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Othman SMIS, Mustaffa AF, Mohd Zahid NII, Che-Othman MH, Samad AFA, Goh HH, Ismail I. Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108387. [PMID: 38266565 DOI: 10.1016/j.plaphy.2024.108387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.
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Affiliation(s)
- Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Nur Irdina Izzatie Mohd Zahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - M Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Abdul Fatah A Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru, 81310, Johor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia; Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia.
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2
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Yang D, Li Y, Zhu M, Cui R, Gao J, Shu Y, Lu X, Zhang H, Zhang K. Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses. Genes (Basel) 2023; 14:2006. [PMID: 38002948 PMCID: PMC10671320 DOI: 10.3390/genes14112006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The FKBP (FK506-binding protein) gene family is an important member of the PPlase protease family and plays a vital role during the processes of plant growth and development. However, no studies of the FKBP gene family have been reported in cucumber. In this study, 19 FKBP genes were identified in cucumber, which were located on chromosomes 1, 3, 4, 6, and 7. Phylogenetic analysis divided the cucumber FKBP genes into three subgroups. The FKBP genes in the same subgroup exhibited similar structures and conserved motifs. The cis-acting elements analysis revealed that the promoters of cucumber FKBP genes contained hormone-, stress-, and development-related cis-acting elements. Synteny analysis of the FKBP genes among cucumber, Arabidopsis, and rice showed that 12 kinds of syntenic relationships were detected between cucumber and Arabidopsis FKBP genes, and 3 kinds of syntenic relationships were observed between cucumber and rice FKBP genes. The tissue-specific expression analysis showed that some FKBP genes were expressed in all tissues, while others were only highly expressed in part of the 10 types of tissues. The expression profile analysis of cucumber FKBP genes under 13 types of stresses showed that the CsaV3_1G007080 gene was differentially expressed under abiotic stresses (high temperature, NaCl, silicon, and photoperiod) and biotic stresses (downy mildew, green mottle mosaic virus, Fusarium wilt, phytophthora capsica, angular leaf spot, and root-knot nematode), which indicated that the CsaV3_1G007080 gene plays an important role in the growth and development of cucumber. The interaction protein analysis showed that most of the proteins in the FKBP gene family interacted with each other. The results of this study will lay the foundation for further research on the molecular biological functions of the cucumber FKBP gene family.
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Affiliation(s)
- Dekun Yang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yahui Li
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Mengdi Zhu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Rongjing Cui
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Jiong Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yingjie Shu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Xiaomin Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
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Hu M, Zhang H, Kong L, Ma J, Wang T, Lu X, Guo Y, Zhang J, Guan R, Chu P. Comparative proteomic and physiological analyses reveal tribenuron-methyl phytotoxicity and nontarget-site resistance mechanisms in Brassica napus. PLANT, CELL & ENVIRONMENT 2023; 46:2255-2272. [PMID: 37102754 DOI: 10.1111/pce.14598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 06/08/2023]
Abstract
The application of herbicides is the most effective strategy for weed control and the development of herbicide-resistant crops will facilitate the weed management. The acetolactate synthase-inhibiting herbicide, tribenuron-methyl (TBM), is broadly used for weed control. However, its application in rapeseed field is restricted since rapeseed is sensitive to TBM. Herein, an integrated study of cytological, physiological and proteomic analysis of the TBM-resistant rapeseed mutant M342 and its wild-type (WT) plants was conducted. After TBM spraying, M342 showed improved tolerance to TBM, and proteins implicated in non-target-site resistance (NTSR) to herbicides had a significantly higher level in M342 as compared with the WT. Differentially accumulated proteins (DAPs) between these two genotypes were enriched in glutathione metabolism and oxidoreduction coenzyme metabolic process, which protected the mutant from oxidative stress triggered by TBM. Important DAPs related to stress or defence response were up-accumulated in M342 regardless of the TBM treatment, which might serve as the constitutive part of NTSR to TBM. These results provide new clues for further exploration of the NTSR mechanism in plants and establish a theoretical basis for the development of herbicide-resistant crops.
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Affiliation(s)
- Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongkun Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Lingna Kong
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Juanjuan Ma
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ting Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xinyu Lu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yue Guo
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Pu Chu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
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Dong Y, Zhou J, Yang Y, Lu W, Jin Y, Huang X, Zhang W, Li J, Ai G, Yin Z, Shen D, Jing M, Dou D, Xia A. Cyclophilin effector Al106 of mirid bug Apolygus lucorum inhibits plant immunity and promotes insect feeding by targeting PUB33. THE NEW PHYTOLOGIST 2023; 237:2388-2403. [PMID: 36519219 DOI: 10.1111/nph.18675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Apolygus lucorum (Meyer-Dur; Heteroptera: Miridae) is a major agricultural pest infesting crops, vegetables, and fruit trees. During feeding, A. lucorum secretes a plethora of effectors into its hosts to promote infestation. However, the molecular mechanisms of these effectors manipulating plant immunity are largely unknown. Here, we investigated the molecular mechanism underlying the effector Al106 manipulation of plant-insect interaction by RNA interference, electrical penetration graph, insect and pathogen bioassays, protein-protein interaction studies, and protein ubiquitination experiment. Expression of Al106 in Nicotiana benthamiana inhibits pathogen-associated molecular pattern-induced cell death and reactive oxygen species burst, and promotes insect feeding and plant pathogen infection. In addition, peptidyl-prolyl cis-trans isomerase (PPIase) activity of Al106 is required for its function to inhibit PTI.Al106 interacts with a plant U-box (PUB) protein, PUB33, from N. benthamiana and Arabidopsis thaliana. We also demonstrated that PUB33 is a positive regulator of plant immunity. Furthermore, an in vivo assay revealed that Al106 inhibits ubiquitination of NbPUB33 depending on PPIase activity. Our findings revealed that a novel cyclophilin effector may interact with plant PUB33 to suppress plant immunity and facilitate insect feeding in a PPIase activity-dependent manner.
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Affiliation(s)
- Yumei Dong
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Jiangxuan Zhou
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Yuxia Yang
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Wangshan Lu
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Yan Jin
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Xingge Huang
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Wendan Zhang
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Jifen Li
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Gan Ai
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Zhiyuan Yin
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Maofeng Jing
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
| | - Ai Xia
- College of Plant Protection, Nanjing Agricultural University, 210000, Nanjing, China
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Genome-Wide Identification and Analysis of FKBP Gene Family in Wheat ( Triticum asetivum). Int J Mol Sci 2022; 23:ijms232314501. [PMID: 36498828 PMCID: PMC9739119 DOI: 10.3390/ijms232314501] [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: 10/17/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
FK506-binding protein (FKBP) genes have been found to play vital roles in plant development and abiotic stress responses. However, limited information is available about this gene family in wheat (Triticum aestivum L.). In this study, a total of 64 FKBP genes were identified in wheat via a genome-wide analysis involving a homologous search of the latest wheat genome data, which was unevenly distributed in 21 chromosomes, encoded 152 to 649 amino acids with molecular weights ranging from 16 kDa to 72 kDa, and was localized in the chloroplast, cytoplasm, nucleus, mitochondria, peroxisome and endoplasmic reticulum. Based on sequence alignment and phylogenetic analysis, 64 TaFKBPs were divided into four different groups or subfamilies, providing evidence of an evolutionary relationship with Aegilops tauschii, Brachypodium distachyon, Triticum dicoccoides, Arabidopsis thaliana and Oryza sativa. Hormone-related, abiotic stress-related and development-related cis-elements were preferentially presented in promoters of TaFKBPs. The expression levels of TaFKBP genes were investigated using transcriptome data from the WheatExp database, which exhibited tissue-specific expression patterns. Moreover, TaFKBPs responded to drought and heat stress, and nine of them were randomly selected for validation by qRT-PCR. Yeast cells expressing TaFKBP19-2B-2 or TaFKBP18-6B showed increased influence on drought stress, indicating their negative roles in drought tolerance. Collectively, our results provide valuable information about the FKBP gene family in wheat and contribute to further characterization of FKBPs during plant development and abiotic stress responses, especially in drought stress.
