucine rich repeat (NLR) domains. Here we show that Ptr is an atypical resistance gene encoding a protein with four Armadillo repeats. Ptr is required for broad-spectrum blast resistance mediated by the NLR R gene Pi-ta and by the associated R gene Pi-ta2. Ptr is expressed constitutively and encodes two isoforms that are mainly localized in the cytoplasm. A two base pair deletion within the Ptr coding region in the fast neutron-generated mutant line M2354 creates a truncated protein, resulting in susceptibility to M. oryzae. Targeted mutation of Ptr in a resistant cultivar using CRISPR/Cas9 leads to blast susceptibility, further confirming its resistance function. The cloning of Ptr may aid in the development of broad spectrum blast resistant rice.
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Zhou B, Zeng L. The Tomato U-Box Type E3 Ligase PUB13 Acts With Group III Ubiquitin E2 Enzymes to Modulate FLS2-Mediated Immune Signaling. FRONTIERS IN PLANT SCIENCE 2018; 9:615. [PMID: 29868071 PMCID: PMC5952000 DOI: 10.3389/fpls.2018.00615] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/18/2018] [Indexed: 06/01/2023]
Abstract
In Arabidopsis and rice, the ubiquitin ligase PUB13-mediated protein degradation plays a significant role in plant pattern-triggered immunity (PTI) and flowering time control. The Arabidopsis PUB13 has been shown to attenuate the pattern recognition receptor FLS2-mediated immune signaling by ubiquitinating FLS2 and consequently promoting its degradation by the 26S proteasome. Nevertheless, the cognate ubiquitin-conjugating enzymes (E2) with which PUB13 acts to modulate FLS2-mediated PTI are unknown. To address this question, we investigate here the tomato (Solanum lycopersicum) homolog of PUB13, SlPUB13 by utilizing the recently characterized complete set of tomato E2s. Of the 13 groups of tomato E2s, only members in group III are found to interact and act with SlPUB13. Knocking-down of the group III E2 genes enhances callose deposition and induction of the RbohB gene in the immunity-associated, early oxidative burst after flg22 treatment. The group III E2s are also found to work with SlPUB13 to ubiquitinate FLS2 in vitro and are required for PUB13-mediated degradation of FLS2 in vivo upon flg22 treatment, suggesting an essential role for group III E2s in the modulation of FLS2-mediated immune signaling by PUB13. Additionally, another immunity-associated E3, NtCMPG1 is shown to also work specifically with members of group III E2 in the in vitro ubiquitination assay, which implies the group III E2 enzymes may cooperate with many E3 ligases to regulate different aspects of PTI. Taken together, these data corroborate the notion that group III E2 enzymes play an important role in PTI and build a foundation for further functional and mechanistic characterization of tomato PUB13.
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Wang W, Fan Y, Niu X, Miao M, Kud J, Zhou B, Zeng L, Liu Y, Xiao F. Functional analysis of the seven in absentia ubiquitin ligase family in tomato. PLANT, CELL & ENVIRONMENT 2018; 41:689-703. [PMID: 29320607 DOI: 10.1111/pce.13140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/01/2018] [Accepted: 01/03/2018] [Indexed: 05/28/2023]
Abstract
Seven in absentia (SINA) protein is one subgroup of ubiquitin ligases possessing an N-terminal cysteine-rich really interesting new gene (RING) domain, two zinc-finger motifs, and a C-terminal domain responsible for substrate-binding and dimerization. In tomato (Solanum lycopersicum), the SINA gene family has six members, and we characterize in this study all tomato SINA (SlSINA) genes and the gene products. Our results show that SlSINA genes are differentially regulated in leaf, bud, stem, flower, and root. All SlSINA proteins possess RING-dependent E3 ubiquitin ligase activity, exhibiting similar specificity towards the E2 ubiquitin-conjugating enzyme. SlSINA1/3/4/5/6 are localized in both cytoplasm and nucleus, whereas SlSINA2 is exclusively localized in the nucleus. Moreover, all SlSINAs can interact with each other for homo- or hetero-dimerization. The functionality of SlSINA proteins has been investigated. SlSINA4 plays a positive role in defense signalling, as manifested by elicitation of E3-dependent hypersensitive response-like cell death; the other SlSINAs are negative regulator and capable to suppress hypersensitive response cell death. Transgenic tomato plants overexpressing SlSINA2 exhibit pale-green leaf phenotype, suggesting SlSINA2 regulates chlorophyll level in plant cells, whereas transgenic tomato plants overexpressing SlSINA5 have altered floral structure with exserted stigma, implicating SlSINA5 plays a role in flower development.
