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Liu S, Wei F, Liu R, Xue C, Chen Y, Zhao C, Chen P. A systematic analysis of ARM genes revealed that GhARM144 regulates the resistance against Verticillium dahliae via interaction with GhOSM34. PHYSIOLOGIA PLANTARUM 2024; 176:e14259. [PMID: 38511474 DOI: 10.1111/ppl.14259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/15/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Proteins of the armadillo repeat gene family play important roles in plant pathogen response. Here, 169 armadillo (ARM) genes were identified in upland cotton (Gossypium hirsutum). Phylogenetic analysis grouped these into 11 subfamilies, with conserved protein structures within each subfamily. The results signify that the expansion of the gene family occurred via whole genome duplication and dispersed duplication. Expression profiling and network analysis suggest that GhARM144 may regulate cotton resistance to Verticillium dahliae. GhARM144 was upregulated in roots by V. dahliae infection or salicylic acid treatment. This upregulation indicates a negative regulatory role of GhARM144' in the cotton immune responses, potentially by manipulating salicylic acid biosynthesis. Protein interaction studies found that GhARM144 associates with an osmotin-like protein, GhOSM34, at the plasma membrane. Silencing GhOSM34 reduced the resistance to V. dahliae, suggesting it may play a positive regulatory role. The results demonstrate that GhARM144 modulates cotton immunity through interaction with GhOSM34 and salicylic acid signalling. Further study of these proteins may yield insights into disease resistance mechanisms in cotton and other plants.
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Affiliation(s)
- Shichao Liu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, China
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan Province, Wanning, Hainan, China
| | - Fei Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, China
| | - Ruibing Liu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, China
| | - Chao Xue
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, China
| | - Yining Chen
- College of Cyber Science, Nankai University, Tianjin, China
| | - Chenchen Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Pengyun Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Liu Y, Li C, Qin A, Deng W, Chen R, Yu H, Wang Y, Song J, Zeng L. Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.). BMC Genomics 2024; 25:132. [PMID: 38302871 PMCID: PMC10832145 DOI: 10.1186/s12864-024-10040-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND The U-box gene family encodes E3 ubiquitin ligases involved in plant hormone signaling pathways and abiotic stress responses. However, there has yet to be a comprehensive analysis of the U-box gene family in maize (Zea mays L.) and its responses to abiotic stress. RESULTS In this study, 85 U-box family proteins were identified in maize and were classified into four subfamilies based on phylogenetic analysis. In addition to the conserved U-box domain, we identified additional functional domains, including Pkinase, ARM, KAP and Tyr domains, by analyzing the conserved motifs and gene structures. Chromosomal localization and collinearity analysis revealed that gene duplications may have contributed to the expansion and evolution of the U-box gene family. GO annotation and KEGG pathway enrichment analysis identified a total of 105 GO terms and 21 KEGG pathways that were notably enriched, including ubiquitin-protein transferase activity, ubiquitin conjugating enzyme activity and ubiquitin-mediated proteolysis pathway. Tissue expression analysis showed that some ZmPUB genes were specifically expressed in certain tissues and that this could be due to their functions. In addition, RNA-seq data for maize seedlings under salt stress revealed 16 stress-inducible plant U-box genes, of which 10 genes were upregulated and 6 genes were downregulated. The qRT-PCR results for genes responding to abiotic stress were consistent with the transcriptome analysis. Among them, ZmPUB13, ZmPUB18, ZmPUB19 and ZmPUB68 were upregulated under all three abiotic stress conditions. Subcellular localization analysis showed that ZmPUB19 and ZmPUB59 were located in the nucleus. CONCLUSIONS Overall, our study provides a comprehensive analysis of the U-box gene family in maize and its responses to abiotic stress, suggesting that U-box genes play an important role in the stress response and providing insights into the regulatory mechanisms underlying the response to abiotic stress in maize.
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Affiliation(s)
- Yongle Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
- College of Life Sciences, Nanjing University, Nanjing, 210095, People's Republic of China
| | - Changgen Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Aokang Qin
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Wenli Deng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Hongyang Yu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Yihua Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Jianbo Song
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
- Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Liming Zeng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
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Liu Z, Wang L, Li Y, Zhu J, Li Z, Chen L, Li H, Shi T, Yao P, Bi Z, Sun C, Bai J, Zhang J, Liu Y. Genome-wide analysis of the U-box E3 ligases gene family in potato (Solanum tuberosum L.) and overexpress StPUB25 enhance drought tolerance in transgenic Arabidopsis. BMC Genomics 2024; 25:10. [PMID: 38166714 PMCID: PMC10759479 DOI: 10.1186/s12864-023-09890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Plant U-box (PUB) E3 ubiquitin ligases have vital effects on various biological processes. Therefore, a comprehensive and systematic identification of the members of the U-box gene family in potato will help to understand the evolution and function of U-box E3 ubiquitin ligases in plants. RESULTS This work identified altogether 74 PUBs in the potato (StPUBs) and examined their gene structures, chromosomal distributions, and conserved motifs. There were seventy-four StPUB genes on ten chromosomes with diverse densities. As revealed by phylogenetic analysis on PUBs within potato, Arabidopsis, tomato (Solanum lycopersicum), cabbage (Brassica oleracea), rice (Oryza sativa), and corn (Zea mays), were clustered into eight subclasses (C1-C8). According to synteny analysis, there were 40 orthologous StPUB genes to Arabidopsis, 58 to tomato, 28 to cabbage, 7 to rice, and 8 to corn. In addition, RNA-seq data downloaded from PGSC were utilized to reveal StPUBs' abiotic stress responses and tissue-specific expression in the doubled-monoploid potato (DM). Inaddition, we performed RNA-seq on the 'Atlantic' (drought-sensitive cultivar, DS) and the 'Qingshu NO.9' (drought-tolerant cultivar, DT) in early flowering, full-blooming, along with flower-falling stages to detect genes that might be involved in response to drought stress. Finally, quantitative real-time PCR (qPCR) was carried out to analyze three candidate genes for their expression levels within 100 mM NaCl- and 10% PEG 6000 (w/v)-treated potato plantlets for a 24-h period. Furthermore, we analyzed the drought tolerance of StPUB25 transgenic plants and found that overexpression of StPUB25 significantly increased peroxidase (POD) activity, reduced ROS (reactive oxygen species) and MDA (malondialdehyde) accumulation compared with wild-type (WT) plants, and enhancing drought tolerance of the transgenic plants. CONCLUSION In this study, three candidate genes related to drought tolerance in potato were excavated, and the function of StPUB25 under drought stress was verified. These results should provide valuable information to understand the potato StPUB gene family and investigate the molecular mechanisms of StPUBs regulating potato drought tolerance.
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Affiliation(s)
- Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lei Wang
- Hebei North University, Zhangjiakou, 075000, China
| | - Yuanming Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jinyong Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhitao Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Limin Chen
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Hongyang Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Tianbin Shi
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhenzhen Bi
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chao Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jiangping Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junlian Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
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Lal MK, Tiwari RK, Kumar A, Dey A, Kumar R, Kumar D, Jaiswal A, Changan SS, Raigond P, Dutt S, Luthra SK, Mandal S, Singh MP, Paul V, Singh B. Mechanistic Concept of Physiological, Biochemical, and Molecular Responses of the Potato Crop to Heat and Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212857. [PMID: 36365310 PMCID: PMC9654185 DOI: 10.3390/plants11212857] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 05/14/2023]
Abstract
Most cultivated potatoes are tetraploid, and the tuber is the main economic part that is consumed due to its calorific and nutritional values. Recent trends in climate change led to the frequent occurrence of heat and drought stress in major potato-growing regions worldwide. The optimum temperature for tuber production is 15-20 °C. High-temperature and water-deficient conditions during the growing season result in several morphological, physiological, biochemical, and molecular alterations. The morphological changes under stress conditions may affect the process of stolon formation, tuberization, and bulking, ultimately affecting the tuber yield. This condition also affects the physiological responses, including an imbalance in the allocation of photoassimilates, respiration, water use efficiency, transpiration, carbon partitioning, and the source-sink relationship. The biochemical responses under stress conditions involve maintaining ionic homeostasis, synthesizing heat shock proteins, achieving osmolyte balance, and generating reactive oxygen species, ultimately affecting various biochemical pathways. Different networks that include both gene regulation and transcription factors are involved at the molecular level due to the combination of hot and water-deficient conditions. This article attempts to present an integrative content of physio-biochemical and molecular responses under the combined effects of heat and drought, prominent factors in climate change. Taking into account all of these aspects and responses, there is an immediate need for comprehensive screening of germplasm and the application of appropriate approaches and tactics to produce potato cultivars that perform well under drought and in heat-affected areas.
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Affiliation(s)
- Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla 171001, India
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Correspondence: (M.K.L.); (R.K.T.); Tel.: +91-9718815448 (M.K.L.)
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla 171001, India
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Correspondence: (M.K.L.); (R.K.T.); Tel.: +91-9718815448 (M.K.L.)
| | - Awadhesh Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | | | - Arvind Jaiswal
- ICAR-Central Potato Research Institute Campus, Jalandhar 144026, India
| | | | - Pinky Raigond
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | - Som Dutt
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | | | - Sayanti Mandal
- Department of Biotechnology, D. Y. Patil Arts, Commerce and Science College, Sant Tukaram Nagar, Pimpri, Pune 411018, India
| | - Madan Pal Singh
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Vijay Paul
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla 171001, India
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Classification and Expression Profile of the U-Box E3 Ubiquitin Ligase Enzyme Gene Family in Maize (Zea mays L.). PLANTS 2022; 11:plants11192459. [PMID: 36235327 PMCID: PMC9573083 DOI: 10.3390/plants11192459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022]
Abstract
The U-box E3 (PUB) family genes encode the E3 ubiquitin ligase enzyme, which determines substrate specific recognition during protein ubiquitination. They are widespread in plants and are critical for plant growth, development, and response to external stresses. However, there are few studies on the functional characteristic of PUB gene family in the important staple crop, maize (Zea mays L.). In this study, the PUB gene in maize was aimed to identify and classify through whole-genome screening. Phylogenetic tree, gene structure, conserved motif, chromosome location, gene duplication (GD), synteny, and cis-acting regulatory element of PUB member were analyzed. The expression profiles of ZmPUB gene family in maize during development and under abiotic stress and hormones treatment were analyzed by the RNA-seq data. A total of 79 PUB genes were identified in maize genome, and they were stratified into seven categories. There were 25 pairs of segmental duplications (SD) and 1 pair of tandem duplication (TD) identified in the maize PUB gene family. A close relationship was observed between the monocot plant maize and rice in PUB gene family. There were 94 kinds of cis-acting elements identified in the maize PUB gene family, which included 46 biotic- and abiotic-responsive elements, 19 hormone-responsive elements, 13 metabolic and growth-related elements. The expression profiles of maize PUB gene family showed characteristics of tissue specificity and response to abiotic stress and hormones treatment. These results provided an extensive overview of the maize PUB gene family.