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Tyagi S, Jha SK, Kumar A, Saripalli G, Bhurta R, Hurali DT, Sathee L, Mallick N, Mir RR, Chinnusamy V. Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.). Front Genet 2022; 13:972474. [PMID: 36246582 PMCID: PMC9561851 DOI: 10.3389/fgene.2022.972474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cyclophilins (CYPs) are a group of highly conserved proteins involved in host-pathogen interactions in diverse plant species. However, the role of CYPs during disease resistance in wheat remains largely elusive. In the present study, the systematic genome-wide survey revealed a set of 81 TaCYP genes from three subfamilies (GI, GII, and GIII) distributed on all 21 wheat chromosomes. The gene structures of TaCYP members were found to be highly variable, with 1–14 exons/introns and 15 conserved motifs. A network of miRNA targets with TaCYPs demonstrated that TaCYPs were targeted by multiple miRNAs and vice versa. Expression profiling was done in leaf rust susceptible Chinese spring (CS) and the CS-Ae. Umbellulata derived resistant IL “Transfer (TR). Three homoeologous TaCYP genes (TaCYP24, TaCYP31, and TaCYP36) showed high expression and three homoeologous TaCYP genes (TaCYP44, TaCYP49, and TaCYP54) showed low expression in TR relative to Chinese Spring. Most of the other TaCYPs showed comparable expression changes (down- or upregulation) in both contrasting TR and CS. Expression of 16 TaCYPs showed significant association (p < 0.05) with superoxide radical and hydrogen peroxide abundance, suggesting the role of TaCYPs in downstream signaling processes during wheat-leaf rust interaction. The differentially expressing TaCYPs may be potential targets for future validation using transgenic (overexpression, RNAi or CRISPR-CAS) approaches and for the development of leaf rust-resistant wheat genotypes.
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Affiliation(s)
- Sandhya Tyagi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Shailendra Kumar Jha, ; Vinod,
| | - Anuj Kumar
- Centre for Agricultural Bioinformatics (CABin), Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Ramesh Bhurta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Deepak T. Hurali
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Niharika Mallick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Wadura Campus, Srinagar, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Sheng D, Qiao L, Zhang X, Li X, Chang L, Guo H, Zhang S, Chen F, Chang Z. Fine mapping of a recessive leaf rust resistance locus on chromosome 2BS in wheat accession CH1539. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:52. [PMID: 37313422 PMCID: PMC10248610 DOI: 10.1007/s11032-022-01318-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust (LR), caused by Puccinia triticina (Pt), is one of the most important fungal diseases of wheat worldwide. The wheat accession CH1539 showed a high level of resistance to leaf rust. A mapping population of 184 recombinant inbred lines (RILs) was developed from a cross between the resistant accession CH1539 and the susceptible cultivar SY95-71. The RILs showed segregating infection responses to Puccinia triticina Eriks. (Pt) race THK at the seedling stage. Genetic analysis showed that leaf rust resistance was controlled by a monogenic gene, and the potential locus was temporarily named LrCH1539. Bulked segregant analysis (BSA) using a 35 K DArTseq array located LrCH1539 on the short arm of chromosome 2B. Subsequently, a genetic linkage map of LrCH1539 was constructed using the developed 2BS chromosome-specific markers, and its flanking markers were sxau-2BS136 and sxau-2BS81. An F2 subpopulation with 3619 lines was constructed by crossing the resistant and susceptible lines selected from the RIL population. The inoculation identification results showed that LrCH1539 was recessively inherited and was fine-mapped to a 779.4-kb region between markers sxau-2BS47 and sxau-2BS255 at the end of 2BS. The linkage marker analysis showed that the positions of LrCH1539 and Lr16 were the same, but the identification results of the resistance spectrum indicated that the causal genes of the two might be different. The resistant materials reported in this study and the cosegregation marker can be used for marker-assisted selection breeding of leaf rust-resistant wheat cultivars. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01318-4.
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Affiliation(s)
- Dece Sheng
- College of Life Science, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Linyi Qiao
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Xin Li
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Lifang Chang
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Huijuan Guo
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Shuwei Zhang
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Fang Chen
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Zhijian Chang
- College of Agronomy, Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
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Offor BC, Mhlongo MI, Dubery IA, Piater LA. Plasma Membrane-Associated Proteins Identified in Arabidopsis Wild Type, lbr2-2 and bak1-4 Mutants Treated with LPSs from Pseudomonas syringae and Xanthomonas campestris. MEMBRANES 2022; 12:membranes12060606. [PMID: 35736313 PMCID: PMC9230897 DOI: 10.3390/membranes12060606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023]
Abstract
Plants recognise bacterial microbe-associated molecular patterns (MAMPs) from the environment via plasma membrane (PM)-localised pattern recognition receptor(s) (PRRs). Lipopolysaccharides (LPSs) are known as MAMPs from gram-negative bacteria that are most likely recognised by PRRs and trigger defence responses in plants. The Arabidopsis PRR(s) and/or co-receptor(s) complex for LPS and the associated defence signalling remains elusive. As such, proteomic identification of LPS receptors and/or co-receptor complexes will help to elucidate the molecular mechanisms that underly LPS perception and defence signalling in plants. The Arabidopsis LPS-binding protein (LBP) and bactericidal/permeability-increasing protein (BPI)-related-2 (LBR2) have been shown to recognise LPS and trigger defence responses while brassinosteroid insensitive 1 (BRI1)-associated receptor kinase 1 (BAK1) acts as a co-receptor for several PRRs. In this study, Arabidopsis wild type (WT) and T-DNA knock out mutants (lbr2-2 and bak1-4) were treated with LPS chemotypes from Pseudomonas syringae pv. tomato DC3000 (Pst) and Xanthomonas campestris pv. campestris 8004 (Xcc) over a 24 h period. The PM-associated protein fractions were separated by liquid chromatography and analysed by tandem mass spectrometry (LC-MS/MS) followed by data analysis using ByonicTM software. Using Gene Ontology (GO) for molecular function and biological processes, significant LPS-responsive proteins were grouped according to defence and stress response, perception and signalling, membrane transport and trafficking, metabolic processes and others. Venn diagrams demarcated the MAMP-responsive proteins that were common and distinct to the WT and mutant lines following treatment with the two LPS chemotypes, suggesting contributions from differential LPS sub-structural moieties and involvement of LBR2 and BAK1 in the LPS-induced MAMP-triggered immunity (MTI). Moreover, the identification of RLKs and RLPs that participate in other bacterial and fungal MAMP signalling proposes the involvement of more than one receptor and/or co-receptor for LPS perception as well as signalling in Arabidopsis defence responses.
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Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis. Curr Biol 2022; 32:2719-2729.e5. [DOI: 10.1016/j.cub.2022.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/14/2022] [Accepted: 05/06/2022] [Indexed: 01/04/2023]
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Yang YN, Kim Y, Kim H, Kim SJ, Cho KM, Kim Y, Lee DS, Lee MH, Kim SY, Hong JC, Kwon SJ, Choi J, Park OK. The transcription factor ORA59 exhibits dual DNA binding specificity that differentially regulates ethylene- and jasmonic acid-induced genes in plant immunity. PLANT PHYSIOLOGY 2021; 187:2763-2784. [PMID: 34890461 PMCID: PMC8644270 DOI: 10.1093/plphys/kiab437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens in a synergistic and interdependent manner, while JA and ET also have independent roles in certain processes, e.g. in responses to wounding and flooding, respectively. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, of which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) GDSL LIPASE 1 (GLIP1) depends on ET for gene expression and pathogen resistance. Here, promoter analysis of GLIP1 revealed ERELEE4 as the critical cis-element for ET-responsive GLIP1 expression. In a yeast one-hybrid screening, ORA59 was isolated as a specific transcription factor that binds to the ERELEE4 element, in addition to the well-characterized GCC box. We found that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in gene promoters. Notably, ORA59 exhibited a differential preference for GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. JA and ET induced ORA59 phosphorylation, which was required for both activity and specificity of ORA59. Furthermore, RNA-seq and virus-induced gene silencing analyses led to the identification of ORA59 target genes of distinct functional categories in JA and ET pathways. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.
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Affiliation(s)
- Young Nam Yang
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Youngsung Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyeri Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Su Jin Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Kwang-Moon Cho
- Molecular Diagnosis Division, AccuGene, Incheon 22006, Korea
| | - Yerin Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Dong Sook Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Myoung-Hoon Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Soo Young Kim
- Department of Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Jong Chan Hong
- Division of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Sun Jae Kwon
- Molecular Diagnosis Division, AccuGene, Incheon 22006, Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Ohkmae K Park
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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11
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Genetic and Proteomic Basis of Sclerotinia Stem Rot Resistance in Indian Mustard [ Brassica juncea (L.) Czern & Coss.]. Genes (Basel) 2021; 12:genes12111784. [PMID: 34828391 PMCID: PMC8621386 DOI: 10.3390/genes12111784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Sclerotinia stem rot is one of the utmost important disease of mustard, causing considerable losses in seed yield and oil quality. The study of the genetic and proteomic basis of resistance to this disease is imperative for its effective utilization in developing resistant cultivars. Therefore, the genetic pattern of Sclerotinia stem rot resistance in Indian mustard was studied using six generations (P1, P2, F1, F2, BC1P1, and BC1P2) developed from the crossing of one resistant (RH 1222-28) and two susceptible (EC 766300 and EC 766123) genotypes. Genetic analysis revealed that resistance was governed by duplicate epistasis. Comparative proteome analysis of resistant and susceptible genotypes indicated that peptidyl-prolyl cis-trans isomerase (A0A078IDN6 PPIase) showed high expression in resistant genotype at the early infection stage while its expression was delayed in susceptible genotypes. This study provides important insight to mustard breeders for designing effective breeding programs to develop resistant cultivars against this devastating disease.
