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Yao S, Xie M, Hu M, Cui X, Wu H, Li X, Hu P, Tong C, Yu X. Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1118339. [PMID: 37021309 PMCID: PMC10067767 DOI: 10.3389/fpls.2023.1118339] [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: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.
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Affiliation(s)
- Shengli Yao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - XiaoBo Cui
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haoming Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Xiaohua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Peng Hu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoli Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
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Song J, Fan B, Shao X, Zang Y, Wang D, Min Y. Single-cell transcriptome sequencing atlas of cassava tuberous root. FRONTIERS IN PLANT SCIENCE 2023; 13:1053669. [PMID: 36684718 PMCID: PMC9848496 DOI: 10.3389/fpls.2022.1053669] [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: 09/26/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Single-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites. RESULTS In this study, we sequenced the single-cell transcriptomes at two developmental phases of cassava tuberous roots using the technology known as 10x Genomics (S1, S2). In total, 14,566 cells were grouped into 15 different cell types, primarily based on the marker genes of model plants known to exist. In the pseudotime study, the cell differentiation trajectory was defined, and the difference in gene expression between the two stages on the pseudotime axis was compared. The differentiation process of the vascular tissue and cerebral tissue was identified by the trajectory. We discovered the rare cell type known as the casparian strip via the use of up-regulated genes and pseudotime analysis, and we explained how it differentiates from endodermis. The successful creation of a protoplast isolation technique for organs rich in starch was also described in our study. DISCUSSION Together, we created the first high-resolution single-cell transcriptome atlas of cassava tuberous roots, which made significant advancements in our understanding of how these roots differentiate and develop.
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Affiliation(s)
- Jinjia Song
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Benji Fan
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Xiaodie Shao
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Yuwei Zang
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Dayong Wang
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Yi Min
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
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Pereira Neto LG, Rossini BC, Marino CL, Toorop PE, Silva EAA. Comparative Seeds Storage Transcriptome Analysis of Astronium fraxinifolium Schott, a Threatened Tree Species from Brazil. Int J Mol Sci 2022; 23:ijms232213852. [PMID: 36430327 PMCID: PMC9696909 DOI: 10.3390/ijms232213852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
Astronium fraxinifolium Schott (Anacardiaceae), also known as a 'gonçalo-alves', is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and in the Amazon biomes. In support of ex situ conservation, this work aimed to study two accessions with different longevity (p50) of A. fraxinifolium collected from two different geographic regions, and to evaluate the transcriptome during aging of the seeds in order to identify genes related to seed longevity. Artificial ageing was performed at a constant temperature of 45 °C and 60% relative humidity. RNA was extracted from 100 embryonic axes exposed to control and aging conditions for 21 days. The transcriptome analysis revealed differentially expressed genes such as Late Embryogenesis Abundant (LEA) genes, genes involved in the photosystem, glycine rich protein (GRP) genes, and several transcription factors associated with embryo development and ubiquitin-conjugating enzymes. Thus, these results contribute to understanding which genes play a role in seed ageing, and may serve as a basis for future functional characterization of the seed aging process in A. fraxinifolium.
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Affiliation(s)
| | - Bruno Cesar Rossini
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Correspondence:
| | - Celso Luis Marino
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Departament of Biological and Chemical Sciences, Biosciences Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18618-689, Brazil
| | - Peter E. Toorop
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
| | - Edvaldo Aparecido Amaral Silva
- Departamento de Produção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu 18610-034, Brazil
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Chen WC, Wang Q, Cao TJ, Lu S. UBC19 is a new interacting protein of ORANGE for its nuclear localization in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2021; 16:1964847. [PMID: 34405771 PMCID: PMC8525976 DOI: 10.1080/15592324.2021.1964847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
ORANGE (OR) is a member of the DnaJ-like zinc finger domain-containing protein family, of which all orthologs share a highly conserved quadruple repeat of the CxxCxxxG signatures at their C-termini. Dual subcellular localization and different interacting partner proteins have been reported for OR. In plastids, OR interacts with phytoene synthase, the entry enzyme for carotenoid biosynthesis, to promote chromoplast biogenesis and carotenoid accumulation in non-pigmented tissues. In the nucleus, OR interacts with the eukaryotic release factor eRF1-2 to regulate cell elongation in the petiole, and with the transcription factor TCP14 to repress the expression of Early Light-Induced Proteins (ELIPs) and chloroplast biogenesis in de-etiolating cotyledons. In this study, we demonstrated the E2 ubiquitin-conjugating enzyme UBC19 as a new interacting partner of OR. The lysine58 of OR was found to be ubiquitinated, and OR lost its nuclear localization and the capability in repressing ELIPs when lysine58 was substituted by alanine. Our findings raised the possibility that the ubiquitination by UBC19 is essential for the nuclear localization of OR.