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Fang Y, Du Q, Yang Q, Jiang J, Hou X, Yang Z, Zhao D, Li X, Xie X. Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor. Front Microbiol 2022; 13:942302. [PMID: 36187972 PMCID: PMC9520534 DOI: 10.3389/fmicb.2022.942302] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
The U-box family is one of the main E3 ubiquitin ligase families in plants. The U-box family has been characterized in several species. However, genome-wide gene identification and expression profiling of the U-box family in response to abiotic stress in Sorghum bicolor remain unclear. In this study, we broadly identified 68 U-box genes in the sorghum genome, including 2 CHIP genes, and 1 typical UFD2 (Ub fusion degradation 2) gene. The U-box gene family was divided into eight subclasses based on homology and conserved domain characteristics. Evolutionary analysis identified 14, 66, and 82 U-box collinear gene pairs in sorghum compared with arabidopsis, rice, and maize, respectively, and a unique tandem repeat pair (SbPUB26/SbPUB27) is present in the sorghum genome. Gene Ontology (GO) enrichment analysis showed that U-box proteins were mainly related to ubiquitination and modification, and various stress responses. Comprehensive analysis of promoters, expression profiling, and gene co-regulation networks also revealed that many sorghum U-box genes may be correlated with multiple stress responses. In summary, our results showed that sorghum contains 68 U-box genes, which may be involved in multiple abiotic stress responses. The findings will support future gene functional studies related to ubiquitination in sorghum.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qiaoli Du
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qian Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Zaifu Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Degang Zhao
- College of Life Sciences, Ministry of Education, Institute of Agricultural Bioengineering, Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Guizhou University, Guiyang, China
- Guizhou Academy of Agricultural Sciences, Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture, Guizhou Institute of Biotechnology, Guiyang, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Academy of Agricultural Sciences, Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture, Guizhou Institute of Biotechnology, Guiyang, China
- *Correspondence: Xin Xie,
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Functional Characterization of Ubiquitination Genes in the Interaction of Soybean—Heterodera glycines. Int J Mol Sci 2022; 23:ijms231810771. [PMID: 36142678 PMCID: PMC9504373 DOI: 10.3390/ijms231810771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022] Open
Abstract
Ubiquitination is a kind of post-translational modification of proteins that plays an important role in plant response to biotic and abiotic stress. The response of soybean GmPUB genes to soybean cyst nematode (SCN, Heterodera glycines) infection is largely unknown. In this study, quantitative real-time PCR (qRT-PCR) was performed to detect the relative expression of 49 GmPUB genes in susceptible cultivar William 82 and resistant cultivar Huipizhi after SCN inoculation. The results show that GmPUB genes responded to cyst nematode infection at 1 day post-inoculation (dpi), 5 dpi, 10 dpi and 15 dpi. The expression levels of GmPUB16A, GmPUB20A, GmCHIPA, GmPUB33A, GmPUB23A and GmPUB24A were dramatically changed during SCN infection. Furthermore, functional analysis of these GmPUB genes by overexpression and RNAi showed that GmPUB20A, GmPUB33A and GmPUB24A negatively regulated soybean resistance under SCN stress. The results from our present study provide insights into the complicated molecular mechanism of the interaction between soybean and SCN.
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Choi JH, Kim JW, Oh MH. Identification of Feronia-interacting proteins in Arabidopsis thaliana. Genes Genomics 2022; 44:1477-1485. [PMID: 36053485 DOI: 10.1007/s13258-022-01292-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Plant growth and development are complex processes modulated by numerous genes, transcription factors, hormones, and peptides. Several reports implicate the membrane-localized Catharanthus roseus receptor-like kinase1 (CrRLK1L) protein, FERONIA (FER), involved in plant development. However, protein targets of FER remain poorly characterized. OBJECTIVE FER recombinant proteins were analyzed, and FER-interacting proteins were identified, to better understand the function of the Arabidopsis thaliana FER (AtFER) gene in plant development. METHODS AtFER-interacting proteins were identified through Yeast-Two Hybrid (Y2H) and validated by bimolecular fluorescence complementation (BiFC). Autophosphorylation activity was evaluated in AtFER site-directed and deletion mutants. RESULTS AtFER cytoplasmic kinase domain (Flag-FER-CD) is autophosphorylated at the Thr residue (s), with T559 and T664 as important sites for AtFER kinase activity. In addition, the carboxy terminal region is essential for AtFER kinase activity. Y2H identified an Armadillo (ARM)-repeat protein (At4g16490) with tandem copies of a degenerate protein sequence motif, a U-BOX 9 (PUB9, At3g07360), IQ-DOMAIN 7 (IQD7, At1g17480), and heteroglycan glucosidase 1 (HGL1, At3g23640) as AtFER-interacting proteins. BiFC confirmed the in vivo interactions between these four proteins and AtFER in tobacco (Nicotiana benthamiana) leaf transient expression assays. The RAPID ALKALINIZATION FACTOR1 (RALF1) peptide, which is a FER ligand, induced the expression of genes encoding the four AtFER-interacting proteins. CONCLUSION The AtFER-interacting proteins identified in this study are likely involved in FER-mediated intracellular signaling pathways that are essential in plant growth and development, and possibly plant immunity.
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Affiliation(s)
- Jae-Han Choi
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea
| | - Ji-Woo Kim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea
| | - Man-Ho Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea.
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Panibe JP, Wang L, Lee YC, Wang CS, Li WH. Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution. BOTANICAL STUDIES 2022; 63:9. [PMID: 35347474 PMCID: PMC8960516 DOI: 10.1186/s40529-022-00336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. RESULTS Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. CONCLUSIONS We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1's blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.
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Affiliation(s)
- Jerome P. Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023 China
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung, 40227 Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
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10
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How Many Faces Does the Plant U-Box E3 Ligase Have? Int J Mol Sci 2022; 23:ijms23042285. [PMID: 35216399 PMCID: PMC8875423 DOI: 10.3390/ijms23042285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Ubiquitination is a major type of post-translational modification of proteins in eukaryotes. The plant U-Box (PUB) E3 ligase is the smallest family in the E3 ligase superfamily, but plays a variety of essential roles in plant growth, development and response to diverse environmental stresses. Hence, PUBs are potential gene resources for developing climate-resilient crops. However, there is a lack of review of the latest advances to fully understand the powerful gene family. To bridge the gap and facilitate its use in future crop breeding, we comprehensively summarize the recent progress of the PUB family, including gene evolution, classification, biological functions, and multifarious regulatory mechanisms in plants.
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11
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Green revolution to grain revolution: Florigen in the frontiers. J Biotechnol 2022; 343:38-46. [PMID: 34673121 DOI: 10.1016/j.jbiotec.2021.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/20/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022]
Abstract
Burgeoning human population dents, globally, the brimming buffer stock as well as gain in food grain production. However, an imminent global starvation was averted through precise scientific intervention and pragmatic policy changes in the 1960s and was eulogized as the "Green Revolution". Miracle rice and wheat obtained through morphometric changes in the ideotype of these two crops yielded bumper harvest that nucleated in Asia and translated into Latin America. The altered agronomic traits in these two crops were the result of tinkering with the phyto-hormone "Gibberellin'. Recently, another plant hormone 'Cytokinin' has gained prominence for its involvement in the grain revolution in rice and other field crops. Suo moto homeostasis of CK by the cytokinin oxidase enzyme governs the cardinal shoot apical meristem that produces new flowering primordia thereby enhancing grain number. Similarly, the flowering hormone 'Florigen' impacts sympodia formation, flowering, and fruit production in tomato. The role of heterozygosity induced heterosis by florigen in revolutionizing tomato production and cellular homeostasis of CK by CK oxidising enzyme (CKX) in enhancing rice production has been path-breaking. This review highlights role of phytohormones in grain revolution and crop specific fine-tuning of gibberellins, cytokinins and florigen to accomplish maximum yield potential in field crops.
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Kim JH, Kim MS, Kim DY, Amoah JN, Seo YW. Molecular Characterization of U-box E3 Ubiquitin Ligases (TaPUB2 and TaPUB3) Involved in the Positive Regulation of Drought Stress Response in Arabidopsis. Int J Mol Sci 2021; 22:13658. [PMID: 34948454 PMCID: PMC8704797 DOI: 10.3390/ijms222413658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 12/25/2022] Open
Abstract
Plant U-box E3 ubiquitin ligase (PUB) is involved in various environmental stress conditions. However, the molecular mechanism of U-box proteins in response to abiotic stress in wheat remains unknown. In this study, two U-box E3 ligase genes (TaPUB2 and TaPUB3), which are highly expressed in response to adverse abiotic stresses, were isolated from common wheat, and their cellular functions were characterized under drought stress. Transient expression assay revealed that TaPUB2 was localized in the cytoplasm and Golgi apparatus, whereas TaPUB3 was expressed only in the Golgi apparatus in wheat protoplasts. Additionally, TaPUB2 and TaPUB3 underwent self-ubiquitination. Moreover, TaPUB2/TaPUB3 heterodimer was identified in yeast and the cytoplasm of wheat protoplasts using a pull-down assay and bimolecular fluorescence complementation analysis. Heterogeneous overexpression of TaPUB2 and TaPUB3 conferred tolerance to drought stress. Taken together, these results implied that the heterodimeric form of U-box E3 ubiquitin ligases (TaPUB2/TaPUB3) responded to abiotic stress and roles as a positive regulator of drought stress tolerance.
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Affiliation(s)
| | | | | | | | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul 02841, Korea; (J.H.K.); (M.S.K.); (D.Y.K.); (J.N.A.)