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12
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Cyclophilins and Their Functions in Abiotic Stress and Plant-Microbe Interactions. Biomolecules 2021; 11:biom11091390. [PMID: 34572603 PMCID: PMC8464771 DOI: 10.3390/biom11091390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 01/12/2023] Open
Abstract
Plants have developed a variety of mechanisms and regulatory pathways to change their gene expression profiles in response to abiotic stress conditions and plant–microbe interactions. The plant–microbe interaction can be pathogenic or beneficial. Stress conditions, both abiotic and pathogenic, negatively affect the growth, development, yield and quality of plants, which is very important for crops. In contrast, the plant–microbe interaction could be growth-promoting. One of the proteins involved in plant response to stress conditions and plant–microbe interactions is cyclophilin. Cyclophilins (CyPs), together with FK506-binding proteins (FKBPs) and parvulins, belong to a big family of proteins with peptidyl-prolyl cis-trans isomerase activity (Enzyme Commission (EC) number 5.2.1.8). Genes coding for proteins with the CyP domain are widely expressed in all organisms examined, including bacteria, fungi, animals, and plants. Their different forms can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, mitochondrion and in the phloem space. They are involved in numerous processes, such as protein folding, cellular signaling, mRNA processing, protein degradation and apoptosis. In the past few years, many new functions, and molecular mechanisms for cyclophilins have been discovered. In this review, we aim to summarize recent advances in cyclophilin research to improve our understanding of their biological functions in plant defense and symbiotic plant–microbe interactions.
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13
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Liu H, Shen J, Yuan C, Lu D, Acharya BR, Wang M, Chen D, Zhang W. The Cyclophilin ROC3 Regulates ABA-Induced Stomatal Closure and the Drought Stress Response of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:668792. [PMID: 34113366 PMCID: PMC8186832 DOI: 10.3389/fpls.2021.668792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/28/2021] [Indexed: 05/28/2023]
Abstract
Drought causes a major constraint on plant growth, development, and crop productivity. Drought stress enhances the synthesis and mobilization of the phytohormone abscisic acid (ABA). Enhanced cellular levels of ABA promote the production of reactive oxygen species (ROS), which in turn induce anion channel activity in guard cells that consequently leads to stomatal closure. Although Cyclophilins (CYPs) are known to participate in the biotic stress response, their involvement in guard cell ABA signaling and the drought response remains to be established. The Arabidopsis thaliana gene ROC3 encodes a CYP. Arabidopsis roc3 T-DNA mutants showed a reduced level of ABA-activated S-type anion currents, and stomatal closure than wild type (WT). Also, roc3 mutants exhibited rapid loss of water in leaf than wild type. Two complementation lines of roc3 mutants showed similar stomatal response to ABA as observed for WT. Both complementation lines also showed similar water loss as WT by leaf detached assay. Biochemical assay suggested that ROC3 positively regulates ROS accumulation by inhibiting catalase activity. In response to ABA treatment or drought stress, roc3 mutant show down regulation of a number of stress responsive genes. All findings indicate that ROC3 positively regulates ABA-induced stomatal closure and the drought response by regulating ROS homeostasis and the expression of various stress-activated genes.
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Affiliation(s)
- Huiping Liu
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Jianlin Shen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Chao Yuan
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Dongxue Lu
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Biswa R. Acharya
- College of Natural and Agricultural Sciences, University of California, Riverside, Riverside, CA, United States
| | - Mei Wang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Donghua Chen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Wei Zhang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
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14
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Pérez-Torres CA, Ibarra-Laclette E, Hernández-Domínguez EE, Rodríguez-Haas B, Pérez-Lira AJ, Villafán E, Alonso-Sánchez A, García-Ávila CDJ, Ramírez-Pool JA, Sánchez-Rangel D. Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq. PeerJ 2021; 9:e11215. [PMID: 33954045 PMCID: PMC8052963 DOI: 10.7717/peerj.11215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/15/2021] [Indexed: 01/13/2023] Open
Abstract
Fusarium kuroshium is a novel member of the Ambrosia Fusarium Clade (AFC) that has been recognized as one of the symbionts of the invasive Kuroshio shot hole borer, an Asian ambrosia beetle. This complex is considered the causal agent of Fusarium dieback, a disease that has severely threatened natural forests, landscape trees, and avocado orchards in the last 8 years. Despite the interest in this species, the molecular responses of both the host and F. kuroshium during the infection process and disease establishment remain unknown. In this work, we established an in vitro pathosystem using Hass avocado stems inoculated with F. kuroshium to investigate differential gene expression at 1, 4, 7 and 14 days post-inoculation. RNA-seq technology allowed us to obtain data from both the plant and the fungus, and the sequences obtained from both organisms were analyzed independently. The pathosystem established was able to mimic Fusarium dieback symptoms, such as carbohydrate exudation, necrosis, and vascular tissue discoloration. The results provide interesting evidence regarding the genes that may play roles in the avocado defense response to Fusarium dieback disease. The avocado data set comprised a coding sequence collection of 51,379 UniGenes, from which 2,403 (4.67%) were identified as differentially expressed. The global expression analysis showed that F. kuroshium responsive UniGenes can be clustered into six groups according to their expression profiles. The biologically relevant functional categories that were identified included photosynthesis as well as responses to stress, hormones, abscisic acid, and water deprivation. Additionally, processes such as oxidation-reduction, organization and biogenesis of the cell wall and polysaccharide metabolism were detected. Moreover, we identified orthologues of nucleotide-binding leucine-rich receptors, and their possible action mode was analyzed. In F. kuroshium, we identified 57 differentially expressed genes. Interestingly, the alcohol metabolic process biological category had the highest number of upregulated genes, and the enzyme group in this category may play an important role in the mechanisms of secondary metabolite detoxification. Hydrolytic enzymes, such as endoglucanases and a pectate lyase, were also identified, as well as some proteases. In conclusion, our research was conducted mainly to explain how the vascular tissue of a recognized host of the ambrosia complex responds during F. kuroshium infection since Fusarium dieback is an ambrosia beetle-vectored disease and many variables facilitate its establishment.
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Affiliation(s)
- Claudia-Anahí Pérez-Torres
- Catedrático CONACyT en la Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | | | | | | | - Alan-Josué Pérez-Lira
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | | | - Clemente de Jesús García-Ávila
- Centro Nacional de Referencia Fitosanitaria, Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Tecámac, Estado de México, México
| | - José-Abrahán Ramírez-Pool
- Centro Nacional de Referencia Fitosanitaria, Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Tecámac, Estado de México, México.,Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Diana Sánchez-Rangel
- Catedrático CONACyT en la Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
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15
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Singh H, Kaur K, Singh M, Kaur G, Singh P. Plant Cyclophilins: Multifaceted Proteins With Versatile Roles. FRONTIERS IN PLANT SCIENCE 2020; 11:585212. [PMID: 33193535 PMCID: PMC7641896 DOI: 10.3389/fpls.2020.585212] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 05/03/2023]
Abstract
Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.
