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Noel K, Wolf IR, Hughes D, Valente GT, Qi A, Huang YJ, Fitt BDL, Stotz HU. Transcriptomics of temperature-sensitive R gene-mediated resistance identifies a WAKL10 protein interaction network. Sci Rep 2024; 14:5023. [PMID: 38424101 PMCID: PMC10904819 DOI: 10.1038/s41598-024-53643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/03/2024] [Indexed: 03/02/2024] Open
Abstract
Understanding temperature-sensitivity of R gene-mediated resistance against apoplastic pathogens is important for sustainable food production in the face of global warming. Here, we show that resistance of Brassica napus cotyledons against Leptosphaeria maculans was temperature-sensitive in introgression line Topas-Rlm7 but temperature-resilient in Topas-Rlm4. A set of 1,646 host genes was differentially expressed in Topas-Rlm4 and Topas-Rlm7 in response to temperature. Amongst these were three WAKL10 genes, including BnaA07g20220D, representing the temperature-sensitive Rlm7-1 allele and Rlm4. Network analysis identified a WAKL10 protein interaction cluster specifically for Topas-Rlm7 at 25 °C. Diffusion analysis of the Topas-Rlm4 network identified WRKY22 as a putative regulatory target of the ESCRT-III complex-associated protein VPS60.1, which belongs to the WAKL10 protein interaction community. Combined enrichment analysis of gene ontology terms considering gene expression and network data linked vesicle-mediated transport to defence. Thus, dysregulation of effector-triggered defence in Topas-Rlm7 disrupts vesicle-associated resistance against the apoplastic pathogen L. maculans.
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Affiliation(s)
- Katherine Noel
- Centre for Agriculture, Food and Environmental Management, University of Hertfordshire, Hatfield, AL10 9AB, UK.
- LS Plant Breeding, North Barn, Manor Farm, Milton Road, Cambridge, CB24 9NG, UK.
| | - Ivan R Wolf
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, 28223, USA
| | - David Hughes
- Intelligent Data Ecosystems, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Guilherme T Valente
- School of Medicine, São Paulo State University - UNESP, Botocatu, SP, 18618687, Brazil
| | - Aiming Qi
- Centre for Agriculture, Food and Environmental Management, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Yong-Ju Huang
- Centre for Agriculture, Food and Environmental Management, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Bruce D L Fitt
- Centre for Agriculture, Food and Environmental Management, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Henrik U Stotz
- Centre for Agriculture, Food and Environmental Management, University of Hertfordshire, Hatfield, AL10 9AB, UK.
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Deng X, Ahmad B, Deng J, Liu L, Lu X, Fan Z, Zha X, Pan Y. MaABI5 and MaABF1 transcription factors regulate the expression of MaJOINTLESS during fruit abscission in mulberry ( Morus alba L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1229811. [PMID: 37670871 PMCID: PMC10475957 DOI: 10.3389/fpls.2023.1229811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023]
Abstract
Mulberry holds significant economic value. However, during the ripening stage of its fruit, the phenomenon of abscission, resulting in heavy fruit drop, can severely impact the yield. The formation of off-zone structures is a critical factor in the fruit abscission process, and this process is regulated by multiple transcription factors. One such key gene that plays a significant role in the development of the off-zone in the model plant tomato is JOINTLESS, which promotes the expression of abscission-related genes and regulates the differentiation of abscission zone tissue cells. However, there is a lack of information about fruit abscission mechanism in mulberry. Here, we analyzed the MaJOINTLESS promoter and identified the upstream regulators MaABF1 and MaABI5. These two regulators showed binding with MaJOINTLESS promoter MaABF1 (the ABA Binding Factor/ABA-Responsive Element Binding Proteins) activated the expression of MaJOINTLESS, while MaABI5 (ABSCISIC ACID-INSENSITIVE 5) inhibited the expression of MaJOINTLESS. Finally, the differentially expressed genes (DEGs) were analyzed by transcriptome sequencing to investigate the expression and synergistic relationship of endogenous genes in mulberry during abscission. GO classification and KEGG pathway enrichment analysis showed that most of the DEGs were concentrated in MAPK signaling pathway, flavonoid biosynthesis, citric acid cycle, phytohormone signaling, amino acid biosynthesis, and glycolysis. These results provide a theoretical basis for subsequent in-depth study of physiological fruit abscission in mulberry.