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Affiliation(s)
- Wei-Cai Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Qi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tian-Jun Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shan Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
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Qin T, Tian Q, Wang G, Xiong L. LOWER TEMPERATURE 1 Enhances ABA Responses and Plant Drought Tolerance by Modulating the Stability and Localization of C2-Domain ABA-Related Proteins in Arabidopsis. MOLECULAR PLANT 2019; 12:1243-1258. [PMID: 31102784 DOI: 10.1016/j.molp.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 05/09/2023]
Abstract
Plasma membrane-associated abscisic acid (ABA) signal transduction is an integral part of ABA signaling. The C2-domain ABA-related (CAR) proteins play important roles in the recruitment of ABA receptors to the plasma membrane to facilitate ABA signaling. However, how CAR proteins are regulated remains unclear. In this study, we conducted a genetic screen for mutants with altered leaf transpiration and identified an uncharacterized protein, LOWER TEMPERATURE 1 (LOT1), which regulates the dynamic localization and stability of CAR proteins. The lot1 mutant had a lower leaf temperature as compared with the wild type due to higher transpiration. We found that LOT1 physically interacts with CAR9 , and ABA reduces LOT1-CAR9 interaction in the nucleus, likely via Ca2+, resulting in increased localization of CAR9 to the plasma membrane. We further found that the stability of CAR9 is affected by LOT1 less CAR9 proteins were accumulated and more were ubiquitinated in lot1. While the lot1, car9 and lot1 car9 mutants were hyposensitive to ABA, the hyposensitive phenotype of lot1 could be rescued by CAR9 overexpression. Collectively, our study reveals that LOT1 regulates plant tolerance to drought stress by affecting ABA signaling through regulating the stability and dynamic localization of CAR9.
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Affiliation(s)
- Tao Qin
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China; Texas A&M Agrilife Research Center, Dallas, TX, USA
| | - Qiuzhen Tian
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guifeng Wang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Liming Xiong
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Texas A&M Agrilife Research Center, Dallas, TX, USA; State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Ma Liu Shui, Hong Kong, China.
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6
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Chen H, Yang Q, Chen K, Zhao S, Zhang C, Pan R, Cai T, Deng Y, Wang X, Chen Y, Chu W, Xie W, Zhuang W. Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.). BMC Genomics 2019; 20:392. [PMID: 31113378 PMCID: PMC6528327 DOI: 10.1186/s12864-019-5770-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
Background Peanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortion in peanut, which provides an opportunity to determine the mechanism underlying this important event. MicroRNA (miRNA)-guided target gene regulation is vital to a wide variety of biological processes. However, whether miRNAs participate in peanut embryo abortion under calcium deficiency has yet to be explored. Results In this study, with the assistance of a recently established platform for genome sequences of wild peanut species, we analyzed small RNAs (sRNAs) in early peanut embryos. A total of 29 known and 132 potential novel miRNAs were discovered in 12 peanut-specific miRNA families. Among the identified miRNAs, 87 were differentially expressed during early embryo development under calcium deficiency and sufficiency conditions, and 117 target genes of the differentially expressed miRNAs were identified. Integrated analysis of miRNAs and transcriptome expression revealed 52 differentially expressed target genes of 20 miRNAs. The expression profiles for some differentially expressed targets by gene chip analysis were consistent with the transcriptome sequencing results. Together, our results demonstrate that seed/embryo development-related genes such as TCP3, AP2, EMB2750, and GRFs; cell division and proliferation-related genes such as HsfB4 and DIVARICATA; plant hormone signaling pathway-related genes such as CYP707A1 and CYP707A3, with which abscisic acid (ABA) is involved; and BR1, with which brassinosteroids (BRs) are involved, were actively modulated by miRNAs during early embryo development. Conclusions Both a number of miRNAs and corresponding target genes likely playing key roles in the regulation of peanut embryo abortion under calcium deficiency were identified. These findings provide for the first time new insights into miRNA-mediated regulatory pathways involved in peanut embryo abortion under calcium deficiency. Electronic supplementary material The online version of this article (10.1186/s12864-019-5770-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hua Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Qiang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Kun Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Shanshan Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Chong Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Ronglong Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan
| | - Tiecheng Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Ye Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Yuting Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Wenting Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Wenping Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Weijian Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. .,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. .,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
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Collum TD, Lutton E, Raines CD, Dardick C, Culver JN. Identification of phloem-associated translatome alterations during leaf development in Prunus domestica L. HORTICULTURE RESEARCH 2019; 6:16. [PMID: 30729006 PMCID: PMC6355854 DOI: 10.1038/s41438-018-0092-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 06/01/2023]
Abstract
Phloem plays a fundamental role in plants by transporting hormones, nutrients, proteins, RNAs, and carbohydrates essential for plant growth and development. However, the identity of the underlying phloem genes and pathways remain enigmatic especially in agriculturally important perennial crops, in part, due to the technical difficulty of phloem sampling. Here, we used two phloem-specific promoters and a translating ribosome affinity purification (TRAP) strategy to characterize the phloem translatome during leaf development at 2, 4, and 6 weeks post vernalization in plum (Prunus domestica L.). Results provide insight into the changing phloem processes that occur during leaf development. These processes included the early activation of DNA replication genes that are likely involved in phloem cell division during leaf expansion, as well as the upregulation of phloem genes associated with sink to source conversion, induction of defense processes, and signaling for reproduction. Combined these results reveal the dynamics of phloem gene expression during leaf development and establish the TRAP system as a powerful tool for studying phloem-specific functions and responses in trees.