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13
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Kim MS, Kang KK, Cho YG. Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice ( Oryzasativa). Int J Mol Sci 2021; 22:ijms222112088. [PMID: 34769518 PMCID: PMC8584879 DOI: 10.3390/ijms222112088] [Citation(s) in RCA: 3] [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: 09/25/2021] [Revised: 10/21/2021] [Accepted: 11/05/2021] [Indexed: 02/03/2023] Open
Abstract
Proteins encoded by U-box type ubiquitin ligase (PUB) genes in rice are known to play an important role in plant responses to abiotic and biotic stresses. Functional analysis has revealed a detailed molecular mechanism involving PUB proteins in relation to abiotic and biotic stresses. In this study, characteristics of 77 OsPUB genes in rice were identified. Systematic and comprehensive analyses of the OsPUB gene family were then performed, including analysis of conserved domains, phylogenetic relationships, gene structure, chromosome location, cis-acting elements, and expression patterns. Through transcriptome analysis, we confirmed that 16 OsPUB genes show similar expression patterns in drought stress and blast infection response pathways. Numerous cis-acting elements were found in promoter sequences of 16 OsPUB genes, indicating that the OsPUB genes might be involved in complex regulatory networks to control hormones, stress responses, and cellular development. We performed qRT-PCR on 16 OsPUB genes under drought stress and blast infection to further identify the reliability of transcriptome and cis-element analysis data. It was confirmed that the expression pattern was similar to RNA-sequencing analysis results. The transcription of OsPUB under various stress conditions indicates that the PUB gene might have various functions in the responses of rice to abiotic and biotic stresses. Taken together, these results indicate that the genome-wide analysis of OsPUB genes can provide a solid basis for the functional analysis of U-box E3 ubiquitin ligase genes. The molecular information of the U-box E3 ubiquitin ligase gene family in rice, including gene expression patterns and cis-acting regulatory elements, could be useful for future crop breeding programs by genome editing.
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Affiliation(s)
- Me-Sun Kim
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea;
| | - Kwon-Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea;
| | - Yong-Gu Cho
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea;
- Correspondence:
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Genome Wide Analysis of U-Box E3 Ubiquitin Ligases in Wheat ( Triticum aestivum L.). Int J Mol Sci 2021; 22:ijms22052699. [PMID: 33800063 PMCID: PMC7962133 DOI: 10.3390/ijms22052699] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/28/2022] Open
Abstract
U-box E3 ligase genes play specific roles in protein degradation by post-translational modification in plant signaling pathways, developmental stages, and stress responses; however, little is known about U-box E3 genes in wheat. We identified 213 U-box E3 genes in wheat based on U-box and other functional domains in their genome sequences. The U-box E3 genes were distributed among 21 chromosomes and most showed high sequence homology with homoeologous U-box E3 genes. Synteny analysis of wheat U-box E3 genes was conducted with other plant species such as Brachypodium distachyon, barley, rice, Triricum uratu, and Aegilops tauschii. A total of 209 RNA-seq samples representing 22 tissue types, from grain, root, leaf, and spike samples across multiple time points, were analyzed for clustering of U-box E3 gene expression during developmental stages, and the genes responded differently in various tissues and developmental stages. In addition, expression analysis of U-box E3 genes under abiotic stress, including drought, heat, and both heat and drought, and cold conditions, was conducted to provide information on U-box E3 gene expression under specific stress conditions. This analysis of U-box E3 genes could provide valuable information to elucidate biological functions for a better understanding of U-box E3 genes in wheat.
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Erfatpour M, Pauls KP. A R2R3-MYB gene-based marker for the non-darkening seed coat trait in pinto and cranberry beans (Phaseolus vulgaris L.) derived from 'Wit-rood boontje'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1977-1994. [PMID: 32112124 PMCID: PMC7237406 DOI: 10.1007/s00122-020-03571-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/21/2020] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE The gene Phvul.010G130600 which codes for a MYB was shown to be tightly associated with seed coat darkening in Phaseolus vulgaris and a single nucleotide deletion in the allele in Wit-rood disrupts a transcription activation region that likely prevents its functioning in this non-darkening genotype. The beige and white background colors of the seed coats of conventional pinto and cranberry beans turn brown through a process known as postharvest darkening (PHD). Seed coat PHD is attributed to proanthocyanidin accumulation and its subsequent oxidation in the seed coat. The J gene is an uncharacterized classical genetic locus known to be responsible for PHD in common bean (P. vulgaris) and individuals that are homozygous for its recessive allele have a non-darkening (ND) seed coat phenotype. A previous study identified a major colorimetrically determined QTL for seed coat color on chromosome 10 that was associated with the ND trait. The objectives of this study were to identify a gene associated with seed coat postharvest darkening in common bean and understand its function in promoting seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL associated with the ND trait revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in non-darkening recombinant inbred lines derived from crosses between ND 'Wit-rood boontje' and a regular darkening pinto genotype. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) with a R2R3-MYB-type transcription factor MtPAR, which has been shown to regulate proanthocyanidin biosynthesis in Medicago truncatula seed coat tissue. The deletion in the 'Wit-rood boontje' allele of Phvul.010G130600 likely causes a translational frame shift that disrupts the function of a transcriptional activation domain contained in the C-terminus of the R2R3-MYB. A gene-based dominant marker was developed for the dominant allele of Phvul.010G130600 which can be used for marker-assisted selection of ND beans.
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Affiliation(s)
- M Erfatpour
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - K P Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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16
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Naeem M, Waseem M, Zhu Z, Zhang L. Downregulation of SlGRAS15 manipulates plant architecture in tomato (Solanum lycopersicum). Dev Genes Evol 2019; 230:1-12. [PMID: 31828522 DOI: 10.1007/s00427-019-00643-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 11/28/2019] [Indexed: 11/25/2022]
Abstract
GRAS family transcription factors (TF) are involved in multiple biological processes in plants. In recent years among the 54 identified GRAS proteins, only few have been studied functionally in tomato (Solanum lycopersicum). In the present study, a novel and previously uncharacterized member of tomato GRAS transcription factors family SlGRAS15 was isolated and functionally characterized. It was observed that SlGRAS15 preferably expressed in roots, followed by young leaves, stem, and comparatively low transcripts levels were noticed in all other tissues. To explore the SlGRAS15 function in detail, an RNA interference (RNAi) vector targeting SlGRAS15 was constructed and transformed into tomato plants. The transgenic plants carrying SlGRAS15-RNAi displayed pleiotropic phenotypes associated with multiple agronomical traits including reduced plant height and small leaf size with pointed margins, increased node number, lateral shoots, and petiolules length. In addition, transcriptional analysis revealed that silencing SlGRAS15 altered vegetative growth by downregulating gibberellin (GA) biosynthesis genes and stimulating the GA deactivating genes, thus lowering the endogenous GA content in tomato transgenic lines. Moreover, the GA signaling downstream gene (SlGAST1) was downregulated but the negative regulator of GA signaling (SlDELLA) was upregulated by SlGRAS15 silencing. The root and hypocotyl length in SlGRAS15-RNAi lines showed reduced growth under normal conditions (Mock) as compared with the wild type (WT) control plants. Taken together, these findings enhanced our understanding that suppression of SlGRAS15 lead to a series of developmental processes by modulating gibberellin signaling and demonstrate an association between the SlGRAS15 and GA signaling pathway during vegetative growth in tomato.
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Affiliation(s)
- Muhammad Naeem
- Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, People's Republic of China.
| | - Muhammad Waseem
- School of Life Sciences, Chongqing University, Huxi Campus, Daxuecheng, Shapingba, Chongqing, People's Republic of China
| | - Zhiguo Zhu
- Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, People's Republic of China
| | - Lincheng Zhang
- Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, People's Republic of China
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17
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Zhang G, Mao Z, Wang Q, Song J, Nie X, Wang T, Zhang H, Guo H. Comprehensive transcriptome profiling and phenotyping of rootstock and scion in a tomato/potato heterografting system. PHYSIOLOGIA PLANTARUM 2019; 166:833-847. [PMID: 30357855 DOI: 10.1111/ppl.12858] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/13/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
Tomato/potato heterografting-triggered phenotypic variations are well documented, yet the molecular mechanisms underlying grafting-induced phenotypic processes remain unknown. To investigate the phenotypic and transcriptomic responses of grafting parents in heterografting in comparison with self-grafting, tomato (Sl) was grafted onto potato rootstocks (St), and comparative phenotyping and transcriptome profiling were performed. Phenotypic analysis showed that Sl/St heterografting induced few phenotypic changes in the tomato scion. A total of 209 upregulated genes were identified in the tomato scion, some of which appear to be involved in starch and sucrose biosynthesis. Sl/St heterografting induced several modifications in the potato rootstocks (St-R), stolon number, stolon length and tuber number decreased significantly, together with an increase in GA3 content of stolon and tuber, compared with self-grafted potato (St-WT). These results indicate that the tomato scion is less effective at producing substances or signals to induce tuberization but promotes stolon development into aerial stems and sprouting. RNA-Seq data analysis showed that 1529 genes were upregulated and 1329 downregulated between St-WT and St-R; some of these genes are involved in plant hormone signal transduction, with GID1-like gibberellin receptor (StGID1) and DELLA protein (StDELLA) being upregulated. Several genes in auxin, abscisic acid and ethylene pathways were differentially expressed as well. Various hormone signals engage in crosstalk to regulate diverse phenotypic events after grafting. This work provides abundant transcriptome profile data and lays a foundation for further research on the molecular mechanisms underlying RNA-based interactions between rootstocks and scions after tomato/potato heterografting.