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Affiliation(s)
- Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- William Harvey Heart Centre, Queen Mary University of London, London, United Kingdom
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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16
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Wang J, Sun W, Kong X, Zhao C, Li J, Chen Y, Gao Z, Zuo K. The peptidyl-prolyl isomerases FKBP15-1 and FKBP15-2 negatively affect lateral root development by repressing the vacuolar invertase VIN2 in Arabidopsis. PLANTA 2020; 252:52. [PMID: 32945964 DOI: 10.1007/s00425-020-03459-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
The peptidyl-prolyl isomerases FKBP15-1 and FKBP15-2 negatively modulate lateral root development by repressing vacuolar invertase VIN2 activity. Lateral root (LR) architecture greatly affects the efficiency of nutrient absorption and the anchorage of plants. Although the internal phytohormone regulatory mechanisms that control LR development are well known, how external nutrients influence lateral root development remains elusive. Here, we characterized the function of two FK506-binding proteins, namely, FKBP15-1 and FKBP15-2, in Arabidopsis. FKBP15-1/15-2 genes were expressed prominently in the vascular bundles of the root basal meristem region, and the FKBP15-1/15-2 proteins were localized to the endoplasmic reticulum of the cells. Using IP-MS, Co-IP, and BiFC assays, we demonstrated that FKBP15-1 and FKBP15-2 interacted with vacuolar invertase 2 (VIN2). Compared to Col-0 and the single mutants, the fkbp15-1fkbp15-2 double mutant had more LRs, and presented higher sucrose catalytic activity. Moreover, genetic analysis showed genetic epistasis of VIN2 over FKBP15-1/FKBP15-2 in controlling LR development. Our results indicate that FKBP15-1 and FKBP15-2 participate in the control of LR number by inhibiting the catalytic activity of VIN2. Owing to the conserved peptidylprolyl cis-trans isomerase activity of FKBP family proteins, our results provide a clue for further analysis of the interplay between lateral root development and protein modification by FKBPs.
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Affiliation(s)
- Jun Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenjie Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiuzhen Kong
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunyan Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianfu Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yun Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Gao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaijing Zuo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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17
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Prator CA, Chooi KM, Jones D, Davy MW, MacDiarmid RM, Almeida RPP. Comparison of two different host plant genera responding to grapevine leafroll-associated virus 3 infection. Sci Rep 2020; 10:8505. [PMID: 32444786 PMCID: PMC7244584 DOI: 10.1038/s41598-020-64972-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/17/2020] [Indexed: 11/08/2022] Open
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses of grapevine but, despite this, there remain several gaps in our understanding of its biology. Because of its narrow host range - limited to Vitis species - and because the virus is restricted to the phloem, most GLRaV-3 research has concentrated on epidemiology and the development of detection assays. The recent discovery that GLRaV-3 can infect Nicotiana benthamiana, a plant model organism, makes new opportunities available for research in this field. We used RNA-seq to compare both V. vinifera and P1/HC-Pro N. benthamiana host responses to GLRaV-3 infection. Our analysis revealed that the majority of DEGs observed between the two hosts were unique although responses between the two hosts also showed several shared gene expression results. When comparing gene expression patterns that were shared between the two hosts, we observed the downregulation of genes associated with stress chaperones, and the induction of gene families involved in primary plant physiological processes. This is the first analysis of gene expression profiles beyond Vitis to mealybug-transmitted GLRaV-3 and demonstrates that N. benthamiana could serve as a useful tool for future studies of GLRaV-3-host interactions.
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Affiliation(s)
- Cecilia A Prator
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Dan Jones
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Marcus W Davy
- The New Zealand Institute for Plant and Food Research Limited, Te Puke, New Zealand
| | - Robin M MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA.
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18
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O'Rourke JA, McCabe CE, Graham MA. Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean. Funct Integr Genomics 2020; 20:321-341. [PMID: 31655948 PMCID: PMC7152590 DOI: 10.1007/s10142-019-00709-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Abstract
Preserving crop yield is critical for US soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by model species such as Arabidopsis. This selection likely resulted in novel stress adaptations, unique to crop species. Given that iron deficiency is a perennial problem in the soybean growing regions of the USA and phosphate deficiency looms as a limitation to global agricultural production, nutrient stress studies in crop species are critically important. In this study, we directly compared whole-genome expression responses of leaves and roots to iron (Fe) and phosphate (Pi) deficiency, representing a micronutrient and macronutrient, respectively. Conducting experiments side by side, we observed soybean responds to both nutrient deficiencies within 24 h. While soybean responds largely to -Fe deficiency, it responds strongly to Pi resupply. Though the timing of the responses was different, both nutrient stress signals used the same molecular pathways. Our study is the first to demonstrate the speed and diversity of the soybean stress response to multiple nutrient deficiencies. We also designed the study to examine gene expression changes in response to multiple stress events. We identified 865 and 3375 genes that either altered their direction of expression after a second stress exposure or were only differentially expressed after a second stress event. Understanding the molecular underpinnings of these responses in crop species could have major implications for improving stress tolerance and preserving yield.
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Affiliation(s)
- Jamie A O'Rourke
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA.
- Department of Agronomy, Iowa State University, 1567 Agronomy Hall, Ames, IA, 50011, USA.
| | - Chantal E McCabe
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
| | - Michelle A Graham
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, 1567 Agronomy Hall, Ames, IA, 50011, USA
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19
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Singh R, Liyanage R, Gupta C, Lay JO, Pereira A, Rojas CM. The Arabidopsis Proteins AtNHR2A and AtNHR2B Are Multi-Functional Proteins Integrating Plant Immunity With Other Biological Processes. FRONTIERS IN PLANT SCIENCE 2020; 11:232. [PMID: 32194606 PMCID: PMC7064621 DOI: 10.3389/fpls.2020.00232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
AtNHR2A (Arabidopsis thaliana nonhost resistance 2A) and AtNHR2B (Arabidopsis thaliana nonhost resistance 2B) are two proteins that participate in nonhost resistance, a broad-spectrum mechanism of plant immunity that protects plants against the majority of potential pathogens. AtNHR2A and AtNHR2B are localized to the cytoplasm, chloroplasts, and other subcellular compartments of unknown identity. The multiple localizations of AtNHR2A and AtNHR2B suggest that these two proteins are highly dynamic and versatile, likely participating in multiple biological processes. In spite of their importance, the specific functions of AtNHR2A and AtNHR2B have not been elucidated. Thus, to aid in the functional characterization of these two proteins and identify the biological processes in which these proteins operate, we used immunoprecipitation coupled with mass spectrometry (IP-MS) to identify proteins interacting with AtNHR2A and AtNHR2B and to generate their interactome network. Further validation of three of the identified proteins provided new insights into specific pathways and processes related to plant immunity where AtNHR2A and AtNHR2B participate. Moreover, the comprehensive analysis of the AtNHR2A- and AtNHR2B-interacting proteins using published empirical information revealed that the functions of AtNHR2A and AtNHR2B are not limited to plant immunity but encompass other biological processes.
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Affiliation(s)
- Raksha Singh
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, United States
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Purdue University, West Lafayette, IN, United States
| | - Rohana Liyanage
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chirag Gupta
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Jackson O. Lay
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Clemencia M. Rojas
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, United States
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20
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Ge Q, Zhang Y, Xu Y, Bai M, Luo W, Wang B, Niu Y, Zhao Y, Li S, Weng Y, Wang Z, Qian Q, Chong K. Cyclophilin OsCYP20-2 with a novel variant integrates defense and cell elongation for chilling response in rice. THE NEW PHYTOLOGIST 2020; 225:2453-2467. [PMID: 31736073 PMCID: PMC7064896 DOI: 10.1111/nph.16324] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/31/2019] [Indexed: 05/20/2023]
Abstract
Coordinating stress defense and plant growth is a survival strategy for adaptation to different environments that contains a series of processes, such as, cell growth, division and differentiation. However, little is known about the coordination mechanism for protein conformation change. A cyclophilin OsCYP20-2 with a variant interacts with SLENDER RICE1 (SLR1) and OsFSD2 in the nucleus and chloroplasts, respectively, to integrate chilling tolerance and cell elongation in rice (Oryza sativa) (FSD2, Fe-superoxide dismutase 2). Mass spectrum assay showed that OsNuCYP20-2 localized at the nucleus (nuclear located OsCYP20-2) was a new variant of OsCYP20-2 that truncated 71 amino-acid residues in N-terminal. The loss-of function OsCYP20-2 mutant showed sensitivity to chilling stress with accumulation of extra reactive oxygen species (ROS). In chloroplasts, the full-length OsCYP20-2 promotes OsFSD2 forming homodimers which enhance its activity, eliminating the accumulation of ROS under chilling stress. However, the mutant had shorter epidermal cells in comparison with wild-type Hwayoung (HY). In the nucleus, OsCYP20-2 caused conformation change of SLR1 to promote its degradation for cell elongation. Our data reveal a cyclophilin with a variant with dual-localization in chloroplasts and the nucleus, which mediate chilling tolerance and cell elongation.