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Affiliation(s)
- Tamara D. Collum
- Institute for Bioscience and Biotechnology Research, College Park, MD USA
| | - Elizabeth Lutton
- USDA-ARS, Appalachian Fruit Research Laboratory, Kearneysville, WV USA
| | - C. Douglas Raines
- USDA-ARS, Appalachian Fruit Research Laboratory, Kearneysville, WV USA
| | | | - James N. Culver
- Institute for Bioscience and Biotechnology Research, College Park, MD USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD USA
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Jia L, Zhao Q, Chen S. Evolution and expression analysis of the sorghum ubiquitin-conjugating enzyme family. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:236-247. [PMID: 32172767 DOI: 10.1071/fp18184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/02/2018] [Indexed: 06/10/2023]
Abstract
Ubiquitin-conjugating enzymes (UBCs), which catalyse the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. Current knowledge regarding the sorghum (Sorghum bicolor (L.) Moench) ubiquitin-conjugating enzyme (SbUBC) family remains very limited. We identified 53 UBC-encoding genes in the sorghum genome and divided these into 18 groups according to their phylogenetic relationship with Arabidopsis thaliana (L.) Heynh., which was further supported by conserved motif and gene structure analyses. Different expression levels under a variety of abiotic stresses suggested that these might participate in distinct signalling pathways and that they underwent functional divergence during evolution. Furthermore, several SbUBC genes responded to single treatments, and individual SbUBC genes responded to multiple treatments, suggesting that sorghum UBCs may mediate crosstalk among different signalling pathways. Overall, the results provide valuable information for better understanding the classification and putative functions of sorghum UBC-encoding genes.
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Affiliation(s)
- Liqiang Jia
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - QiuFang Zhao
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Shu Chen
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
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Abstract
Nitrogen (N) fertilizer has a major influence on the yield and quality. Understanding and optimising the response of crop plants to nitrogen fertilizer usage is of central importance in enhancing food security and agricultural sustainability. In this study, the analysis of gene regulatory networks reveals multiple genes and biological processes in response to N. Two microarray studies have been used to infer components of the nitrogen-response network. Since they used different array technologies, a map linking the two probe sets to the maize B73 reference genome has been generated to allow comparison. Putative Arabidopsis homologues of maize genes were used to query the Biological General Repository for Interaction Datasets (BioGRID) network, which yielded the potential involvement of three transcription factors (TFs) (GLK5, MADS64 and bZIP108) and a Calcium-dependent protein kinase. An Artificial Neural Network was used to identify influential genes and retrieved bZIP108 and WRKY36 as significant TFs in both microarray studies, along with genes for Asparagine Synthetase, a dual-specific protein kinase and a protein phosphatase. The output from one study also suggested roles for microRNA (miRNA) 399b and Nin-like Protein 15 (NLP15). Co-expression-network analysis of TFs with closely related profiles to known Nitrate-responsive genes identified GLK5, GLK8 and NLP15 as candidate regulators of genes repressed under low Nitrogen conditions, while bZIP108 might play a role in gene activation.
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10
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Ma X, Zhang X, Zhao K, Li F, Li K, Ning L, He J, Xin Z, Yin D. Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Seed Expansion in Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2018; 9:349. [PMID: 29662498 PMCID: PMC5890158 DOI: 10.3389/fpls.2018.00349] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 05/22/2023]
Abstract
Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering (DAF) in two peanut eighth-generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1,082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.