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Affiliation(s)
- Wenjie Wang
- School of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Youhong Fan
- School of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Xiangli Niu
- School of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Min Miao
- School of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Joanna Kud
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Bangjun Zhou
- Plant Science Innovation Center and Plant Pathology Department, University of Nebraska, Lincoln, NE, 68583, USA
| | - Lirong Zeng
- Plant Science Innovation Center and Plant Pathology Department, University of Nebraska, Lincoln, NE, 68583, USA
| | - Yongsheng Liu
- School of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610064, China
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
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Li S, Liu K, Zhou B, Li M, Zhang S, Zeng L, Zhang C, Yu B. MAC3A and MAC3B, Two Core Subunits of the MOS4-Associated Complex, Positively Influence miRNA Biogenesis. THE PLANT CELL 2018; 30:481-494. [PMID: 29437988 PMCID: PMC5868694 DOI: 10.1105/tpc.17.00953] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/16/2018] [Accepted: 01/31/2018] [Indexed: 05/18/2023]
Abstract
MAC3A and MAC3B are conserved U-box-containing proteins in eukaryotes. They are subunits of the MOS4-associated complex (MAC) that plays essential roles in plant immunity and development in Arabidopsis thaliana However, their functional mechanisms remain elusive. Here, we show that Arabidopsis MAC3A and MAC3B act redundantly in microRNA (miRNA) biogenesis. Lack of both MAC3A and MAC3B in the mac3b mac3b double mutant reduces the accumulation of miRNAs, causing elevated transcript levels of miRNA targets. mac3a mac3b also decreases the levels of primary miRNA transcripts (pri-miRNAs). However, MAC3A and MAC3B do not affect the promoter activity of genes encoding miRNAs (MIR genes), suggesting that they may not affect MIR transcription. This result, together with the fact that MAC3A associates with pri-miRNAs in vivo, indicates that MAC3A and MAC3B may stabilize pri-miRNAs. Furthermore, we find that MAC3A and MAC3B interact with the DCL1 complex that catalyzes miRNA maturation, promote DCL1 activity, and are required for the localization of HYL1, a component of the DCL1 complex. Besides MAC3A and MAC3B, two other MAC subunits, CDC5 and PRL1, also function in miRNA biogenesis. Based on these results, we propose that MAC functions as a complex to control miRNA levels through modulating pri-miRNA transcription, processing, and stability.
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Affiliation(s)
- Shengjun Li
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Kan Liu
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Bangjun Zhou
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| | - Mu Li
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Shuxin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Lirong Zeng
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| | - Chi Zhang
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Bin Yu
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
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Immunity-Associated Programmed Cell Death as a Tool for the Identification of Genes Essential for Plant Innate Immunity. Methods Mol Biol 2018. [PMID: 29332285 DOI: 10.1007/978-1-4939-7668-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Plants have evolved a sophisticated innate immune system to contend with potential infection by various pathogens. Understanding and manipulation of key molecular mechanisms that plants use to defend against various pathogens are critical for developing novel strategies in plant disease control. In plants, resistance to attempted pathogen infection is often associated with hypersensitive response (HR), a form of rapid programmed cell death (PCD) at the site of attempted pathogen invasion. In this chapter, we describe a method for rapid identification of genes that are essential for plant innate immunity. It combines virus-induced gene silencing (VIGS), a tool that is suitable for studying gene function in high-throughput, with the utilization of immunity-associated PCD, particularly HR-linked PCD as the readout of changes in plant innate immunity. The chapter covers from the design of gene fragment for VIGS, the agroinfiltration of the Nicotiana benthamian plants, to the use of immunity-associated PCD induced by twelve elicitors as the indicator of activation of plant immunity.
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Sharma B, Bhatt TK. Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato. Sci Rep 2017; 7:8613. [PMID: 28819320 PMCID: PMC5561181 DOI: 10.1038/s41598-017-09121-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/14/2017] [Indexed: 11/27/2022] Open
Abstract
The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme. We have utilized in-silico methods to analyze E2 enzymes in Solanum lycopersicum and 59 genes were identified with UBC family domains. The physio-chemical properties, chromosomal localization, structural organization, gene duplication, promoter analysis, gene ontology and conserved motifs were investigated along with phylogenetic analysis of tomato E2 genes exploring evolutionary relations. The gene expression analysis of RNA sequencing data revealed expression profile of tomato E2 genes in seedling, root, leaf, seed, fruit, and flower tissues. Our study aid in the understanding of distribution, expansion, evolutionary relation and probable participation in plant biological processes of tomato E2 enzymes that will facilitate strong base for future research on ubiquitin-mediated regulations in tomato and other plant systems.