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Affiliation(s)
- Qiang Ge
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- Innovation Academy for Seed DesignChinese Academy of SciencesBeijing100101China
| | - Mingyi Bai
- The Key Laboratory of Plant Cell Engineering and Germplasm InnovationMinistry of EducationSchool of Life SciencesShandong UniversityJinan250100China
| | - Wei Luo
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Bo Wang
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yuda Niu
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Yuan Zhao
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
| | - Shanshan Li
- Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Yuxiang Weng
- Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Zhiyong Wang
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCA94305USA
| | - Qian Qian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Kang Chong
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
- Innovation Academy for Seed DesignChinese Academy of SciencesBeijing100101China
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21
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Tarazona A, Forment J, Elena SF. Identifying Early Warning Signals for the Sudden Transition from Mild to Severe Tobacco Etch Disease by Dynamical Network Biomarkers. Viruses 2019; 12:E16. [PMID: 31861938 PMCID: PMC7019593 DOI: 10.3390/v12010016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022] Open
Abstract
Complex systems exhibit critical thresholds at which they transition among alternative phases. Complex systems theory has been applied to analyze disease progression, distinguishing three stages along progression: (i) a normal noninfected state; (ii) a predisease state, in which the host is infected and responds and therapeutic interventions could still be effective; and (iii) an irreversible state, where the system is seriously threatened. The dynamical network biomarker (DNB) theory sought for early warnings of the transition from health to disease. Such DNBs might range from individual genes to complex structures in transcriptional regulatory or protein-protein interaction networks. Here, we revisit transcriptomic data obtained during infection of tobacco plants with tobacco etch potyvirus to identify DNBs signaling the transition from mild/reversible to severe/irreversible disease. We identified genes showing a sudden transition in expression along disease categories. Some of these genes cluster in modules that show the properties of DNBs. These modules contain both genes known to be involved in response to pathogens (e.g., ADH2, CYP19, ERF1, KAB1, LAP1, MBF1C, MYB58, PR1, or TPS5) and other genes not previously related to biotic stress responses (e.g., ABCI6, BBX21, NAP1, OSM34, or ZPN1).
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Affiliation(s)
- Adrián Tarazona
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna, 46980 València, Spain;
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, 46022 València, Spain;
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna, 46980 València, Spain;
- The Santa Fe Institute, Santa Fe, NM 87501, USA
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22
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Donato M, Geisler M. HSP
90 and co‐chaperones: a multitaskers’ view on plant hormone biology. FEBS Lett 2019; 593:1415-1430. [DOI: 10.1002/1873-3468.13499] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Martin Donato
- Department of Biology University of Fribourg Switzerland
| | - Markus Geisler
- Department of Biology University of Fribourg Switzerland
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23
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Enzyme activity and structural features of three single-domain phloem cyclophilins from Brassica napus. Sci Rep 2019; 9:9368. [PMID: 31249367 PMCID: PMC6597583 DOI: 10.1038/s41598-019-45856-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 06/14/2019] [Indexed: 01/05/2023] Open
Abstract
Cyclophilins (CYPs) are a group of ubiquitous prolyl cis/trans isomerases (PPIases). It was shown that plants possess the most diverse CYP families and that these are abundant in the phloem long-distance translocation stream. Since phloem exudate showed PPIase activity, three single-domain CYPs that occur in phloem samples from Brassica napus were characterised on functional and structural levels. It could be shown that they exhibit isomerase activity and that this activity is controlled by a redox regulation mechanism, which has been postulated for divergent CYPs. The structure determination by small-angle X-ray scattering experiments revealed a conserved globular shape. In addition, the high-resolution crystal structure of BnCYP19-1 was resolved and refined to 2.0 Å resolution, and the active sites of related CYPs as well as substrate binding were modelled. The obtained data and results support the hypothesis that single domain phloem CYPs are active phloem PPIases that may function as chaperones.
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24
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Yang J, Wang G, Ke H, Zhang Y, Ji L, Huang L, Zhang C, Wang X, Ma Z. Genome-wide identification of cyclophilin genes in Gossypium hirsutum and functional characterization of a CYP with antifungal activity against Verticillium dahliae. BMC PLANT BIOLOGY 2019; 19:272. [PMID: 31226952 PMCID: PMC6588949 DOI: 10.1186/s12870-019-1848-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/24/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cyclophilins (CYPs), belonging to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily, play important roles during plant responses to biotic and abiotic stresses. RESULTS Here, a total of 79 CYPs were identified in the genome of Gossypium hirsutum. Of which, 65 GhCYPs only contained one cyclophilin type PPIase domain, others 14 GhCYPs contain additional domains. A number of cis-acting elements related to phytohormone signaling were predicated in the upstream of GhCYPs ORF. The expression analysis revealed that GhCYPs were induced in response to cold, hot, salt, PEG and Verticillium dahliae infection. In addition, the functional importance of GhCYP-3 in Verticillium wilt resistance was also presented in this study. GhCYP-3 showed both cytoplasmic and nuclear localization. Overexpression of GhCYP-3 in Arabidopsis significantly improved Verticillium wilt resistance of the plants. Recombinant GhCYP-3 displayed PPIase activity and evident inhibitory effects on V. dahliae in vitro. Moreover, the extracts from GhCYP-3 transgenic Arabidopsis displayed significantly inhibit activity to conidia germinating and hyphal growth of V. dahliae. CONCLUSIONS Our study identified the family members of cotton CYP genes using bioinformatics tools. Differential expression patterns of GhCYPs under various abiotic stress and V. dahliae infection conditions provide a comprehensive understanding of the biological functions of candidate genes. Moreover, GhCYP-3 involved in the resistance of cotton to V. dahliae infection presumably through antifungal activity.
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Affiliation(s)
- Jun Yang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Guoning Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Huifeng Ke
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Yan Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Lianlian Ji
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Lizhi Huang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Chunying Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Xingfen Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
| | - Zhiying Ma
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001 China
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25
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Pogorelko GV, Juvale PS, Rutter WB, Hütten M, Maier TR, Hewezi T, Paulus J, van der Hoorn RA, Grundler FM, Siddique S, Lionetti V, Zabotina OA, Baum TJ. Re-targeting of a plant defense protease by a cyst nematode effector. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:1000-1014. [PMID: 30801789 DOI: 10.1111/tpj.14295] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 02/08/2019] [Accepted: 02/15/2019] [Indexed: 05/29/2023]
Abstract
Plants mount defense responses during pathogen attacks, and robust host defense suppression by pathogen effector proteins is essential for infection success. 4E02 is an effector of the sugar beet cyst nematode Heterodera schachtii. Arabidopsis thaliana lines expressing the effector-coding sequence showed altered expression levels of defense response genes, as well as higher susceptibility to both the biotroph H. schachtii and the necrotroph Botrytis cinerea, indicating a potential suppression of defenses by 4E02. Yeast two-hybrid analyses showed that 4E02 targets A. thaliana vacuolar papain-like cysteine protease (PLCP) 'Responsive to Dehydration 21A' (RD21A), which has been shown to function in the plant defense response. Activity-based protein profiling analyses documented that the in planta presence of 4E02 does not impede enzymatic activity of RD21A. Instead, 4E02 mediates a re-localization of this protease from the vacuole to the nucleus and cytoplasm, which is likely to prevent the protease from performing its defense function and at the same time, brings it in contact with novel substrates. Yeast two-hybrid analyses showed that RD21A interacts with multiple host proteins including enzymes involved in defense responses as well as carbohydrate metabolism. In support of a role in carbohydrate metabolism of RD21A after its effector-mediated re-localization, we observed cell wall compositional changes in 4E02 expressing A. thaliana lines. Collectively, our study shows that 4E02 removes RD21A from its defense-inducing pathway and repurposes this enzyme by targeting the active protease to different cell compartments.
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Affiliation(s)
- Gennady V Pogorelko
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - William B Rutter
- USDA-ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Marion Hütten
- Rheinische Friedrich-Wilhelms-University Bonn, INRES - Molecular Phytomedicine, Bonn, Germany
| | - Thomas R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Judith Paulus
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Florian Mw Grundler
- Rheinische Friedrich-Wilhelms-University Bonn, INRES - Molecular Phytomedicine, Bonn, Germany
| | - Shahid Siddique
- Rheinische Friedrich-Wilhelms-University Bonn, INRES - Molecular Phytomedicine, Bonn, Germany
| | - Vincenzo Lionetti
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185, Rome, Italy
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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26
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Barbosa Dos Santos I, Park SW. Versatility of Cyclophilins in Plant Growth and Survival: A Case Study in Arabidopsis. Biomolecules 2019; 9:biom9010020. [PMID: 30634678 PMCID: PMC6358970 DOI: 10.3390/biom9010020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/22/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Cyclophilins (CYPs) belong to a peptidyl-prolyl cis-trans isomerase family, and were first characterized in mammals as a target of an immunosuppressive drug, cyclosporin A, preventing proinflammatory cytokine production. In Arabidopsis, 29 CYPs and CYP-like proteins are found across all subcellular compartments, involved in various physiological processes including transcriptional regulation, organogenesis, photosynthetic and hormone signaling pathways, stress adaptation and defense responses. These important but diverse activities of CYPs must be reflected by their versatility as cellular and molecular modulators. However, our current knowledge regarding their mode of actions is still far from complete. This review will briefly revisit recent progresses on the roles and mechanisms of CYPs in Arabidopsis studies, and information gaps within, which help understanding the phenotypic and environmental plasticity of plants.