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Affiliation(s)
| | | | | | | | | | | | | | - Zeyu Xin
- *Correspondence: Dongmei Yin, Zeyu Xin,
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11
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Proteome scale identification, classification and structural analysis of iron-binding proteins in bread wheat. J Inorg Biochem 2017; 170:63-74. [DOI: 10.1016/j.jinorgbio.2017.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/23/2017] [Accepted: 02/10/2017] [Indexed: 12/26/2022]
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12
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Wang S, Cao L, Wang H. Arabidopsis ubiquitin-conjugating enzyme UBC22 is required for female gametophyte development and likely involved in Lys11-linked ubiquitination. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3277-88. [PMID: 27069118 PMCID: PMC4892721 DOI: 10.1093/jxb/erw142] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Protein ubiquitination is critical for numerous processes in eukaryotes. The ubiquitin-conjugating enzyme (E2) is required for ubiquitination. The Arabidopsis genome has approximately 37 E2 genes, but in vivo functions for most of them remain unknown. In this study we observed that knockout mutants of Arabidopsis UBC22 had much-reduced silique length and seed number, with nearly 90% of ovules aborted. Analyses revealed that the majority of mutant embryo sacs displayed severe defects and often contained no gamete nuclei. There was no difference between mutant and wild-type Arabidopsis at the megaspore mother cell stage; however, the functional megaspore was either not present or appeared abnormal in a large portion of mutant ovules, suggesting that the defect started with functional megaspore degeneration in the mutants. Degeneration continued during megagametogenesis, such that the percentage of mature embryo sacs without any gamete nuclei was much greater than the percentage of developing ovules without a functional megaspore and, in addition, various abnormalities in megagametogenesis were observed. Additionally, heterozygous plants had only 13.1% of ovules aborted, indicating that the heterozygous sporophytic tissues could affect the development of the mutant female gametophyte. UBC22 is the sole member of an Arabidopsis E2 subfamily, and is more closely related to one type of E2s in animals that catalyzes Lys11-specific ubiquitination. Indeed, our results showed that Arabidopsis UBC22 could catalyze ubiquitin dimer formation in vitro in a Lys11-dependent manner, suggesting that it likely catalyzes Lys11-linked ubiquitination in plants. This study has thus identified one biochemical property of UBC22 and revealed a novel function in female gametophyte development.
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Affiliation(s)
- Sheng Wang
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Ling Cao
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Wang
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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Dong C, Hu H, Jue D, Zhao Q, Chen H, Xie J, Jia L. The banana E2 gene family: Genomic identification, characterization, expression profiling analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:11-24. [PMID: 26940488 DOI: 10.1016/j.plantsci.2016.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/23/2015] [Accepted: 01/13/2016] [Indexed: 05/06/2023]
Abstract
The E2 is at the center of a cascade of Ub1 transfers, and it links activation of the Ub1 by E1 to its eventual E3-catalyzed attachment to substrate. Although the genome-wide analysis of this family has been performed in some species, little is known about analysis of E2 genes in banana. In this study, 74 E2 genes of banana were identified and phylogenetically clustered into thirteen subgroups. The predicted banana E2 genes were distributed across all 11 chromosomes at different densities. Additionally, the E2 domain, gene structure and motif compositions were analyzed. The expression of all of the banana E2 genes was analyzed in the root, stem, leaf, flower organs, five stages of fruit development and under abiotic stresses. All of the banana E2 genes, with the exception of few genes in each group, were expressed in at least one of the organs and fruit developments, which indicated that the E2 genes might involve in various aspects of the physiological and developmental processes of the banana. Quantitative RT-PCR (qRT-PCR) analysis identified that 45 E2s under drought and 33 E2s under salt were induced. To the best of our knowledge, this report describes the first genome-wide analysis of the banana E2 gene family, and the results should provide valuable information for understanding the classification, cloning and putative functions of this family.
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Affiliation(s)
- Chen Dong
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Huigang Hu
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Dengwei Jue
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Qiufang Zhao
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Hongliang Chen
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Jianghui Xie
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Liqiang Jia
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China.
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Jue D, Sang X, Lu S, Dong C, Zhao Q, Chen H, Jia L. Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize. PLoS One 2015; 10:e0143488. [PMID: 26606743 PMCID: PMC4659669 DOI: 10.1371/journal.pone.0143488] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ubiquitination is a post-translation modification where ubiquitin is attached to a substrate. Ubiquitin-conjugating enzymes (E2s) play a major role in the ubiquitin transfer pathway, as well as a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). METHODOLOGY/PRINCIPAL FINDINGS In the present study, a total of 75 putative ZmUBC genes have been identified and located in the maize genome. Phylogenetic analysis revealed that ZmUBC proteins could be divided into 15 subfamilies, which include 13 ubiquitin-conjugating enzymes (ZmE2s) and two independent ubiquitin-conjugating enzyme variant (UEV) groups. The predicted ZmUBC genes were distributed across 10 chromosomes at different densities. In addition, analysis of exon-intron junctions and sequence motifs in each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Tissue expression analysis indicated that most ZmUBC genes were expressed in at least one of the tissues, indicating that these are involved in various physiological and developmental processes in maize. Moreover, expression profile analyses of ZmUBC genes under different stress treatments (4°C, 20% PEG6000, and 200 mM NaCl) and various expression patterns indicated that these may play crucial roles in the response of plants to stress. CONCLUSIONS Genome-wide identification, chromosome organization, gene structure, evolutionary and expression analyses of ZmUBC genes have facilitated in the characterization of this gene family, as well as determined its potential involvement in growth, development, and stress responses. This study provides valuable information for better understanding the classification and putative functions of the UBC-encoding genes of maize.