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Affiliation(s)
- Xuan Deng
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Bilal Ahmad
- State Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jing Deng
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Lianlian Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Xiuping Lu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Zelin Fan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Xingfu Zha
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Yu Pan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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Cheng Z, Zhang X, Yao W, Zhao K, Liu L, Fan G, Zhou B, Jiang T. Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar. BMC PLANT BIOLOGY 2021; 21:110. [PMID: 33627082 PMCID: PMC7903804 DOI: 10.1186/s12870-021-02872-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/02/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. RESULTS On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. CONCLUSION Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.
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Affiliation(s)
- Zihan Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xuemei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Kai Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Lin Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Gaofeng Fan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
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Abstract
Plants balance their competing requirements for growth and stress tolerance via a sophisticated regulatory circuitry that controls responses to the external environments. We have identified a plant-specific gene, COST1 (constitutively stressed 1), that is required for normal plant growth but negatively regulates drought resistance by influencing the autophagy pathway. An Arabidopsis thaliana cost1 mutant has decreased growth and increased drought tolerance, together with constitutive autophagy and increased expression of drought-response genes, while overexpression of COST1 confers drought hypersensitivity and reduced autophagy. The COST1 protein is degraded upon plant dehydration, and this degradation is reduced upon treatment with inhibitors of the 26S proteasome or autophagy pathways. The drought resistance of a cost1 mutant is dependent on an active autophagy pathway, but independent of other known drought signaling pathways, indicating that COST1 acts through regulation of autophagy. In addition, COST1 colocalizes to autophagosomes with the autophagosome marker ATG8e and the autophagy adaptor NBR1, and affects the level of ATG8e protein through physical interaction with ATG8e, indicating a pivotal role in direct regulation of autophagy. We propose a model in which COST1 represses autophagy under optimal conditions, thus allowing plant growth. Under drought, COST1 is degraded, enabling activation of autophagy and suppression of growth to enhance drought tolerance. Our research places COST1 as an important regulator controlling the balance between growth and stress responses via the direct regulation of autophagy.
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Sadhukhan A, Enomoto T, Kobayashi Y, Watanabe T, Iuchi S, Kobayashi M, Sahoo L, Yamamoto YY, Koyama H. Sensitive to Proton Rhizotoxicity1 Regulates Salt and Drought Tolerance of Arabidopsis thaliana through Transcriptional Regulation of CIPK23. PLANT & CELL PHYSIOLOGY 2019; 60:2113-2126. [PMID: 31241160 DOI: 10.1093/pcp/pcz120] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/11/2019] [Indexed: 05/10/2023]
Abstract
The transcription factor sensitive to proton rhizotoxicity 1 (STOP1) regulates multiple stress tolerances. In this study, we confirmed its involvement in NaCl and drought tolerance. The root growth of the T-DNA insertion mutant of STOP1 (stop1) was sensitive to NaCl-containing solidified MS media. Transcriptome analysis of stop1 under NaCl stress revealed that STOP1 regulates several genes related to salt tolerance, including CIPK23. Among all available homozygous T-DNA insertion mutants of the genes suppressed in stop1, only cipk23 showed a NaCl-sensitive root growth phenotype comparable to stop1. The CIPK23 promoter had a functional STOP1-binding site, suggesting a strong CIPK23 suppression led to NaCl sensitivity of stop1. This possibility was supported by in planta complementation of CIPK23 in the stop1 background, which rescued the short root phenotype under NaCl. Both stop1 and cipk23 exhibited a drought tolerant phenotype and increased abscisic acid-regulated stomatal closure, while the complementation of CIPK23 in stop1 reversed these traits. Our findings uncover additional pleiotropic roles of STOP1 mediated by CIPK23, which regulates various ion transporters including those regulating K+-homeostasis, which may induce a trade-off between drought tolerance and other traits.