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Affiliation(s)
| | - Sang-Wook Park
- Department of Entomology and Plant Pathology Auburn University, Auburn, AL 36849, USA.
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27
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Fan G, Yang Y, Li T, Lu W, Du Y, Qiang X, Wen Q, Shan W. A Phytophthora capsici RXLR Effector Targets and Inhibits a Plant PPIase to Suppress Endoplasmic Reticulum-Mediated Immunity. MOLECULAR PLANT 2018; 11:1067-1083. [PMID: 29864524 DOI: 10.1016/j.molp.2018.05.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 05/25/2018] [Accepted: 05/27/2018] [Indexed: 05/20/2023]
Abstract
Phytophthora pathogens secrete a large arsenal of effectors that manipulate host processes to create an environment conducive to pathogen colonization. However, the underlying mechanisms by which Phytophthora effectors manipulate host plant cells still remain largely unclear. In this study, we report that PcAvr3a12, a Phytophthora capsici RXLR effector and a member of the Avr3a effector family, suppresses plant immunity by targeting and inhibiting host plant peptidyl-prolyl cis-trans isomerase (PPIase). Overexpression of PcAvr3a12 in Arabidopsis thaliana enhanced plant susceptibility to P. capsici. FKBP15-2, an endoplasmic reticulum (ER)-localized protein, was identified as a host target of PcAvr3a12 during early P. capsici infection. Analyses of A. thaliana T-DNA insertion mutant (fkbp15-2), RNAi, and overexpression lines consistently showed that FKBP15-2 positively regulates plant immunity in response to Phytophthora infection. FKBP15-2 possesses PPIase activity essential for its contribution to immunity but is directly suppressed by PcAvr3a12. Interestingly, we found that FKBP15-2 is involved in ER stress sensing and is required for ER stress-mediated plant immunity. Taken together, these results suggest that P. capsici deploys an RXLR effector, PcAvr3a12, to facilitate infection by targeting and suppressing a novel ER-localized PPIase, FKBP15-2, which is required for ER stress-mediated plant immunity.
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Affiliation(s)
- Guangjin Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tingting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenqin Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoyu Qiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qujiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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28
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Search for Partner Proteins of A. thaliana Immunophilins Involved in the Control of Plant Immunity. Molecules 2018; 23:molecules23040953. [PMID: 29671793 PMCID: PMC6017422 DOI: 10.3390/molecules23040953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 12/04/2022] Open
Abstract
The involvement of plant immunophilins in multiple essential processes such as development, various ways of adapting to biotic and abiotic stresses, and photosynthesis has already been established. Previously, research has demonstrated the involvement of three immunophilin genes (AtCYP19-1/ROC3, AtFKBP65/ROF2, and AtCYP57) in the control of plant response to invasion by various pathogens. Current research attempts to identify host target proteins for each of the selected immunophilins. As a result, candidate interactors have been determined and confirmed using a yeast 2-hybrid (Y2H) system for protein–protein interaction assays. The generation of mutant isoforms of ROC3 and AtCYP57 harboring substituted amino acids in the in silico-predicted active sites became essential to achieving significant binding to its target partners. This data shows that ROF2 targets calcium-dependent lipid-binding domain-containing protein (At1g70790; AT1) and putative protein phosphatase (At2g30020; АТ2), whereas ROC3 interacts with GTP-binding protein (At1g30580; ENGD-1) and RmlC-like cupin (At5g39120). The immunophilin AtCYP57 binds to putative pyruvate decarboxylase-1 (Pdc1) and clathrin adaptor complex-related protein (At5g05010). Identified interactors confirm our previous findings that immunophilins ROC3, ROF2, and AtCYP57 are directly involved with stress response control. Further, these findings extend our understanding of the molecular functional pathways of these immunophilins.
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29
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Takáč T, Šamajová O, Pechan T, Luptovčiak I, Šamaj J. Feedback Microtubule Control and Microtubule-Actin Cross-talk in Arabidopsis Revealed by Integrative Proteomic and Cell Biology Analysis of KATANIN 1 Mutants. Mol Cell Proteomics 2017; 16:1591-1609. [PMID: 28706004 DOI: 10.1074/mcp.m117.068015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/06/2017] [Indexed: 12/20/2022] Open
Abstract
Microtubule organization and dynamics are critical for key developmental processes such as cell division, elongation, and morphogenesis. Microtubule severing is an essential regulator of microtubules and is exclusively executed by KATANIN 1 in Arabidopsis In this study, we comparatively studied the proteome-wide effects in two KATANIN 1 mutants. Thus, shotgun proteomic analysis of roots and aerial parts of single nucleotide mutant fra2 and T-DNA insertion mutant ktn1-2 was carried out. We have detected 42 proteins differentially abundant in both fra2 and ktn1-2 KATANIN 1 dysfunction altered the abundance of proteins involved in development, metabolism, and stress responses. The differential regulation of tubulins and microtubule-destabilizing protein MDP25 implied a feedback microtubule control in KATANIN 1 mutants. Furthermore, deregulation of profilin 1, actin-depolymerizing factor 3, and actin 7 was observed. These findings were confirmed by immunoblotting analysis of actin and by microscopic observation of actin filaments using fluorescently labeled phalloidin. Results obtained by quantitative RT-PCR analysis revealed that changed protein abundances were not a consequence of altered expression levels of corresponding genes in the mutants. In conclusion, we show that abundances of several cytoskeletal proteins as well as organization of microtubules and the actin cytoskeleton are amended in accordance with defective microtubule severing.
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Affiliation(s)
- Tomáš Takáč
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Tibor Pechan
- §Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Starkville, Mississippi 39759
| | - Ivan Luptovčiak
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic;
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30
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Hanhart P, Thieß M, Amari K, Bajdzienko K, Giavalisco P, Heinlein M, Kehr J. Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. Sci Rep 2017; 7:1514. [PMID: 28473712 PMCID: PMC5431436 DOI: 10.1038/s41598-017-01596-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse important roles, e.g. in protein degradation, mRNA processing, development, and stress responses. We performed a genome-wide database survey and identified a total of 94 CYP genes encoding 91 distinct proteins. Sequence alignment analysis of the putative BnCYP cyclophilin-like domains revealed highly conserved motifs. By using RNA-Seq, we could verify the presence of 77 BnCYP genes under control conditions. To identify phloem-specific BnCYP proteins in a complementary approach, we used LC-MS/MS to determine protein abundances in leaf and phloem extracts. We detected 26 BnCYPs in total with 12 being unique to phloem sap. Our analysis provides the basis for future studies concentrating on the functional characterization of individual members of this gene family in a plant of dual importance: as a crop and a model system for polyploidization and long-distance signalling.
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Affiliation(s)
- Patrizia Hanhart
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Melanie Thieß
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Khalid Amari
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Krzysztof Bajdzienko
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Manfred Heinlein
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Julia Kehr
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany.
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31
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Quantitative Proteomics Reveals the Defense Response of Wheat against Puccinia striiformis f. sp. tritici. Sci Rep 2016; 6:34261. [PMID: 27678307 PMCID: PMC5039691 DOI: 10.1038/srep34261] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 09/12/2016] [Indexed: 01/09/2023] Open
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is considered one of the most aggressive diseases to wheat production. In this study, we used an iTRAQ-based approach for the quantitative proteomic comparison of the incompatible Pst race CYR23 in infected and non-infected leaves of the wheat cultivar Suwon11. A total of 3,475 unique proteins were identified from three key stages of interaction (12, 24, and 48 h post-inoculation) and control groups. Quantitative analysis showed that 530 proteins were differentially accumulated by Pst infection (fold changes >1.5, p < 0.05). Among these proteins, 10.54% was classified as involved in the immune system process and stimulus response. Intriguingly, bioinformatics analysis revealed that a set of reactive oxygen species metabolism-related proteins, peptidyl–prolyl cis–trans isomerases (PPIases), RNA-binding proteins (RBPs), and chaperonins was involved in the response to Pst infection. Our results were the first to show that PPIases, RBPs, and chaperonins participated in the regulation of the immune response in wheat and even in plants. This study aimed to provide novel routes to reveal wheat gene functionality and better understand the early events in wheat–Pst incompatible interactions.