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Affiliation(s)
- Dengwei Jue
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Xuelian Sang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Shengqiao Lu
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530227, China
| | - Chen Dong
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Qiufang Zhao
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Hongliang Chen
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Liqiang Jia
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
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15
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E Z, Zhang Y, Li T, Wang L, Zhao H. Characterization of the Ubiquitin-Conjugating Enzyme Gene Family in Rice and Evaluation of Expression Profiles under Abiotic Stresses and Hormone Treatments. PLoS One 2015; 10:e0122621. [PMID: 25902049 PMCID: PMC4406754 DOI: 10.1371/journal.pone.0122621] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/23/2015] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin-conjugating enzyme E2s (UBCs), which catalyze the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. However, little is known about the knowledge of UBC gene family in rice. In this study, a total of 39 UBC encoding genes, which all contained an UBC domain with a cysteine active site, were identified in the rice genome. These were classified into fifteen distinct subfamilies based upon their sequence similarity and phylogenetic relationships. A subset of 19 OsUBC genes exhibited chromosomal duplication; 4 and 15 OsUBC genes were tandemly and segmentally duplicated, respectively. Comprehensive analyses were performed to investigate the expression profiles of OsUBC genes in various stages of vegetative and reproductive development using data from EST, Microarrays, MPSS, and real-time PCR. Many OsUBC genes exhibited abundant and tissue-specific expression patterns. Moreover, 14 OsUBCs were found to be differentially expressed under treatments with drought, or salt stresses. The expression analysis after treatments with IAA, 6-BA, GA and ABA indicated that almost all OsUBC genes were responsive to at least two of the four hormones. Several genes were significantly down-regulated under all of the hormone treatments, and most of the genes reduced by 6-BA were also reduced by GA. This study will facilitate further studies of the OsUBC gene family and provide useful clues for functional validation of OsUBCs in rice.
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Affiliation(s)
- Zhiguo E
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Yuping Zhang
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Tingting Li
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Lei Wang
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Heming Zhao
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
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Callis J. The ubiquitination machinery of the ubiquitin system. THE ARABIDOPSIS BOOK 2014; 12:e0174. [PMID: 25320573 PMCID: PMC4196676 DOI: 10.1199/tab.0174] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The protein ubiquitin is a covalent modifier of proteins, including itself. The ubiquitin system encompasses the enzymes required for catalysing attachment of ubiquitin to substrates as well as proteins that bind to ubiquitinated proteins leading them to their final fate. Also included are activities that remove ubiquitin independent of, or in concert with, proteolysis of the substrate, either by the proteasome or proteases in the vacuole. In addition to ubiquitin encoded by a family of fusion proteins, there are proteins with ubiquitin-like domains, likely forming ubiquitin's β-grasp fold, but incapable of covalent modification. However, they serve as protein-protein interaction platforms within the ubiquitin system. Multi-gene families encode all of these types of activities. Within the ubiquitination machinery "half" of the ubiquitin system are redundant, partially redundant, and unique components affecting diverse developmental and environmental responses in plants. Notably, multiple aspects of biotic and abiotic stress responses require, or are modulated by, ubiquitination. Finally, aspects of the ubiquitin system have broad utility: as components to enhance gene expression or to regulate protein abundance. This review focuses on the ubiquitination machinery: ubiquitin, unique aspects about the synthesis of ubiquitin and organization of its gene family, ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2) and ubiquitin ligases, or E3s. Given the large number of E3s in Arabidopsis this review covers the U box, HECT and RING type E3s, with the exception of the cullin-based E3s.
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Affiliation(s)
- Judy Callis
- Department of Molecular and Cellular Biology, University of California-Davis, Davis CA 95616
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17
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Wang Y, Wang W, Cai J, Zhang Y, Qin G, Tian S. Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. Genome Biol 2014; 15:548. [PMID: 25464976 DOI: 10.1186/preaccept-3895766441330481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. RESULTS Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening. CONCLUSIONS Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
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18
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Wang Y, Wang W, Cai J, Zhang Y, Qin G, Tian S. Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. Genome Biol 2014; 15:548. [PMID: 25464976 PMCID: PMC4269173 DOI: 10.1186/s13059-014-0548-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/18/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. RESULTS Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening. CONCLUSIONS Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
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Affiliation(s)
- Yuying Wang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
| | - Weihao Wang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Jianghua Cai
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Yanrui Zhang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Guozheng Qin
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
| | - Shiping Tian
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
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Chung E, Cho CW, So HA, Kang JS, Chung YS, Lee JH. Overexpression of VrUBC1, a Mung Bean E2 Ubiquitin-Conjugating Enzyme, Enhances Osmotic Stress Tolerance in Arabidopsis. PLoS One 2013; 8:e66056. [PMID: 23824688 PMCID: PMC3688854 DOI: 10.1371/journal.pone.0066056] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/01/2013] [Indexed: 12/02/2022] Open
Abstract
The ubiquitin conjugating enzyme E2 (UBC E2) mediates selective ubiquitination, acting with E1 and E3 enzymes to designate specific proteins for subsequent degradation. In the present study, we characterized the function of the mung bean VrUBC1 gene (Vigna radiata UBC 1). RNA gel-blot analysis showed that VrUBC1 mRNA expression was induced by either dehydration, high salinity or by the exogenous abscisic acid (ABA), but not by low temperature or wounding. Biochemical studies of VrUBC1 recombinant protein and complementation of yeast ubc4/5 by VrUBC1 revealed that VrUBC1 encodes a functional UBC E2. To understand the function of this gene in development and plant responses to osmotic stresses, we overexpressed VrUBC1 in Arabidopsis (Arabidopsis thaliana). The VrUBC1-overexpressing plants displayed highly sensitive responses to ABA and osmotic stress during germination, enhanced ABA- or salt-induced stomatal closing, and increased drought stress tolerance. The expression levels of a number of key ABA signaling genes were increased in VrUBC1-overexpressing plants compared to the wild-type plants. Yeast two-hybrid and bimolecular fluorescence complementation demonstrated that VrUBC1 interacts with AtVBP1 (A. thalianaVrUBC1 Binding Partner 1), a C3HC4-type RING E3 ligase. Overall, these results demonstrate that VrUBC1 plays a positive role in osmotic stress tolerance through transcriptional regulation of ABA-related genes and possibly through interaction with a novel RING E3 ligase.