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Affiliation(s)
- Ayan Sadhukhan
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Japan
| | - Takuo Enomoto
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Japan
| | - Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Japan
| | - Toshihiro Watanabe
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, Japan
| | - Satoshi Iuchi
- Experimental Plant Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Masatomo Kobayashi
- Experimental Plant Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Lingaraj Sahoo
- Department of Biosciences and bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Yoshiharu Y Yamamoto
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Japan
| | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Japan
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Ilias IA, Negishi K, Yasue K, Jomura N, Morohashi K, Baharum SN, Goh HH. Transcriptome-wide effects of expansin gene manipulation in etiolated Arabidopsis seedling. JOURNAL OF PLANT RESEARCH 2019; 132:159-172. [PMID: 30341720 DOI: 10.1007/s10265-018-1067-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/19/2018] [Indexed: 05/24/2023]
Abstract
Expansin is a non-enzymatic protein which plays a pivotal role in cell wall loosening by inducing stress relaxation and extension in the plant cell wall. Previous studies on Arabidopsis, Petunia × hybrida, and tomato demonstrated that the suppression of expansin gene expression reduced plant growth but expansin overexpression does not necessarily promotes growth. In this study, both expansin gene suppression and overexpression in dark-grown transgenic Arabidopsis seedlings resulted in reduced hypocotyl length at late growth stages with a more pronounced effect for the overexpression. This defect in hypocotyl elongation raises questions about the molecular effect of expansin gene manipulation. RNA-seq analysis of the transcriptomic changes between day 3 and day 5 seedlings for both transgenic lines found numerous differentially expressed genes (DEGs) including transcription factors and hormone-related genes involved in different aspects of cell wall development. These DEGs imply that the observed hypocotyl growth retardation is a consequence of the concerted effect of regulatory factors and multiple cell-wall related genes, which are important for cell wall remodelling during rapid hypocotyl elongation. This is further supported by co-expression analysis through network-centric approach of differential network cluster analysis. This first transcriptome-wide study of expansin manipulation explains why the effect of expansin overexpression is greater than suppression and provides insights into the dynamic nature of molecular regulation during etiolation.
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Affiliation(s)
- Iqmal Asyraf Ilias
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Darul Ehsan, Malaysia
| | - Kohei Negishi
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Keito Yasue
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Naohiro Jomura
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Kengo Morohashi
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Syarul Nataqain Baharum
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Darul Ehsan, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Darul Ehsan, Malaysia.