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Affiliation(s)
- Guanghai Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qiong Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China
| | - Jie Song
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuheng Nie
- Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China
| | - Tingting Wang
- Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China
| | - Han Zhang
- Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China
| | - Huachun Guo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China
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18
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Song S, Tan B, Dong X, Yang Q, Chi S, Liu H, Zhang H, Zhang S. Molecular cloning, characterization and expression analysis of ARMC6, ARMC7, ARMC8 from Pacific white shrimp, Litopenaeus vannamei. Gene 2019; 682:50-66. [PMID: 30292870 DOI: 10.1016/j.gene.2018.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/30/2018] [Accepted: 10/04/2018] [Indexed: 10/28/2022]
Abstract
Armadillo repeat-containing proteins (ARMCs) comprise a large family that is widely distributed in eukaryotes and plays prominent roles in cell-cell adhesion, intracellular signaling, and cytoskeletal regulation. In this study, three ARMC genes, termed LvARMC6, LvARMC7 and LvARMC8, were identified and characterized from Litopenaeus vannamei. The complete cDNAs open reading frames (ORF) of LvARMC6, LvARMC7, and LvARMC8 (GenBank accession no. MG735126, MG728109 and KX058562) were 1410 bp, 570 bp and 2046 bp, encoding 469, 189, and 681 amino acids, respectively. Topology analysis indicated that three ARM domains were present in LvARMC6, one in LvARMC7 and six in LvARMC8. The identities of all the three LvARMCs with other species were between 50% and 71%. Phylogenetic analysis illustrated that different subtype of ARMCs formed their own separate branches and LvARMCs were placed in branch of invertebrates respectively with strong bootstrap support. The constitutive expressions of LvARMCs were confirmed by real-time quantitative PCR. LvARMC6, LvARMC7 and LvARMC8 were expressed highest in heart, gills and epithelium, respectively. After challenge with either white spot syndrome virus (WSSV), Vibrio parahemolyticus, or Staphylococcus aureus, all of the LvARMCs demonstrated differential expression profiles in hemocytes, hepatopancreas, intestine and gills. Taken together, our results suggest that LvARMCs may play a role in the innate immune defense against pathogenic viral and bacterial infections of L. vannamei.
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Affiliation(s)
- Shougang Song
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Beiping Tan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, PR China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, PR China
| | - Xiaohui Dong
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, PR China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, PR China
| | - Qihui Yang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, PR China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, PR China
| | - Shuyan Chi
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, PR China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, PR China
| | - Hongyu Liu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, PR China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, PR China
| | - Haitao Zhang
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, PR China; The Research Center of Guangdong Evergreen Feed Industry Co., Ltd., Zhanjiang 524022, PR China
| | - Shuang Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, PR China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, PR China.
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19
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Li M, Wang X, Li C, Li H, Zhang J, Ye Z. Silencing GRAS2 reduces fruit weight in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:498-513. [PMID: 29359472 DOI: 10.1111/jipb.12636] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
GRAS family transcription factors are involved in multiple biological processes in plants. Here, we report that GRAS2 plays a vital role in regulating fruit weight in tomato (Solanum lycopersicum). We establish that the expression of GRAS2 was elevated in ovaries and maintained at a constant level in fertilized ovules. Reduction of GRAS2 expression in transgenic plants reduced fruit weight through modulating ovary growth and cell size. At the metabolic level, downregulation of GRAS2 decreased activities of the gibberellic acid biosynthesis and signal transduction pathways, leading to insufficient levels of active gibberellic acid during the initial ovary development of tomato. Moreover, genotypic diversity of GRAS2 was consistent with the molecular basis of fruit weight evolution, suggesting that GRAS2 contributes to the molecular basis of the evolution of fruit weight in tomato. Collectively, these findings enhance our understanding of GRAS2 functions, in fruit development of tomato, and demonstrate a strong association between the GRAS gene family and fruit development.
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Affiliation(s)
- Miao Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Changxing Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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20
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Mandal A, Mishra AK, Dulani P, Muthamilarasan M, Shweta S, Prasad M. Identification, characterization, expression profiling, and virus-induced gene silencing of armadillo repeat-containing proteins in tomato suggest their involvement in tomato leaf curl New Delhi virus resistance. Funct Integr Genomics 2017; 18:101-111. [PMID: 29250708 DOI: 10.1007/s10142-017-0578-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/08/2017] [Accepted: 12/07/2017] [Indexed: 11/28/2022]
Abstract
Armadillo repeat family is well-characterized in several plant species for their involvement in multiple regulatory processes including growth, development, and stress response. We have previously shown a three-fold higher expression of ARM protein-encoding in tomato cultivar tolerant to tomato leaf curl New Delhi virus (ToLCNDV) compared to susceptible cultivar upon virus infection. This suggests the putative involvement of ARM proteins in defense response against virus infection; however, no comprehensive investigation has been performed to address this inference. In the present study, we have identified a total of 46 ARM-repeat proteins (SlARMs), and 41 U-box-containing proteins (SlPUBs) in tomato. These proteins and their corresponding genes were studied for their physicochemical properties, gene structure, domain architecture, chromosomal localization, phylogeny, and cis-regulatory elements in the upstream promoter region. Expression profiling of candidate genes in response to ToLCNDV infection in contrasting tomato cultivars showed significant upregulation of SlARM18 in the tolerant cultivar. Virus-induced gene silencing of SlARM18 in the tolerant tomato cultivar conferred susceptibility, which suggests the involvement of this gene in resistance mechanism. Further studies are underway to functionally characterize SlARM18 to delineate its precise role in defense mechanism.
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Affiliation(s)
- Arunava Mandal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Awdhesh Kumar Mishra
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Priya Dulani
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | | | - Shweta Shweta
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
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21
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Zhang M, Zhang GQ, Kang HH, Zhou SM, Wang W. TaPUB1, a Putative E3 Ligase Gene from Wheat, Enhances Salt Stress Tolerance in Transgenic Nicotiana benthamiana. PLANT & CELL PHYSIOLOGY 2017; 58:1673-1688. [PMID: 29016965 DOI: 10.1093/pcp/pcx101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/15/2017] [Indexed: 05/25/2023]
Abstract
High salinity is one of the most severe environmental stresses and limits the growth and yield of diverse crop plants. We isolated a gene named TaPUB1 from wheat (Triticum aestivum L. cv HF9703) that encodes a novel protein containing a U-box domain, the precursor RNA processing 19p (Prp19) superfamily and WD-40 repeats. Real-time reverse transcription-PCR analysis showed that TaPUB1 transcript accumulation was up-regulated by high salinity, drought and phytohormones, suggesting that it plays a role in the abiotic-related defense response. We overexpressed TaPUB1 in Nicotiana benthamiana to evaluate the function of TaPUB1 in the regulation of the salt stress response. Transgenic N. benthamiana plants (OE) with constitutively overexpressed TaPUB1 under the control of the Cauliflower mosaic virus 35S (CaMV 35S) promoter exhibited a higher germination rate, less growth inhibition, less Chl loss and higher photosynthetic capacity than wild-type (WT) plants under salt stress conditions. These results demonstrated the increased tolerance of OE plants to salt stress compared with the WT. The OE plants had lower osmotic potential (OP), reduced Na+ toxicity and less reactive oxygen species accumulation compared with the WT, which may be related to their higher level of osmolytes, lower Na+/K+ ratio and higher antioxidant enzyme activities under salt stress conditions. Consistent with these results, the up-regulated expression of osmic- and antioxidant-related genes in OE plants indicated a role for TaPUB1 in plant salt tolerance.
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Affiliation(s)
- Meng Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
- Collaborative Innovation Center, Jining Medical University, Jining, Shandong 272067, PR China
| | - Guang-Qiang Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Han-Han Kang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Shu-Mei Zhou
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
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22
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Liu F, Wang Y, Ding Z, Zhao L, Xiao J, Wang L, Ding S. Transcriptomic analysis of flower development in tea (Camellia sinensis (L.)). Gene 2017; 631:39-51. [PMID: 28844668 DOI: 10.1016/j.gene.2017.08.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 07/08/2017] [Accepted: 08/23/2017] [Indexed: 01/07/2023]
Abstract
Flowering is a critical and complicated process in plant development, involving interactions of numerous endogenous and environmental factors, but little is known about the complex network regulating flower development in tea plants. In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptomic analysis assembles gene-related information involved in reproductive growth of C. sinensis. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction were enriched among the DEGs. Furthermore, 207 flowering-associated unigenes were identified from our database. Some transcription factors, such as WRKY, ERF, bHLH, MYB and MADS-box were shown to be up-regulated in floral transition, which might play the role of progression of flowering. Furthermore, 14 genes were selected for confirmation of expression levels using quantitative real-time PCR (qRT-PCR). The comprehensive transcriptomic analysis presents fundamental information on the genes and pathways which are involved in flower development in C. sinensis. Our data also provided a useful database for further research of tea and other species of plants.
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Affiliation(s)
- Feng Liu
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China.
| | - Lei Zhao
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - Jun Xiao
- School of Biological Science and Winery Engineering, Taishan University, Taian 271021, China
| | - Linjun Wang
- Fruit Tree and Tea Workstation of Weihai City, 264200, China
| | - Shibo Ding
- Rizhao Tea Research Institute of Shandong, Rizhao, Shandong 276800, China
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Wang N, Liu Y, Cong Y, Wang T, Zhong X, Yang S, Li Y, Gai J. Genome-Wide Identification of Soybean U-Box E3 Ubiquitin Ligases and Roles of GmPUB8 in Negative Regulation of Drought Stress Response in Arabidopsis. PLANT & CELL PHYSIOLOGY 2016; 57:1189-209. [PMID: 27057003 DOI: 10.1093/pcp/pcw068] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 03/13/2016] [Indexed: 05/05/2023]
Abstract
Plant U-box (PUB) E3 ubiquitin ligases play important roles in hormone signaling pathways and response to abiotic stresses, but little is known about them in soybean, Glycine max. Here, we identified and characterized 125 PUB genes from the soybean genome, which were classified into eight groups according to their protein domains. Soybean PUB genes (GmPUB genes) are broadly expressed in many tissues and are a little more abundant in the roots than in the other tissues. Nine GmPUB genes, GmPUB1-GmPUB9, showed induced expression patterns by drought, and the expression of GmPUB8 was also induced by exogenous ABA and NaCl. GmPUB8 was localized to post-Golgi compartments, interacting with GmE2 protein as demonstrated by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) experiments, and showed E3 ubiquitin ligase activity by in vitro ubiquitination assay. Heterogeneous overexpression of GmPUB8 in Arabidopsis showed decreased drought tolerance, enhanced sensitivity with respect to osmotic and salt stress inhibition of seed germination and seedling growth, and inhibited ABA- and mannitol-mediated stomatal closure. Eight drought stress-related genes were less induced in GmPUB8-overexpressing Arabidopsis after drought treatment compared with the wild type and the pub23 mutant. Taken together, our results suggested that GmPUB8 might negatively regulate plant response to drought stress. In addition, Y2H and BiFC showed that GmPUB8 interacted with soybean COL (CONSTANS LIKE) protein. GmPUB8-overexpressing Arabidopsis flowered earlier under middle- and short-day conditions but later under long-day conditions, indicating that GmPUB8 might regulate flowering time in the photoperiod pathway. This study helps us to understand the functions of PUB E3 ubiquitin ligases in soybean.