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Affiliation(s)
- Eunsook Chung
- Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
| | - Chang-Woo Cho
- Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
| | - Hyun-Ah So
- Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
| | - Jee-Sook Kang
- Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
| | - Young Soo Chung
- Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
| | - Jai-Heon Lee
- Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
- * E-mail:
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Zhao Q, Tian M, Li Q, Cui F, Liu L, Yin B, Xie Q. A plant-specific in vitro ubiquitination analysis system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:524-33. [PMID: 23350615 DOI: 10.1111/tpj.12127] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/15/2013] [Accepted: 01/23/2013] [Indexed: 05/23/2023]
Abstract
Protein ubiquitination requires the concerted action of three enzymes: ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). These ubiquitination enzymes belong to an abundant protein family that is encoded in all eukaryotic genomes. Describing their biochemical characteristics is an important part of their functional analysis. It has been recognized that various E2/E3 specificities exist, and that detection of E3 ubiquitination activity in vitro may depend on the recruitment of E2s. Here, we describe the development of an in vitro ubiquitination system based on proteins encoded by genes from Arabidopsis. It includes most varieties of Arabidopsis E2 proteins, which are tested with several RING-finger type E3 ligases. This system permits determination of E3 activity in combination with most of the E2 sub-groups that have been identified in the Arabidopsis genome. At the same time, E2/E3 specificities have also been explored. The components used in this system are all from plants, particularly Arabidopsis, making it very suitable for ubiquitination assays of plant proteins. Some E2 proteins that are not easily expressed in Escherichia coli were transiently expressed and purified from plants before use in ubiquitination assays. This system is also adaptable to proteins of species other than plants. In this system, we also analyzed two mutated forms of ubiquitin, K48R and K63R, to detect various types of ubiquitin conjugation.
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Affiliation(s)
- Qingzhen Zhao
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beichen West Road, Beijing 100101, China
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21
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Ambrosone A, Di Giacomo M, Leone A, Grillo MS, Costa A. Identification of early induced genes upon water deficit in potato cell cultures by cDNA-AFLP. JOURNAL OF PLANT RESEARCH 2013; 126:169-178. [PMID: 22772750 DOI: 10.1007/s10265-012-0505-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 06/06/2012] [Indexed: 06/01/2023]
Abstract
For plant cells in the early phases of water stress exposure, the genes induced under such conditions play a key role in detecting and responding to water deficit. In this study, potato cell suspensions were used as a simplified model system to dissect early molecular changes upon low water potential. In particular, the cDNA-amplified fragment length polymorphism approach was used to capture genes rapidly activated in potato cell cultures in response to water deficit induced by short-term exposure (up to 1 h) to polyethylene glycol. Selective amplifications with 38 primer combinations allowed the visualization of about 167 transcript-derived fragments (TDFs) differentially expressed upon exposure to low water potential. The gene expression pattern of 18 up-regulated genes was further investigated by semi-quantitative reverse transcriptase polymerase chain reaction analysis. Sequencing and similarity analysis revealed that TDFs present homologies chiefly with proteins involved in chaperone activity and protein degradation (hsps, proteinase precursor), in protein synthesis (elongation factor, ribosomal proteins) and in the ROS scavenging pathway (phenylalanine ammonia-lyase, peroxidase). Our findings might contribute to describe the potential role of genes activated in the early phases of plant response to drought.