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Affiliation(s)
- Bhaskar Sharma
- Department of Biotechnology, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Tarun Kumar Bhatt
- Department of Biotechnology, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
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Kushwaha NK, Bhardwaj M, Chakraborty S. The replication initiator protein of a geminivirus interacts with host monoubiquitination machinery and stimulates transcription of the viral genome. PLoS Pathog 2017; 13:e1006587. [PMID: 28859169 PMCID: PMC5597257 DOI: 10.1371/journal.ppat.1006587] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/13/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022] Open
Abstract
Geminiviruses constitute a group of plant viruses, with a ssDNA genome, whose replication in the nucleus of an infected cell requires the function of geminivirus-encoded replication initiator protein (Rep). Our results suggest that monoubiquitinated histone 2B (H2B-ub) promotes tri-methylation of histone 3 at lysine 4 (H3-K4me3) on the promoter of Chilli leaf curl virus (ChiLCV). We isolated homologues of two major components of the monoubiquitination machinery: UBIQUITIN-CONJUGATING ENZYME2 (NbUBC2) and HISTONE MONOUBIQUITINATION1 (NbHUB1) from N. benthamiana. ChiLCV failed to cause disease in NbUBC2-, and NbHUB1-silenced plants, at the same time, H2B-ub and H3-K4me3 modifications were decreased, and the occupancy of RNA polymerase II on the viral promoter was reduced as well. In further investigations, Rep protein of ChiLCV was found to re-localize NbUBC2 from the cytoplasm to the nucleoplasm, like NbHUB1, the cognate partner of NbUBC2. Rep was observed to interact and co-localize with NbHUB1 and NbUBC2 in the nuclei of the infected cells. In summary, the current study reveals that the ChiLCV Rep protein binds the viral genome and interacts with NbUBC2 and NbHUB1 for the monoubiquitination of histone 2B that subsequently promotes trimethylation of histone 3 at lysine 4 on ChiLCV mini-chromosomes and enhances transcription of the viral genes.
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Affiliation(s)
- Nirbhay Kumar Kushwaha
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mansi Bhardwaj
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Zhou B, Zeng L. Elucidating the role of highly homologous Nicotiana benthamiana ubiquitin E2 gene family members in plant immunity through an improved virus-induced gene silencing approach. PLANT METHODS 2017; 13:59. [PMID: 28736574 PMCID: PMC5521103 DOI: 10.1186/s13007-017-0210-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/17/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Virus-induced gene silencing (VIGS) has been used in many plant species as an attractive post transcriptional gene silencing (PTGS) method for studying gene function either individually or at large-scale in a high-throughput manner. However, the specificity and efficiency for knocking down members of a highly homologous gene family have remained to date a significant challenge in VIGS due to silencing of off-targets. RESULTS Here we present an improved method for the selection and evaluation of gene fragments used for VIGS to specifically and efficiently knock down members of a highly homologous gene family. Using this method, we knocked down twelve and four members, respectively of group III of the gene family encoding ubiquitin-conjugating enzymes (E2) in Nicotiana benthamiana. Assays using these VIGS-treated plants revealed that the group III E2s are essential for plant development, plant immunity-associated reactive oxygen species (ROS) production, expression of the gene NbRbohB that is required for ROS production, and suppression of immunity-associated programmed cell death (PCD) by AvrPtoB, an effector protein of the bacterial pathogen Pseudomons syringae. Moreover, functional redundancy for plant development and ROS production was found to exist among members of group III E2s. CONCLUSIONS We have found that employment of a gene fragment as short as approximately 70 base pairs (bp) that contains at least three mismatched nucleotides to other genes within any 21-bp sequences prevents silencing of off-target(s) in VIGS. This improved approach in the selection and evaluation of gene fragments allows for specific and efficient knocking down of highly homologous members of a gene family. Using this approach, we implicated N. benthamiana group III E2s in plant development, immunity-associated ROS production, and suppression of multiple immunity-associated PCD by AvrPtoB. We also unraveled functional redundancy among group III members in their requirement for plant development and plant immunity-associated ROS production.
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Affiliation(s)
- Bangjun Zhou
- Center for Plant Science Innovation, Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
| | - Lirong Zeng
- Center for Plant Science Innovation, Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583 USA
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128 China
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