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Affiliation(s)
- Ning Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yaping Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yahui Cong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiujuan Zhong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Shouping Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Zhu Y, Li Y, Fei F, Wang Z, Wang W, Cao A, Liu Y, Han S, Xing L, Wang H, Chen W, Tang S, Huang X, Shen Q, Xie Q, Wang X. E3 ubiquitin ligase gene CMPG1-V from Haynaldia villosa L. contributes to powdery mildew resistance in common wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:154-68. [PMID: 26287740 DOI: 10.1111/tpj.12966] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 08/07/2015] [Accepted: 08/11/2015] [Indexed: 05/20/2023]
Abstract
Powdery mildew is one of the most devastating wheat fungal diseases. A diploid wheat relative, Haynaldia villosa L., is highly resistant to powdery mildew, and its genetic resource of resistances, such as the Pm21 locus, is now widely used in wheat breeding. Here we report the cloning of a resistance gene from H. villosa, designated CMPG1-V, that encodes a U-box E3 ubiquitin ligase. Expression of the CMPG1-V gene was induced in the leaf and stem of H. villosa upon inoculation with Blumeria graminis f. sp. tritici (Bgt) fungus, and the presence of Pm21 is essential for its rapid induction of expression. CMPG1-V has conserved key residues for E3 ligase, and possesses E3 ligase activity in vitro and in vivo. CMPG1-V is localized in the nucleus, endoplasmic reticulum, plasma membrane and partially in trans-Golgi network/early endosome vesicles. Transgenic wheat over-expressing CMPG1-V showed improved broad-spectrum powdery mildew resistance at seedling and adult stages, associated with an increase in expression of salicylic acid-responsive genes, H2 O2 accumulation, and cell-wall protein cross-linking at the Bgt infection sites, and the expression of CMPG1-V in H. villosa was increased when treated with salicylic acid, abscisic acid and H2 O2 . These results indicate the involvement of E3 ligase in defense responses to Bgt fungus in wheat, particularly in broad-spectrum disease resistance, and suggest association of reactive oxidative species and the phytohormone pathway with CMPG1-V-mediated powdery mildew resistance.
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Affiliation(s)
- Yanfei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Yingbo Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Fei Fei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Zongkuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Wei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Aizhong Cao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Yuan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Shuang Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Liping Xing
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Wei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Sanyuan Tang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiahe Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qianhua Shen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
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Luo Q, Li Y, Wang W, Fei X, Deng X. Genome-wide survey and expression analysis of Chlamydomonas reinhardtii U-box E3 ubiquitin ligases (CrPUBs) reveal a functional lipid metabolism module. PLoS One 2015; 10:e0122600. [PMID: 25822994 PMCID: PMC4378952 DOI: 10.1371/journal.pone.0122600] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/11/2015] [Indexed: 11/18/2022] Open
Abstract
E3 ubiquitin ligases determine the substrate specificity of ubiquitination. Plant U-box (PUB) E3 ligases, with a typical 70-amino acid U-box domain, participate in plant developmental processes and environmental responses. Thus far, 64 PUB proteins have been identified in Arabidopsis and 77 PUB proteins have been identified in Oryza. However, detailed studies on U-box genes in the model microalgae Chlamydomonas reinhardtii are lacking. Here, we present a comprehensive analysis of the genes encoding U-box family proteins in C. reinhardtii. Following BLASTP analysis, 30 full-length U-box genes were identified in the C. reinhardtii genome sequence. Bioinformatics analyses of CrPUB genes were performed to characterize the phylogenetic relationships, chromosomal locations and gene structures of each member. The 30 identified CrPUB proteins are clustered into 3 distinct subfamilies, and the genes for these proteins are unevenly distributed among 14 chromosomes. Furthermore, the quantitative real-time RT-PCR or semi-quantitative RT-PCR analysis of 30 CrPUB mRNA abundances under nitrogen starvation showed that 18 CrPUB genes were induced by N starvation and that 7 genes were repressed in the N-poor environment. We selected five CrPUB genes exhibiting marked changes in expression under N-free conditions for further analysis in RNAi experiments and examined the oil content of these gene-silenced transgenic strains. The silencing of CrPUB5 and CrPUB14, which are typically down-regulated under N starvation, induced 9.8%-45.0% and 14.4%-61.8% lipid accumulation, respectively. In contrast, the silencing of CrPUB11, CrPUB23 and CrPUB28, which are markedly up-regulated under N-free conditions, decreased the lipid content by 5.5%-27.8%, 8.1%-27.3% and 6.6%-27.9%, respectively. These results provide a useful reference for the identification and functional analysis of this gene family and fundamental information for microalgae lipid metabolism research.
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Affiliation(s)
- Qiulan Luo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Yajun Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Wenquan Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Xiaowen Fei
- School of Science, Hainan Medical College, Haikou, 571101, China
| | - Xiaodong Deng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
- * E-mail:
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26
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Wang J, Qu B, Dou S, Li L, Yin D, Pang Z, Zhou Z, Tian M, Liu G, Xie Q, Tang D, Chen X, Zhu L. The E3 ligase OsPUB15 interacts with the receptor-like kinase PID2 and regulates plant cell death and innate immunity. BMC PLANT BIOLOGY 2015; 15:49. [PMID: 25849162 PMCID: PMC4330927 DOI: 10.1186/s12870-015-0442-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/28/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rice blast disease is one of the most destructive diseases of rice worldwide. We previously cloned the rice blast resistance gene Pid2, which encodes a transmembrane receptor-like kinase containing an extracellular B-lectin domain and an intracellular serine/threonine kinase domain. However, little is known about Pid2-mediated signaling. RESULTS Here we report the functional characterization of the U-box/ARM repeat protein OsPUB15 as one of the PID2-binding proteins. We found that OsPUB15 physically interacted with the kinase domain of PID2 (PID2K) in vitro and in vivo and the ARM repeat domain of OsPUB15 was essential for the interaction. In vitro biochemical assays indicated that PID2K possessed kinase activity and was able to phosphorylate OsPUB15. We also found that the phosphorylated form of OsPUB15 possessed E3 ligase activity. Expression pattern analyses revealed that OsPUB15 was constitutively expressed and its encoded protein OsPUB15 was localized in cytosol. Transgenic rice plants over-expressing OsPUB15 at early stage displayed cell death lesions spontaneously in association with a constitutive activation of plant basal defense responses, including excessive accumulation of hydrogen peroxide, up-regulated expression of pathogenesis-related genes and enhanced resistance to blast strains. We also observed that, along with plant growth, the cell death lesions kept spreading over the whole seedlings quickly resulting in a seedling lethal phenotype. CONCLUSIONS These results reveal that the E3 ligase OsPUB15 interacts directly with the receptor-like kinase PID2 and regulates plant cell death and blast disease resistance.
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Affiliation(s)
- Jing Wang
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- />Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130 China
| | - Baoyuan Qu
- />State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shijuan Dou
- />College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001 China
| | - Liyun Li
- />College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001 China
| | - Dedong Yin
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhiqian Pang
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- />CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
| | - Zhuangzhi Zhou
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Miaomiao Tian
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Guozhen Liu
- />College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001 China
| | - Qi Xie
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Dingzhong Tang
- />State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xuewei Chen
- />Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130 China
| | - Lihuang Zhu
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
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Navarro C, Cruz-Oró E, Prat S. Conserved function of FLOWERING LOCUS T (FT) homologues as signals for storage organ differentiation. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:45-53. [PMID: 25449726 DOI: 10.1016/j.pbi.2014.10.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 05/24/2023]
Abstract
Due to their high carbohydrate content and relative low farming demands, tuber-bearing species are an important contribution to human dietary needs in many climatic zones, and interest in these staple crops for processed food and other industrial uses is increasing. Over the past years we have seen remarkable advances in our understanding of the signalling mechanisms involved in the differentiation of these organs, partly aided by their conservation with the well-characterized photoperiodic control of flowering in Arabidopsis. Recent studies have led to the identification of members of the FT gene family as major component of the tuber-inducing signal and the characterization of circadian and photoperiodic components involved in the regulation of these genes. A relevant role of microRNAs in the control of storage organ formation has been established, and hormonal balance requirements similar to those controlling shoot branching were shown to be implicated in the activation of stolon meristem cells. Hence, the recent finding that FT controls branching through direct interaction with the TCP factors holds great promise for the identification of genes acting as FT signal integrators in the stolon.
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Affiliation(s)
- Cristina Navarro
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
| | - Eduard Cruz-Oró
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
| | - Salomé Prat
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain.
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Sharma M, Pandey GK. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1218. [PMID: 26793205 PMCID: PMC4707873 DOI: 10.3389/fpls.2015.01218] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants.
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29
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De novo transcriptome assembly and the identification of gene-associated single-nucleotide polymorphism markers in Asian and American ginseng roots. Mol Genet Genomics 2014; 290:1055-65. [PMID: 25527477 DOI: 10.1007/s00438-014-0974-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
We performed de novo transcriptome sequencing for Panax ginseng and Panax quinquefolius accessions using the 454 GS FLX Titanium System and discovered annotation-based genome-wide single-nucleotide polymorphism (SNPs) using next-generation ginseng transcriptome data without reference genome sequence. The comprehensive transcriptome characterization with the mature roots of four ginseng accessions generated 297,170 reads for 'Cheonryang' cultivar, 305,673 reads for 'Yunpoong' cultivar, 311,861 reads for the G03080 breeding line, and 308,313 reads for P. quinquefolius. In transcriptome assembly, the lengths of the sample read were 156.42 Mb for 'Cheonryang', 161.95 Mb for 'Yunpoong', 165.07 Mb for G03080 breeding line, and 166.48 Mb for P. quinquefolius. A total of 97 primer pairs were designed with the homozygous SNP presented in all four accessions. SNP genotyping using high-resolution melting (HRM) analysis was performed to validate the putative SNP markers of 97 primer pairs. Out of the 73 primer pairs, 73 primer pairs amplified the target sequence and 34 primer pairs showed polymorphic melting curves in samples from 11 P. ginseng cultivars and one P. quinquefolius accession. Among the 34 polymorphic HRM-SNP primers, four primers were useful to distinguish ginseng cultivars. In the present study, we demonstrated that de novo transcriptome assembly and mapping analyses are useful in providing four HRM-SNP primer pairs that reliably show a high degree of polymorphism among ginseng cultivars.