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Affiliation(s)
- Alfredo Ambrosone
- National Research Council of Italy, Institute of Plant Genetics (CNR-IGV), Via Università 133, Portici, Naples, Italy
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Heyman J, De Veylder L. The anaphase-promoting complex/cyclosome in control of plant development. MOLECULAR PLANT 2012; 5:1182-94. [PMID: 23034505 DOI: 10.1093/mp/sss094] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Temporal controlled degradation of key cell division proteins ensures a correct onset of the different cell cycle phases and exit from the cell division program. In light of the cell cycle, the Anaphase-Promoting Complex/Cyclosome (APC/C) is an important conserved multi-subunit ubiquitin ligase, marking targets for degradation by the 26S proteasome. However, whereas the APC/C has been studied extensively in yeast and mammals, only in the last decade has the plant APC/C started to unveil its secrets. Research results have shown the importance of the APC/C core complex and its activators during gametogenesis, growth, hormone signaling, symbiotic interactions, and endoreduplication onset. In addition, recently, the first plant APC/C inhibitors have been reported, allowing a fine-tuning of APC/C activity during the cell cycle. Together with the identification of the first APC/C targets, a picture emerges of APC/C activity being essential for many different developmental processes.
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Affiliation(s)
- Jefri Heyman
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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Eswaran N, Parameswaran S, Sathram B, Anantharaman B, Kumar G RK, Tangirala SJ. Yeast functional screen to identify genetic determinants capable of conferring abiotic stress tolerance in Jatropha curcas. BMC Biotechnol 2010; 10:23. [PMID: 20302659 PMCID: PMC2851662 DOI: 10.1186/1472-6750-10-23] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 03/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Environmentally inflicted stresses such as salinity and drought limit the plant productivity both in natural and agricultural system. Increasing emphasis has been directed to molecular breeding strategies to enhance the intrinsic ability of plant to survive stress conditions. Functional screens in microorganisms with heterologous genes are a rapid, effective and powerful tool to identify stress tolerant genes in plants. Jatropha curcas (Physic nut) has been identified as a potential source of biodiesel plant. In order to improve its productivity under stress conditions to benefit commercial plantations, we initiated prospecting of novel genes expressed during stress in J. curcas that can be utilized to enhance stress tolerance ability of plant. RESULTS To identify genes expressed during salt tolerance, cDNA expression libraries were constructed from salt-stressed roots of J. curcas, regulated under the control of the yeast GAL1 system. Using a replica based screening, twenty thousand yeast transformants were screened to identify transformants expressing heterologous gene sequences from J. curcas with enhanced ability to tolerate stress. From the screen we obtained 32 full length genes from J. curcas [GenBank accession numbers FJ489601-FJ489611, FJ619041-FJ619057 and FJ623457-FJ623460] that can confer abiotic stress tolerance. As a part of this screen, we optimized conditions for salt stress in J. curcas, defined parameters for salt stress in yeast, as well as isolated three salt hypersensitive yeast strains shs-2, shs-6 and shs-8 generated through a process of random mutagenesis, and exhibited growth retardation beyond 750 mM NaCl. Further, we demonstrated complementation of the salt sensitive phenotypes in the shs mutants, and analyzed the expression patterns for selected J. curcas genes obtained from the screen in both leaf and root tissues after salt stress treatments. CONCLUSIONS The approach described in this report provides a rapid and universal assay system for large scale screening of genes for varied abiotic stress tolerance within a short span of time. Using this screening strategy we could isolate both genes with previously known function in stress tolerance as well as novel sequences with yet unknown function in salt stress tolerance from J. curcas. The isolated genes could be over-expressed using plant expression system to generate and evaluate transgenic plants for stress tolerance as well as be used as markers for breeding salt stress tolerance in plants.
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Affiliation(s)
- Nalini Eswaran
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Sriram Parameswaran
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
- DuPont Knowledge Centre, ICICI Knowledge Park, Genome Valley, Turkapalli, Shamirpet, Hyderabad 500 078, India
| | - Balaji Sathram
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Bhagyam Anantharaman
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Raja Krishna Kumar G
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Sudhakar Johnson Tangirala
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
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Topp SH, Rasmussen SK, Mibus H, Sander L. A search for growth related genes in Kalanchoë blossfeldiana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2009; 47:1024-30. [PMID: 19819156 DOI: 10.1016/j.plaphy.2009.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Indexed: 05/28/2023]
Abstract
Differential display of mRNA from four sets of contrasting phenotypes were carried out in order to identify and isolate genes associated with elongating growth of Kalanchoë blossfeldiana. A total of 17 unique differential expressed cDNA fragments were sequenced and 12 showed homology to genes in other plant species. Three genes were subsequently tested for growth related activity by Virus Induced Gene Silencing (VIGS) in Nicotiana benthamiana. One gene fragment (13C) resulted in plants with significantly reduced growth (N = 20, P = 0.05, one-tailed students t-test) from day 25 after virus infection. Full-length cDNA and genomic DNA sequences were obtained by inverse PCR and thermal asymmetric interlaced (TAIL) PCR and the gene was named KbORF1. The predicted gene is 2244 bp long with three exons of 411 bp in total encoding a protein of 137 amino acid residues with homologs widespread among plants. The protein has no known function, but its expression has been confirmed in a proteomic study of Arabidopsis. Southern blot analysis shows two hybridizing fragments in agreement with the tetraploid nature of K. blossfeldiana. Fragment 13C comprises 446 bp of the gene, and the portion of 13C conferring growth retardation by VIGS is located 10 bp into the second intron indicating a regulatory function of this part of the KbORF1 mRNA. Differential display in combination with VIGS as a screening method proved to be a good functional approach not only to search for genes of interest, but also to isolate expressed genetic regulatory domains.