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32
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Pogorelko G, Juvale PS, Rutter WB, Hewezi T, Hussey R, Davis EL, Mitchum MG, Baum TJ. A cyst nematode effector binds to diverse plant proteins, increases nematode susceptibility and affects root morphology. MOLECULAR PLANT PATHOLOGY 2016; 17:832-44. [PMID: 26575318 PMCID: PMC6638508 DOI: 10.1111/mpp.12330] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 05/20/2023]
Abstract
Cyst nematodes are plant-parasitic roundworms that are of significance in many cropping systems around the world. Cyst nematode infection is facilitated by effector proteins secreted from the nematode into the plant host. The cDNAs of the 25A01-like effector family are novel sequences that were isolated from the oesophageal gland cells of the soybean cyst nematode (Heterodera glycines). To aid functional characterization, we identified an orthologous member of this protein family (Hs25A01) from the closely related sugar beet cyst nematode H. schachtii, which infects Arabidopsis. Constitutive expression of the Hs25A01 CDS in Arabidopsis plants caused a small increase in root length, accompanied by up to a 22% increase in susceptibility to H. schachtii. A plant-expressed RNA interference (RNAi) construct targeting Hs25A01 transcripts in invading nematodes significantly reduced host susceptibility to H. schachtii. These data document that Hs25A01 has physiological functions in planta and a role in cyst nematode parasitism. In vivo and in vitro binding assays confirmed the specific interactions of Hs25A01 with an Arabidopsis F-box-containing protein, a chalcone synthase and the translation initiation factor eIF-2 β subunit (eIF-2bs), making these proteins probable candidates for involvement in the observed changes in plant growth and parasitism. A role of eIF-2bs in the mediation of Hs25A01 virulence function is further supported by the observation that two independent eIF-2bs Arabidopsis knock-out lines were significantly more susceptible to H. schachtii.
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Affiliation(s)
- Gennady Pogorelko
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - William B Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66505, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard Hussey
- Department of Plant Pathology, The University of Georgia, Athens, GA, 30602, USA
| | - Eric L Davis
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Melissa G Mitchum
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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Kaur G, Singh S, Singh H, Chawla M, Dutta T, Kaur H, Bender K, Snedden WA, Kapoor S, Pareek A, Singh P. Characterization of Peptidyl-Prolyl Cis-Trans Isomerase- and Calmodulin-Binding Activity of a Cytosolic Arabidopsis thaliana Cyclophilin AtCyp19-3. PLoS One 2015; 10:e0136692. [PMID: 26317213 PMCID: PMC4552658 DOI: 10.1371/journal.pone.0136692] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/06/2015] [Indexed: 12/25/2022] Open
Abstract
Cyclophilins, which bind to immunosuppressant cyclosporin A (CsA), are ubiquitous proteins and constitute a multigene family in higher organisms. Several members of this family are reported to catalyze cis-trans isomerisation of the peptidyl-prolyl bond, which is a rate limiting step in protein folding. The physiological role of these proteins in plants, with few exceptions, is still a matter of speculation. Although Arabidopsis genome is predicted to contain 35 cyclophilin genes, biochemical characterization, imperative for understanding their cellular function(s), has been carried only for few of the members. The present study reports the biochemical characterization of an Arabidopsis cyclophilin, AtCyp19-3, which demonstrated that this protein is enzymatically active and possesses peptidyl-prolyl cis-trans isomerase (PPIase) activity that is specifically inhibited by CsA with an inhibition constant (Ki) of 18.75 nM. The PPIase activity of AtCyp19-3 was also sensitive to Cu(2+), which covalently reacts with the sulfhydryl groups, implying redox regulation. Further, using calmodulin (CaM) gel overlay assays it was demonstrated that in vitro interaction of AtCyp19-3 with CaM is Ca(2+)-dependent, and CaM-binding domain is localized to 35-70 amino acid residues in the N-terminus. Bimolecular fluorescence complementation assays showed that AtCyp19-3 interacts with CaM in vivo also, thus, validating the in vitro observations. However, the PPIase activity of the Arabidopsis cyclophilin was not affected by CaM. The implications of these findings are discussed in the context of Ca(2+) signaling and cyclophilin activity in Arabidopsis.
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Affiliation(s)
- Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Supreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidayalaya, Jalandhar, Punjab, India
| | - Mrinalini Chawla
- Interdiscipinary Center for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Tanima Dutta
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Harsimran Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Kyle Bender
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
| | - W. A. Snedden
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
| | - Sanjay Kapoor
- Interdiscipinary Center for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal, Nehru University, New Delhi, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
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Kumari S, Joshi R, Singh K, Roy S, Tripathi AK, Singh P, Singla-Pareek SL, Pareek A. Expression of a cyclophilin OsCyp2-P isolated from a salt-tolerant landrace of rice in tobacco alleviates stress via ion homeostasis and limiting ROS accumulation. Funct Integr Genomics 2015; 15:395-412. [PMID: 25523384 DOI: 10.1007/s10142-014-0429-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/23/2014] [Accepted: 11/30/2014] [Indexed: 10/24/2022]
Abstract
Cyclophilins are a set of ubiquitous proteins present in all subcellular compartments, involved in a wide variety of cellular processes. Comparative bioinformatics analysis of the rice and Arabidopsis genomes led us to identify novel putative cyclophilin gene family members in both the genomes not reported previously. We grouped cyclophilin members with similar molecular weight and subtypes together in the phylogenetic tree which indicated their co-evolution in rice and Arabidopsis. We also characterized a rice cyclophilin gene, OsCyp2-P (Os02g0121300), isolated from a salinity-tolerant landrace, Pokkali. Publicly available massively parallel signature sequencing (MPSS) and microarray data, besides our quantitative real time PCR (qRT-PCR) data suggest that transcript abundance of OsCyp2-P is regulated under different stress conditions in a developmental and organ specific manner. Ectopic expression of OsCyp2-P imparted multiple abiotic stress tolerance to transgenic tobacco plants as evidenced by higher root length, shoot length, chlorophyll content, and K(+)/Na(+) ratio under stress conditions. Transgenic plants also showed reduced lipid peroxidase content, electrolyte leakage, and superoxide content under stress conditions suggesting better ion homeostasis than WT plants. Localization studies confirmed that OsCyp2-P is localized in both cytosol and nucleus, indicating its possible interaction with several other proteins. The overall results suggest the explicit role of OsCyp2-P in bestowing multiple abiotic stress tolerance at the whole plant level. OsCyp2-P operates via reactive oxygen species (ROS) scavenging and ion homeostasis and thus is a promising candidate gene for enhancing multiple abiotic stress tolerance in crop plants.
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Affiliation(s)
- Sumita Kumari
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Singh K, Zouhar M, Mazakova J, Rysanek P. Genome wide identification of the immunophilin gene family in Leptosphaeria maculans: a causal agent of Blackleg disease in Oilseed Rape (Brassica napus). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:645-57. [PMID: 25259854 DOI: 10.1089/omi.2014.0081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract Phoma stem canker (blackleg) is a disease of world-wide importance on oilseed rape (Brassica napus) and can cause serious losses for crops globally. The disease is caused by dothideomycetous fungus, Leptosphaeria maculans, which is highly virulent/aggressive. Cyclophilins (CYPs) and FK506-binding proteins (FKBPs) are ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) family. They are collectively referred to as immunophilins (IMMs). In the present study, IMM genes, CYP and FKBP in haploid strain v23.1.3 of L. maculans genome, were identified and classified. Twelve CYPs and five FKBPs were determined in total. Domain architecture analysis revealed the presence of a conserved cyclophilin-like domain (CLD) in the case of CYPs and FKBP_C in the case of FKBPs. Interestingly, IMMs in L. maculans also subgrouped into single domain (SD) and multidomain (MD) proteins. They were primarily found to be localized in cytoplasm, nuclei, and mitochondria. Homologous and orthologous gene pairs were also determined by comparison with the model organism Saccharomyces cerevisiae. Remarkably, IMMs of L. maculans contain shorter introns in comparison to exons. Moreover, CYPs, in contrast with FKBPs, contain few exons. However, two CYPs were determined as being intronless. The expression profile of IMMs in both mycelium and infected primary leaves of B. napus demonstrated their potential role during infection. Secondary structure analysis revealed the presence of atypical eight β strands and two α helices fold architecture. Gene ontology analysis of IMMs predicted their significant role in protein folding and PPIase activity. Taken together, our findings for the first time present new prospects of this highly conserved gene family in phytopathogenic fungus.