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30
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Moses T, Papadopoulou KK, Osbourn A. Metabolic and functional diversity of saponins, biosynthetic intermediates and semi-synthetic derivatives. Crit Rev Biochem Mol Biol 2014; 49:439-62. [PMID: 25286183 PMCID: PMC4266039 DOI: 10.3109/10409238.2014.953628] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 01/11/2023]
Abstract
Saponins are widely distributed plant natural products with vast structural and functional diversity. They are typically composed of a hydrophobic aglycone, which is extensively decorated with functional groups prior to the addition of hydrophilic sugar moieties, to result in surface-active amphipathic compounds. The saponins are broadly classified as triterpenoids, steroids or steroidal glycoalkaloids, based on the aglycone structure from which they are derived. The saponins and their biosynthetic intermediates display a variety of biological activities of interest to the pharmaceutical, cosmetic and food sectors. Although their relevance in industrial applications has long been recognized, their role in plants is underexplored. Recent research on modulating native pathway flux in saponin biosynthesis has demonstrated the roles of saponins and their biosynthetic intermediates in plant growth and development. Here, we review the literature on the effects of these molecules on plant physiology, which collectively implicate them in plant primary processes. The industrial uses and potential of saponins are discussed with respect to structure and activity, highlighting the undoubted value of these molecules as therapeutics.
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Affiliation(s)
- Tessa Moses
- Department of Metabolic Biology, John Innes CentreColney Lane, NorwichUK
| | | | - Anne Osbourn
- Department of Metabolic Biology, John Innes CentreColney Lane, NorwichUK
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31
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Sharma M, Pandey A, Pandey GK. β-catenin in plants and animals: common players but different pathways. FRONTIERS IN PLANT SCIENCE 2014; 5:143. [PMID: 24782881 PMCID: PMC3989760 DOI: 10.3389/fpls.2014.00143] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/25/2014] [Indexed: 05/24/2023]
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32
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Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, Kapoor S, Tyagi AK, Pandey GK. Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development. DNA Res 2014; 21:267-83. [PMID: 24398598 PMCID: PMC4060948 DOI: 10.1093/dnares/dst056] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genes in the Armadillo (ARM)-repeat superfamily encode proteins with a range of developmental and physiological processes in unicellular and multicellular eukaryotes. These 42 amino acid, long tandem repeat-containing proteins have been abundantly recognized in many plant species. Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis. In this study, we performed a computational analysis in the rice genome (Oryza sativa L. subsp. japonica), and identified 158 genes of Armadillo superfamily. Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them. An in-depth analysis of gene expression through microarray and Q-PCR revealed a number of ARM proteins expressing differentially in abiotic stresses and developmental conditions, suggesting a potential roles of this superfamily in development and stress signalling. Comparative phylogenetic analysis between Arabidopsis and rice Armadillo genes revealed a high degree of evolutionary conservation between the orthologues in two plant species. The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection. This genome-wide identification and expression analysis provides a basis for further functional analysis of Armadillo genes under abiotic stress and reproductive developmental condition in the plant lineage.
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Affiliation(s)
- Manisha Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Amarjeet Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Alka Shankar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Amita Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Vinay Baranwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Akhilesh K Tyagi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi 110067, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
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Vogelmann K, Subert C, Danzberger N, Drechsel G, Bergler J, Kotur T, Burmester T, Hoth S. Plasma membrane-association of SAUL1-type plant U-box armadillo repeat proteins is conserved in land plants. FRONTIERS IN PLANT SCIENCE 2014; 5:37. [PMID: 24600457 PMCID: PMC3928556 DOI: 10.3389/fpls.2014.00037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/27/2014] [Indexed: 05/08/2023]
Abstract
Post-translational protein modification plays a pivotal role in the regulation and specific turnover of proteins. One of these important modifications is the ubiquitination of target proteins, which can occur at distinct cellular compartments. At the plasma membrane, ubiquitination regulates the internalization and thus trafficking of membrane proteins such as receptors and channels. The Arabidopsis plant U-box (PUB) armadillo repeat (PUB-ARM) ubiquitin ligase SAUL1 (SENESCENCE-ASSOCIATED UBIQUITIN LIGASE1) is part of the ubiquitination machinery at the plasma membrane. In contrast to most other PUB-ARM proteins, SAUL1 carries additional C-terminal ARM repeats responsible for plasma membrane-association. Here, we demonstrated that the C-terminal ARM repeat domain is also essential and sufficient to mediate plasma membrane-association of the closest Arabidopis paralog AtPUB43. We investigated targeting of PUB-ARM ubiquitin ligases of different plant species to find out whether plasma membrane-association of SAUL1-type PUB-ARM proteins is conserved. Phylogenetic analysis identified orthologs of SAUL1 in these plant species. Intracellular localization of transiently expressed GFP fusion proteins revealed that indeed plasma membrane-association due to additional C-terminal ARM repeats represents a conserved feature of SAUL1-type proteins. Analyses of transgenic Arabidopsis plants overexpressing N-terminally masked or truncated proteins revealed that interfering with the function of SAUL1-type proteins resulted in severe growth defects. Our results suggest an ancient origin of ubiquitination at the plasma membrane in the evolution of land plants.
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Affiliation(s)
- Katja Vogelmann
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Christa Subert
- Department Biologie, Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Nina Danzberger
- Department Biologie, Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Gabriele Drechsel
- Zentrum für Molekularbiologie der Pflanzen, Allgemeine Genetik, Universität TübingenTübingen, Germany
| | - Johannes Bergler
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Tanja Kotur
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Thorsten Burmester
- Stoffwechselphysiologie, Biozentrum Grindel, Universität HamburgHamburg, Germany
| | - Stefan Hoth
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
- *Correspondence: Stefan Hoth, Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststrasse 18, D-22609 Hamburg, Germany e-mail:
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Abstract
E3 ligases comprise a highly diverse and important group of enzymes that act within the 26S ubiquitin proteasome pathway. They facilitate the transfer of ubiquitin moieties to substrate proteins which may be marked for degradation by this step. As such, they serve as central regulators in many cellular and physiological processes in plants. The review provides an update on the multitude of different E3 ligases currently known in plants, and illustrates the central role in plant biology of specific examples.
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Affiliation(s)
- Liyuan Chen
- Plant Stress Physiology, School of Biological Sciences, Abelson 435, PO Box 644236, Washington State University, Pullman, WA 99164-4236, USA
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Upadhyaya HD, Wang YH, Gowda CLL, Sharma S. Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2003-15. [PMID: 23649651 DOI: 10.1007/s00122-013-2113-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/26/2013] [Indexed: 05/20/2023]
Abstract
Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools and to identify genes underlying the traits for molecular breeding, we developed 14,739 SNP markers used to genotype the complete sorghum [Sorghum bicolor (L.) Moench] mini core collection. The collection was evaluated in four rainy and three post-rainy season environments for plant height and maturity. Association analysis identified six marker loci linked to height and ten to maturity in at least two environments with at least two SNPs in each locus. Of these, 14 were in close proximity to previously mapped height/maturity QTL in sorghum. Candidate genes for maturity or plant height close to the marker loci include a sugar transporter (SbSUC9), an auxin response factor (SbARF3), an FLC and FT regulator (SbMED12), and a photoperiod response gene (SbPPR1) for maturity and peroxidase 53, and an auxin transporter (SbLAX4) for plant height. Linkage disequilibrium analysis showed that SbPPR1 and SbARF3 were in regions with reduced sequence variation among early-maturing accessions, suggestive of past purifying selection. We also found a linkage disequilibrium block that existed only among the accessions with short plant height in rainy season environments. The block contains a gene homologous to the Arabidopsis flowering time gene, LUMINIDEPENDENS (LD). Functional LD promotes early maturity while mutation delays maturity, affecting plant height. Previous studies also found reduced sequence variations within this gene. These newly-mapped SNP markers will facilitate further efforts to identify plant height or maturity genes in sorghum.
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Affiliation(s)
- Hari D Upadhyaya
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India
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Wang H, Lu Y, Jiang T, Berg H, Li C, Xia Y. The Arabidopsis U-box/ARM repeat E3 ligase AtPUB4 influences growth and degeneration of tapetal cells, and its mutation leads to conditional male sterility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:511-23. [PMID: 23398263 DOI: 10.1111/tpj.12146] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/29/2013] [Accepted: 02/01/2013] [Indexed: 05/06/2023]
Abstract
Pollen formation is a complex developmental process that has been extensively investigated to unravel underlying fundamental developmental mechanisms and for genetic manipulation of the male-sterility trait for hybrid crop production. Here we describe identification of AtPUB4, a U-box/ARM repeat-containing E3 ubiquitin ligase, as a novel player in male fertility in Arabidopsis. Loss of AtPUB4 function causes hypertrophic growth of the tapetum layer. The Atpub4 mutation also leads to incomplete degeneration of the tapetal cells and strikingly abnormal exine structures of pollen grains. As a result, although the Atpub4 mutant produces viable pollen, the pollen grains adhere to each other and to the remnants of incompletely degenerated tapetal cells, and do not properly disperse from dehisced anthers for successful pollination. We found that the male-sterility phenotype caused by the Atpub4 mutation is temperature-dependent: the mutant plants are sterile when grown at 22°C but are partially fertile at 16°C. Our study also indicates that the AtPUB4-mediated pathway acts in parallel with the brassinosteroid pathway in controlling developmental fates of the tapetal cells to ensure male fertility.