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Lawaju BR, Lawrence KS, Lawrence GW, Klink VP. Harpin-inducible defense signaling components impair infection by the ascomycete Macrophomina phaseolina. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:331-348. [PMID: 29936240 DOI: 10.1016/j.plaphy.2018.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 05/23/2023]
Abstract
Soybean (Glycine max) infection by the charcoal rot (CR) ascomycete Macrophomina phaseolina is enhanced by the soybean cyst nematode (SCN) Heterodera glycines. We hypothesized that G. max genetic lines impairing infection by M. phaseolina would also limit H. glycines parasitism, leading to resistance. As a part of this M. phaseolina resistance process, the genetic line would express defense genes already proven to impair nematode parasitism. Using G. max[DT97-4290/PI 642055], exhibiting partial resistance to M. phaseolina, experiments show the genetic line also impairs H. glycines parasitism. Furthermore, comparative studies show G. max[DT97-4290/PI 642055] exhibits induced expression of the effector triggered immunity (ETI) gene NON-RACE SPECIFIC DISEASE RESISTANCE 1/HARPIN INDUCED1 (NDR1/HIN1) that functions in defense to H. glycines as compared to the H. glycines and M. phaseolina susceptible line G. max[Williams 82/PI 518671]. Other defense genes that are induced in G. max[DT97-4290/PI 642055] include the pathogen associated molecular pattern (PAMP) triggered immunity (PTI) genes ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1), NONEXPRESSOR OF PR1 (NPR1) and TGA2. These observations link G. max defense processes that impede H. glycines parasitism to also potentially function toward impairing M. phaseolina pathogenicity. Testing this hypothesis, G. max[Williams 82/PI 518671] genetically engineered to experimentally induce GmNDR1-1, EDS1-2, NPR1-2 and TGA2-1 expression leads to impaired M. phaseolina pathogenicity. In contrast, G. max[DT97-4290/PI 642055] engineered to experimentally suppress the expression of GmNDR1-1, EDS1-2, NPR1-2 and TGA2-1 by RNA interference (RNAi) enhances M. phaseolina pathogenicity. The results show components of PTI and ETI impair both nematode and M. phaseolina pathogenicity.
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Affiliation(s)
- Bisho R Lawaju
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, College of Agriculture and Life Sciences, Mississippi State, MS, 39762, USA.
| | - Kathy S Lawrence
- Department of Entomology and Plant Pathology, Auburn University, 209 Life Science Building, Auburn, AL, 36849, USA.
| | - Gary W Lawrence
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, College of Agriculture and Life Sciences, Mississippi State University, Mississippi State, MS, 39762, USA.
| | - Vincent P Klink
- Department of Biological Sciences, College of Arts and Sciences, Mississippi State University, Mississippi State, MS, 39762, USA.
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Kraner ME, Müller C, Sonnewald U. Comparative proteomic profiling of the choline transporter-like1 (CHER1) mutant provides insights into plasmodesmata composition of fully developed Arabidopsis thaliana leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:696-709. [PMID: 28865150 DOI: 10.1111/tpj.13702] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 05/23/2023]
Abstract
In plants, intercellular communication and exchange are highly dependent on cell wall bridging structures between adhering cells, so-called plasmodesmata (PD). In our previous genetic screen for PD-deficient Arabidopsis mutants, we described choline transporter-like 1 (CHER1) being important for PD genesis and maturation. Leaves of cher1 mutant plants have up to 10 times less PD, which do not develop to complex structures. Here we utilize the T-DNA insertion mutant cher1-4 and report a deep comparative proteomic workflow for the identification of cell-wall-embedded PD-associated proteins. Analyzing triplicates of cell-wall-enriched fractions in depth by fractionation and quantitative high-resolution mass spectrometry, we compared > 5000 proteins obtained from fully developed leaves. Comparative data analysis and subsequent filtering generated a list of 61 proteins being significantly more abundant in Col-0. This list was enriched for previously described PD-associated proteins. To validate PD association of so far uncharacterized proteins, subcellular localization analyses were carried out by confocal laser-scanning microscopy. This study confirmed the association of PD for three out of four selected candidates, indicating that the comparative approach indeed allowed identification of so far undescribed PD-associated proteins. Performing comparative cell wall proteomics of Nicotiana benthamiana tissue, we observed an increase in abundance of these three selected candidates during sink to source transition. Taken together, our comparative proteomic approach revealed a valuable data set of potential PD-associated proteins, which can be used as a resource to unravel the molecular composition of complex PD and to investigate their function in cell-to-cell communication.
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Affiliation(s)
- Max E Kraner
- Division of Biochemistry, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstr 5, D-91058, Erlangen, Germany
| | - Carmen Müller
- Division of Biochemistry, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstr 5, D-91058, Erlangen, Germany
| | - Uwe Sonnewald
- Division of Biochemistry, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstr 5, D-91058, Erlangen, Germany
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