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Affiliation(s)
- Khushwant Singh
- Department of Plant Protection, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Czech Republic
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Microbial peptidyl-prolyl cis/trans isomerases (PPIases): virulence factors and potential alternative drug targets. Microbiol Mol Biol Rev 2015; 78:544-71. [PMID: 25184565 DOI: 10.1128/mmbr.00015-14] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (PPIases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. Intense searches revealed that PPIases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. Despite the clear-cut enzymatic activity and ubiquitous distribution of PPIases, reports on solely PPIase-dependent biological roles remain scarce. Nevertheless, they have been found to be involved in a plethora of biological processes, such as gene expression, signal transduction, protein secretion, development, and tissue regeneration, underscoring their general importance. Hence, it is not surprising that PPIases have also been identified as virulence-associated proteins. The extent of contribution to virulence is highly variable and dependent on the pleiotropic roles of a single PPIase in the respective pathogen. The main objective of this review is to discuss this variety in virulence-related bacterial and protozoan PPIases as well as the involvement of host PPIases in infectious processes. Moreover, a special focus is given to Legionella pneumophila macrophage infectivity potentiator (Mip) and Mip-like PPIases of other pathogens, as the best-characterized virulence-related representatives of this family. Finally, the potential of PPIases as alternative drug targets and first tangible results are highlighted.
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Samayoa LF, Malvar RA, Olukolu BA, Holland JB, Butrón A. Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel. BMC PLANT BIOLOGY 2015; 15:35. [PMID: 25652257 PMCID: PMC4340109 DOI: 10.1186/s12870-014-0403-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/22/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Corn borers are the primary maize pest; their feeding on the pith results in stem damage and yield losses. In this study, we performed a genome-wide association study (GWAS) to identify SNPs associated with resistance to Mediterranean corn borer in a maize diversity panel using a set of more than 240,000 SNPs. RESULTS Twenty five SNPs were significantly associated with three resistance traits: 10 were significantly associated with tunnel length, 4 with stem damage, and 11 with kernel resistance. Allelic variation at each significant SNP was associated with from 6 to 9% of the phenotypic variance. A set of genes containing or physically close to these SNPs are proposed as candidate genes for borer resistance, supported by their involvement in plant defense-related mechanisms in previously published evidence. The linkage disequilibrium decayed (r(2) < 0.10) rapidly within short distance, suggesting high resolution of GWAS associations. CONCLUSIONS Most of the candidate genes found in this study are part of signaling pathways, others act as regulator of expression under biotic stress condition, and a few genes are encoding enzymes with antibiotic effect against insects such as the cystatin1 gene and the defensin proteins. These findings contribute to the understanding the complex relationship between plant-insect interactions.
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Affiliation(s)
- Luis Fernando Samayoa
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.
| | - Rosa Ana Malvar
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.
| | - Bode A Olukolu
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, 27695, USA.
| | - James B Holland
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, 27695, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, Raleigh, North Carolina, 27695, USA.
| | - Ana Butrón
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.
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Ünal CM, Steinert M. FKBPs in bacterial infections. Biochim Biophys Acta Gen Subj 2014; 1850:2096-102. [PMID: 25529296 DOI: 10.1016/j.bbagen.2014.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/11/2014] [Accepted: 12/13/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND FK506-binding proteins (FKBPs) contain a domain with peptidyl-prolyl-cis/trans-isomerase (PPIase) activity and bind the immunosuppressive drugs FK506 and rapamycin. FKBPs belong to the immunophilin family and are found in eukaryotes and bacteria. SCOPE OF REVIEW In this review we describe two major groups of bacterial virulence-associated FKBPs, the trigger factor and Mip-like PPIases. Moreover, we discuss the contribution of host FKBPs in bacterial infection processes. MAJOR CONCLUSIONS Since PPIases are regarded as alternative antiinfective drug targets we highlight current research strategies utilizing pipecolinic acid and cycloheximide derivatives as well as substrate based inhibitors. GENERAL SIGNIFICANCE The current research strategies suggest a beneficial synergism of drug development and basic research. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Can M Ünal
- Türk-Alman Üniversitesi, Fen Fakültesi, Istanbul, Turkey; Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany
| | - Michael Steinert
- Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany; Helmholtz Centre for Infection Research, Braunschweig, Germany.
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Plant immunophilins: a review of their structure-function relationship. Biochim Biophys Acta Gen Subj 2014; 1850:2145-58. [PMID: 25529299 DOI: 10.1016/j.bbagen.2014.12.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 01/02/2023]
Abstract
BACKGROUND Originally discovered as receptors for immunosuppressive drugs, immunophilins consist of two major groups, FK506 binding proteins (FKBPs) and cyclosporin A binding proteins (cyclophilins, CYPs). Many members in both FKBP and CYP families are peptidyl prolyl isomerases that are involved in protein folding processes, though they share little sequence homology. It is not surprising to find immunophilins in all organisms examined so far, including viruses, bacteria, fungi, plants and animals, as protein folding represents a common process in all living systems. SCOPE OF REVIEW Studies on plant immunophilins have revealed new functions beyond protein folding and new structural properties beyond that of typical PPIases. This review focuses on the structural and functional diversity of plant FKBPs and CYPs. MAJOR CONCLUSIONS The differences in sequence, structure as well as subcellular localization, have added on to the diversity of this family of molecular chaperones. In particular, the large number of immunophilins present in the thylakoid lumen of the photosynthetic organelle, promises to deliver insights into the regulation of photosynthesis, a unique feature of plant systems. However, very little structural information and functional data are available for plant immunophilins. GENERAL SIGNIFICANCE Studies on the structure and function of plant immunophilins are important in understanding their role in plant biology. By reviewing the structural and functional properties of some immunophilins that represent the emerging area of research in plant biology, we hope to increase the interest of researchers in pursuing further research in this area. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Li M, Ma X, Chiang YH, Yadeta KA, Ding P, Dong L, Zhao Y, Li X, Yu Y, Zhang L, Shen QH, Xia B, Coaker G, Liu D, Zhou JM. Proline isomerization of the immune receptor-interacting protein RIN4 by a cyclophilin inhibits effector-triggered immunity in Arabidopsis. Cell Host Microbe 2014; 16:473-83. [PMID: 25299333 PMCID: PMC4768788 DOI: 10.1016/j.chom.2014.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/24/2014] [Accepted: 08/25/2014] [Indexed: 11/15/2022]
Abstract
In the absence of pathogen infection, plant effector-triggered immune (ETI) receptors are maintained in a preactivation state by intermolecular interactions with other host proteins. Pathogen effector-induced alterations activate the receptor. In Arabidopsis, the ETI receptor RPM1 is activated via bacterial effector AvrB-induced phosphorylation of the RPM1-interacting protein RIN4 at Threonine 166. We find that RIN4 also interacts with the prolyl-peptidyl isomerase (PPIase) ROC1, which is reduced upon RIN4 Thr166 phosphorylation. ROC1 suppresses RPM1 immunity in a PPIase-dependent manner. Consistent with this, RIN4 Pro149 undergoes cis/trans isomerization in the presence of ROC1. While the RIN4(P149V) mutation abolishes RPM1 resistance, the deletion of Pro149 leads to RPM1 activation in the absence of RIN4 phosphorylation. These results support a model in which RPM1 directly senses conformational changes in RIN4 surrounding Pro149 that is controlled by ROC1. RIN4 Thr166 phosphorylation indirectly regulates RPM1 resistance by modulating the ROC1-mediated RIN4 isomerization.
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Affiliation(s)
- Meng Li
- College of Life Sciences, Peking University, No. 5 YiheYuan Road, Beijing 100871, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Xiqing Ma
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, Tsinghua Yuan 1, School of Life Sciences, Beijing 100084, China
| | - Yi-Hsuan Chiang
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Koste A Yadeta
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Pengfei Ding
- College of Life Sciences, Peking University, No. 5 YiheYuan Road, Beijing 100871, China
| | - Liansai Dong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Xiuming Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Yufei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Ling Zhang
- Center for Molecular Agrobiology and State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Qian-Hua Shen
- Center for Molecular Agrobiology and State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China
| | - Bin Xia
- College of Life Sciences, Peking University, No. 5 YiheYuan Road, Beijing 100871, China
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Dong Liu
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, Tsinghua Yuan 1, School of Life Sciences, Beijing 100084, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, CAS, No. 1 West Beichen Road, Beijing 100101, China.
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