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Affiliation(s)
- Hai Wang
- Department of Biology, Hong Kong Baptist University, 224 Waterloo Rd, Hong Kong, China
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Zhang J, Wu K, Zeng S, Teixeira da Silva JA, Zhao X, Tian CE, Xia H, Duan J. Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development. BMC Genomics 2013; 14:279. [PMID: 23617896 PMCID: PMC3639151 DOI: 10.1186/1471-2164-14-279] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 04/15/2013] [Indexed: 12/25/2022] Open
Abstract
Background Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countries. The control of flowering time is a major bottleneck in the industrialized development of C. sinense. Little is known about the mechanisms responsible for floral development in this orchid. Moreover, genome references for entire transcriptome sequences do not currently exist for C. sinense. Thus, transcriptome and expression profiling data for this species are needed as an important resource to identify genes and to better understand the biological mechanisms of floral development in C. sinense. Results In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptome analysis assembles gene-related information related to vegetative and reproductive growth of C. sinense. Illumina sequencing generated 54,248,006 high quality reads that were assembled into 83,580 unigenes with an average sequence length of 612 base pairs, including 13,315 clusters and 70,265 singletons. A total of 41,687 (49.88%) unique sequences were annotated, 23,092 of which were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Furthermore, 120 flowering-associated unigenes, 73 MADS-box unigenes and 28 CONSTANS-LIKE (COL) unigenes were identified from our collection. In addition, three digital gene expression (DGE) libraries were constructed for the vegetative phase (VP), floral differentiation phase (FDP) and reproductive phase (RP). The specific expression of many genes in the three development phases was also identified. 32 genes among three sub-libraries with high differential expression were selected as candidates connected with flower development. Conclusion RNA-seq and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral development at three development phases of C. sinense. This data could be used as an important resource for investigating the genetics of the flowering pathway and various biological mechanisms in this orchid.
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Affiliation(s)
- Jianxia Zhang
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
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The U-box E3 ubiquitin ligase TUD1 functions with a heterotrimeric G α subunit to regulate Brassinosteroid-mediated growth in rice. PLoS Genet 2013; 9:e1003391. [PMID: 23526892 PMCID: PMC3597501 DOI: 10.1371/journal.pgen.1003391] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 01/31/2013] [Indexed: 11/19/2022] Open
Abstract
Heterotrimeric G proteins are an important group of signaling molecules found in eukaryotes. They function with G-protein-coupled-receptors (GPCRs) to transduce various signals such as steroid hormones in animals. Nevertheless, their functions in plants are not well-defined. Previous studies suggested that the heterotrimeric G protein α subunit known as D1/RGA1 in rice is involved in a phytohormone gibberellin-mediated signaling pathway. Evidence also implicates D1 in the action of a second phytohormone Brassinosteroid (BR) and its pathway. However, it is unclear how D1 functions in this pathway, because so far no partner has been identified to act with D1. In this study, we report a D1 genetic interactor Taihu Dwarf1 (TUD1) that encodes a functional U-box E3 ubiquitin ligase. Genetic, phenotypic, and physiological analyses have shown that tud1 is epistatic to d1 and is less sensitive to BR treatment. Histological observations showed that the dwarf phenotype of tud1 is mainly due to decreased cell proliferation and disorganized cell files in aerial organs. Furthermore, we found that D1 directly interacts with TUD1. Taken together, these results demonstrate that D1 and TUD1 act together to mediate a BR-signaling pathway. This supports the idea that a D1-mediated BR signaling pathway occurs in rice to affect plant growth and development.
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O’Rourke JA, Yang SS, Miller SS, Bucciarelli B, Liu J, Rydeen A, Bozsoki Z, Uhde-Stone C, Tu ZJ, Allan D, Gronwald JW, Vance CP. An RNA-Seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. PLANT PHYSIOLOGY 2013; 161:705-24. [PMID: 23197803 PMCID: PMC3561014 DOI: 10.1104/pp.112.209254] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/21/2012] [Indexed: 05/18/2023]
Abstract
Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.
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Affiliation(s)
- Jamie A. O’Rourke
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - S. Samuel Yang
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Susan S. Miller
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Bruna Bucciarelli
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Junqi Liu
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Ariel Rydeen
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Zoltan Bozsoki
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Claudia Uhde-Stone
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | | | - Deborah Allan
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - John W. Gronwald
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Carroll P. Vance
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
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Zawaski C, Ma C, Strauss SH, French D, Meilan R, Busov VB. PHOTOPERIOD RESPONSE 1 (PHOR1)-like genes regulate shoot/root growth, starch accumulation, and wood formation in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5623-34. [PMID: 22915748 PMCID: PMC3444277 DOI: 10.1093/jxb/ers217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
This study describes functional characterization of two putative poplar PHOTOPERIOD RESPONSE 1 (PHOR1) orthologues. The expression and sequence analyses indicate that the two poplar genes diverged, at least partially, in function. PtPHOR1_1 is most highly expressed in roots and induced by short days, while PtPHOR1_2 is more uniformly expressed throughout plant tissues and is not responsive to short days. The two PHOR1 genes also had distinct effects on shoot and root growth when their expression was up- and downregulated transgenically. PtPHOR1_1 effects were restricted to roots while PtPHOR1_2 had similar effects on aerial and below-ground development. Nevertheless, both genes seemed to be upregulated in transgenic poplars that are gibberellin-deficient and gibberellin-insensitive, suggesting interplay with gibberellin signalling. PHOR1 suppression led to increased starch accumulation in both roots and stems. The effect of PHOR1 suppression on starch accumulation was coupled with growth-inhibiting effects in both roots and shoots, suggesting that PHOR1 is part of a mechanism that regulates the allocation of carbohydrate to growth or storage in poplar. PHOR1 downregulation led to significant reduction of xylem formation caused by smaller fibres and vessels suggesting that PHOR1 likely plays a role in the growth of xylem cells.
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Affiliation(s)
- Christine Zawaski
- School of Forest Resources and Environmental Science, Michigan Technological UniversityHoughton, MI 49931-1295USA
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR 97331-5752USA
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR 97331-5752USA
| | - Darla French
- Department of Forestry and Natural Resources, Purdue UniversityWest Lafayette, IN 47907-2061USA
| | - Richard Meilan
- Department of Forestry and Natural Resources, Purdue UniversityWest Lafayette, IN 47907-2061USA
| | - Victor B. Busov
- School of Forest Resources and Environmental Science, Michigan Technological UniversityHoughton, MI 49931-1295USA
- *To whom correspondence should be addressed: E-mail:
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Phillips SM, Dubery IA, van Heerden H. Molecular characterization of an elicitor-responsive Armadillo repeat gene (GhARM) from cotton (Gossypium hirsutum). Mol Biol Rep 2012; 39:8513-23. [PMID: 22714909 DOI: 10.1007/s11033-012-1706-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/06/2012] [Indexed: 11/28/2022]
Abstract
Only a few Armadillo (ARM) repeat proteins have been characterized in plants where they appear to have diverse functions, including the regulation of defence responses. In this study, the identification, cloning and characterization of a gene, encoding an ARM repeat protein (GhARM), is described. GhARM exists as multiple copies in cotton, with an 1713 bp ORF encoding 570 amino acids. The predicted protein contains three consecutive ARM repeats within an Armadillo-type fold, with no other distinguishing domains. Sequence alignments and phylogenetic analysis revealed that GhARM has a high homology with other ARM proteins in plants. The predicted three dimensional model of GhARM displayed a characteristic right-handed superhelical twist. In silico analysis of the promoter sequence revealed that it contains several defence- and hormone-responsive cis-regulatory elements. Expression of GhARM was significantly down-regulated in response to treatment with a V. dahliae elicitor suggesting that GhARM may function as a negative-regulator of cotton defence signalling against V. dahliae. To date, GhARM is the only ARM repeat gene that has been completely sequenced and characterized in cotton.
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Affiliation(s)
- Sonia M Phillips
- Department of Biochemistry, University of Johannesburg, Kingsway Campus, Auckland Park, 2006, P.O. Box 524, Johannesburg, South Africa.
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Viswanath V, Ma C, Etherington E, Dharmawardhana P, Pearce DW, Rood SB, Busov VB, Strauss SH. Greenhouse and field evaluation of transgenic poplars with modified gibberellin metabolism and signaling genes. BMC Proc 2011. [PMCID: PMC3239892 DOI: 10.1186/1753-6561-5-s7-o22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Altered germination and subcellular localization patterns for PUB44/SAUL1 in response to stress and phytohormone treatments. PLoS One 2011; 6:e21321. [PMID: 21738636 PMCID: PMC3124495 DOI: 10.1371/journal.pone.0021321] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 05/24/2011] [Indexed: 11/25/2022] Open
Abstract
Background In plants, the ubiquitin-proteasome system is emerging as a significant regulatory system throughout the plant lifecycle. The ubiquitination of a target protein requires the sequential actions of the E1, E2 and E3 enzymes, with the latter E3 enzyme conferring target selection in this process. There are a large number of predicted E3 enzymes in plant genomes, and very little is known about the functions of many of these predicted genes. Here we report here an analysis of two closely-related members of the Arabidopsis Plant U-box (PUB) family of E3 ubiquitin ligases, PUB43 and PUB44. Principal Findings Homozygous pub44/pub44 mutant seedlings were found displayed a seedling lethal phenotype and this corresponded with widespread cell death lesions throughout the cotyledons and roots. Interestingly, heterozygous PUB44/pub44 seedlings were wild-type in appearance yet displayed intermediate levels of cell death lesions in comparison to pub44/pub44 seedlings. In contrast, homozygous pub43/pub43 mutants were viable and did not show any signs of cell death despite the PUB43 gene being more highly expressed than PUB44. The PUB44 mutants are not classical lesion mimic mutants as they did not have increased resistance to plant pathogens. We also observed increased germination rates in mutant seeds for both PUB44 and PUB43 under inhibitory concentrations of abscisic acid. Finally, the subcellular localization of PUB44 was investigated with transient expression assays in BY-2 cells. Under varying conditions, PUB44 was observed to be localized to the cytoplasm, plasma membrane, or nucleus. Conclusions Based on mutant plant analyses, the Arabidopsis PUB43 and PUB44 genes are proposed to function during seed germination and early seedling growth. Given PUB44's ability to shuttle from the nucleus to the plasma membrane, PUB44 may be active in different subcellular compartments as part of these biological functions.
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Merkle T. Nucleo-cytoplasmic transport of proteins and RNA in plants. PLANT CELL REPORTS 2011; 30:153-76. [PMID: 20960203 PMCID: PMC3020307 DOI: 10.1007/s00299-010-0928-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 09/30/2010] [Indexed: 05/19/2023]
Abstract
Transport of macromolecules between the nucleus and the cytoplasm is an essential necessity in eukaryotic cells, since the nuclear envelope separates transcription from translation. In the past few years, an increasing number of components of the plant nuclear transport machinery have been characterised. This progress, although far from being completed, confirmed that the general characteristics of nuclear transport are conserved between plants and other organisms. However, plant-specific components were also identified. Interestingly, several mutants in genes encoding components of the plant nuclear transport machinery were investigated, revealing differential sensitivity of plant-specific pathways to impaired nuclear transport. These findings attracted attention towards plant-specific cargoes that are transported over the nuclear envelope, unravelling connections between nuclear transport and components of signalling and developmental pathways. The current state of research in plants is summarised in comparison to yeast and vertebrate systems, and special emphasis is given to plant nuclear transport mutants.
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Affiliation(s)
- Thomas Merkle
- Faculty of Biology, Institute for Genome Research and Systems Biology, University of Bielefeld, 33594 Bielefeld, Germany.
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Park JJ, Yi J, Yoon J, Cho LH, Ping J, Jeong HJ, Cho SK, Kim WT, An G. OsPUB15, an E3 ubiquitin ligase, functions to reduce cellular oxidative stress during seedling establishment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:194-205. [PMID: 21223385 DOI: 10.1111/j.1365-313x.2010.04416.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The plant U-box (PUB) protein functions as an E3 ligase to poly-ubiquitinate a target protein for its degradation or post-translational modification. Here, we report functional roles for OsPUB15, which encodes a cytosolic U-box protein in the class-II PUB family. Self-ubiquitination assays showed that bacterially expressed MBP-OsPUB15 protein has E3 ubiquitin ligase activity. A T-DNA insertional mutation in OsPUB15 caused severe growth retardation and a seedling-lethal phenotype. Mutant seeds did not produce primary roots, and their shoot development was significantly delayed. Transgenic plants expressing the OsPUB15 antisense transcript phenocopied these mutant characters. The abnormal phenotypes were partially rescued by two antioxidants, catechin and ascorbic acid. Germinating seeds in the dark also recovered the rootless defect. Levels of H2O2 and oxidized proteins were higher in the knock-out mutant compared with the wild type. OsPUB15 transcript levels were increased upon H2O2, salt and drought stresses; plants overexpressing the gene grew better than the wild type under high salinity. These results indicate that PUB15 is a regulator that reduces reactive oxygen species (ROS) stress and cell death.
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Affiliation(s)
- Jong-Jin Park
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
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Delis C, Krokida A, Georgiou S, Peña-Rodríguez LM, Kavroulakis N, Ioannou E, Roussis V, Osbourn AE, Papadopoulou KK. Role of lupeol synthase in Lotus japonicus nodule formation. THE NEW PHYTOLOGIST 2011; 189:335-46. [PMID: 20868395 DOI: 10.1111/j.1469-8137.2010.03463.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
• Triterpenes are plant secondary metabolites, derived from the cyclization of 2,3-oxidosqualene by oxidosqualene cyclases (OSCs). Here, we investigated the role of lupeol synthase, encoded by OSC3, and its product, lupeol, in developing roots and nodules of the model legume Lotus japonicus. • The expression patterns of OSC3 in different developmental stages of uninfected roots and in roots infected with Mesorhizobium loti were determined. The tissue specificity of OSC3 expression was analysed by in situ hybridization. Functional analysis, in which transgenic L. japonicus roots silenced for OSC3 were generated, was performed. The absence of lupeol in the silenced plant lines was determined by GC-MS. • The expression of ENOD40, a marker gene for nodule primordia initiation, was increased significantly in the OSC3-silenced plant lines, suggesting that lupeol influences nodule formation. Silenced plants also showed a more rapid nodulation phenotype, consistent with this. Exogenous application of lupeol to M. loti-infected wild-type plants provided further evidence for a negative regulatory effect of lupeol on the expression of ENOD40. • The synthesis of lupeol in L. japonicus roots and nodules can be solely attributed to OSC3. Taken together, our data suggest a role for lupeol biosynthesis in nodule formation through the regulation of ENOD40 gene expression.
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Affiliation(s)
- Costas Delis
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
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47
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Drechsel G, Bergler J, Wippel K, Sauer N, Vogelmann K, Hoth S. C-terminal armadillo repeats are essential and sufficient for association of the plant U-box armadillo E3 ubiquitin ligase SAUL1 with the plasma membrane. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:775-85. [PMID: 20956359 PMCID: PMC3003819 DOI: 10.1093/jxb/erq313] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 09/13/2010] [Indexed: 05/21/2023]
Abstract
Ubiquitination plays important roles in plant growth and development. Whereas ubiquitin-dependent protein degradation and modulation in the cytoplasm and nucleus are well established in plants, ubiquitination events mediated by E3 ubiquitin ligases at the plasma membrane are largely unknown. Here, it is demonstrated that the suppressor of premature senescence and cell death SENESCENCE-ASSOCIATED UBIQUITIN LIGASE 1 (SAUL1), a plant U-box armadillo repeat (PUB-ARM) E3 ubiquitin ligase, localizes at the plasma membrane. Among the members of the PUB-ARM protein family, this localization is unique to SAUL1 and its two closest homologues. A novel armadillo repeat domain was identified at the SAUL1 C-terminus that directs specific association with the plasma membrane and is crucial for SAUL1 function in vivo. The data suggest that a small subgroup of PUB-ARM proteins including SAUL1 have functions at the plasma membrane probably by modifying target proteins by ubiquitination.
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Affiliation(s)
| | | | | | | | | | - Stefan Hoth
- To whom correspondence should be addressed. E-mail:
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Li B, Xu W, Xu Y, Zhang Y, Wang T, Bai Y, Han C, Zhang A, Xu Z, Chong K. Integrative study on proteomics, molecular physiology, and genetics reveals an accumulation of cyclophilin-like protein, TaCYP20-2, leading to an increase of Rht protein and dwarf in a novel GA-insensitive mutant (gaid) in Wheat. J Proteome Res 2010; 9:4242-53. [PMID: 20527814 DOI: 10.1021/pr100560v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dwarfism with a "Green Revolution" phenotype is a desirable agronomic trait for crop cultivators as associated with increased yield, improved lodging resistance and higher fertility. Few dwarf mutants of hexaploid wheat (Triticum aestivum), except for Rht-B1 and Rht-D1, have been identified. Here, we report on a novel dwarf natural wheat mutant, which is identified as a gibberellic acid (GA)-insensitive dwarf (gaid) mutant for its semidominant blocking GA signaling pathway. Physiological and morphological investigations showed that the shoot elongation of gaid mutant plants is insensitive to exogenous GA(3) treatment. Expression of TaGA20ox1 in the gaid mutant was enhanced after GA(3) treatment. The short stem of gaid resulted from reduced cell elongation. The transcript expression of Rht, encoding a DELLA protein negatively regulating GA signaling in wheat, displayed similar patterns between gaid and wild type. Contrarily, the degradation of Rht induced by GA(3) treatment was suppressed in the mutant. 2-DE screening assay showed that the expression patterns of the mutant, as well as their responses to GA(3), were changed as compared with the wild type. In the mutant, one of enriched proteins was identified as TaCYP20-2 by Q-TOF MS approach and immunoblotting. TaCYP20-2 was localized in the chloroplast and cell plasma membrane. The transcript of TaCYP20-2 was higher in gaid than that in wild type. Molecular genetic data showed that overexpression of TaCYP20-2 in wheat resulted in a dwarfism similar to that of gaid. It suggests that TaCYP20-2 is a new member that regulates wheat stem development mediated by DELLA protein degradation of GA signaling pathway.
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Affiliation(s)
- Beibei Li
- Research Center for Molecular Developmental Biology, Key Lab of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, CAS, Beijing, China
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Gu Y, Somerville C. Cellulose synthase interacting protein: a new factor in cellulose synthesis. PLANT SIGNALING & BEHAVIOR 2010; 5:1571-4. [PMID: 21150290 PMCID: PMC3115106 DOI: 10.4161/psb.5.12.13621] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 09/14/2010] [Indexed: 05/17/2023]
Abstract
Cellulose is the most abundant biopolymer on earth. The great abundance of cellulose places it at the forefront as a primary source of biomass for renewable biofuels. However, the knowledge of how plant cells make cellulose remains very rudimentary. Cellulose microfibrils are synthesized at the plasma membrane by hexameric protein complexes, also known as cellulose synthase complexes. The only known components of cellulose synthase complexes are cellulose synthase (CESA) proteins until the recent identification of a novel component. CSI1, which encodes CESA interacting protein 1 (CSI1) in Arabidopsis. CSI1, as the first non-CESA proteins associated with cellulose synthase complexes, opens up many opportunities.
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Affiliation(s)
- Ying Gu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
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Park GG, Park JJ, Yoon J, Yu SN, An G. A RING finger E3 ligase gene, Oryza sativa Delayed Seed Germination 1 (OsDSG1), controls seed germination and stress responses in rice. PLANT MOLECULAR BIOLOGY 2010; 74:467-78. [PMID: 20878348 DOI: 10.1007/s11103-010-9687-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 09/03/2010] [Indexed: 05/02/2023]
Abstract
Seed germination is an important character for plant growth and seed quality. We identified a rice mutant that was delayed in its germination. There, T-DNA was inserted into Oryza sativa Delayed Seed Germination 1 (OsDSG1), causing a recessive null mutation. Overexpression of the gene enhanced seed germination. OsDSG1 is most similar to Arabidopsis AIP2, an E3 ligase targeting ABI3.Yeast two-hybrid experiments showed that our OsDSG1 binds to OsABI3, indicating that OsDSG1 is a rice ortholog of AIP2. Self-ubiquitination assay indicated that bacterially expressed OsDSG1 protein has E3 ubiquitin ligase activity. Real-time PCR analysis revealed that OsDSG1 was expressed in leaves and roots, and strongly in developing seeds. In addition to the delayed-germination phenotype, mutant plants were shorter and had greater tolerance to high-salt and drought stresses. In the osdsg1 mutant, transcript levels of ABA signaling genes and ABA responsive genes were significantly increased. By contrast, expressions of OsGAMYB and its downstream genes that encode hydrolytic enzymes were markedly reduced. These observations support that OsDSG1 is a major regulator of ABA signaling in germinating seeds. Finally, we observed that the germination rates of various rice cultivars depended upon the transcript levels of OsDSG1 and other ABA-signaling genes.
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Affiliation(s)
- Gi-Gyeong Park
- Crop Biotech Institute & Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea
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