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Affiliation(s)
- Sine H Topp
- University of Copenhagen, Faculty of Life Sciences, Department of Agriculture and Ecology, Plant and Soil Sciences Laboratory, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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25
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de Almeida Engler J, De Veylder L, De Groodt R, Rombauts S, Boudolf V, De Meyer B, Hemerly A, Ferreira P, Beeckman T, Karimi M, Hilson P, Inzé D, Engler G. Systematic analysis of cell-cycle gene expression during Arabidopsis development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:645-60. [PMID: 19392699 DOI: 10.1111/j.1365-313x.2009.03893.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The steady-state distribution of cell-cycle transcripts in Arabidopsis thaliana seedlings was studied in a broad in situ survey to provide a better understanding of the expression of cell-cycle genes during plant development. The 61 core cell-cycle genes analyzed were expressed at variable levels throughout the different plant tissues: 23 genes generally in dividing and young differentiating tissues, 34 genes mostly in both dividing and differentiated tissues and four gene transcripts primarily in differentiated tissues. Only 21 genes had a typical patchy expression pattern, indicating tight cell-cycle regulation. The increased expression of 27 cell-cycle genes in the root elongation zone hinted at their involvement in the switch from cell division to differentiation. The induction of 20 cell-cycle genes in differentiated cortical cells of etiolated hypocotyls pointed to their possible role in the process of endoreduplication. Of seven cyclin-dependent kinase inhibitor genes, five were upregulated in etiolated hypocotyls, suggesting a role in cell-cycle arrest. Nineteen genes were preferentially expressed in pericycle cells activated by auxin that give rise to lateral root primordia. Approximately 1800 images have been collected and can be queried via an online database. Our in situ analysis revealed that 70% of the cell-cycle genes, although expressed at different levels, show a large overlap in their localization. The lack of regulatory motifs in the upstream regions of the analyzed genes suggests the absence of a universal transcriptional control mechanism for all cell-cycle genes.
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Affiliation(s)
- Janice de Almeida Engler
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Gent, Belgium
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26
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Castillejo MÁ, Maldonado AM, Dumas-Gaudot E, Fernández-Aparicio M, Susín R, Diego R, Jorrín JV. Differential expression proteomics to investigate responses and resistance to Orobanche crenata in Medicago truncatula. BMC Genomics 2009; 10:294. [PMID: 19575787 PMCID: PMC2714000 DOI: 10.1186/1471-2164-10-294] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 07/03/2009] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Parasitic angiosperm Orobanche crenata infection represents a major constraint for the cultivation of legumes worldwide. The level of protection achieved to date is either incomplete or ephemeral. Hence, an efficient control of the parasite requires a better understanding of its interaction and associated resistance mechanisms at molecular levels. RESULTS In order to study the plant response to this parasitic plant and the molecular basis of the resistance we have used a proteomic approach. The root proteome of two accessions of the model legume Medicago truncatula displaying differences in their resistance phenotype, in control as well as in inoculated plants, over two time points (21 and 25 days post infection), has been compared. We report quantitative as well as qualitative differences in the 2-DE maps between early- (SA 27774) and late-resistant (SA 4087) genotypes after Coomassie and silver-staining: 69 differential spots were observed between non-inoculated genotypes, and 42 and 25 spots for SA 4087 and SA 27774 non-inoculated and inoculated plants, respectively. In all, 49 differential spots were identified by peptide mass fingerprinting (PMF) following MALDI-TOF/TOF mass spectrometry. Many of the proteins showing significant differences between genotypes and after parasitic infection belong to the functional category of defense and stress-related proteins. A number of spots correspond to proteins with the same function, and might represent members of a multigenic family or post-transcriptional forms of the same protein. CONCLUSION The results obtained suggest the existence of a generic defense mechanism operating during the early stages of infection and differing in both genotypes. The faster response to the infection observed in the SA 27774 genotype might be due to the action of proteins targeted against key elements needed for the parasite's successful infection, such as protease inhibitors. Our data are discussed and compared with those previously obtained with pea 1 and transcriptomic analysis of other plant-pathogen and plant-parasitic plant systems.
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Affiliation(s)
- Ma Ángeles Castillejo
- Institute for Sustainable Agriculture, CSIC, Alameda del Obispo s/n, Apdo. 4084, 14080 Córdoba, Spain
| | - Ana M Maldonado
- Department of Biochemistry and Molecular Biology, University of Cordoba, Rabanales Campus, Córdoba, Spain
| | - Eliane Dumas-Gaudot
- UMR 1088 INRA/CNRS/UB (Plant-Microbe Environment) INRA-CMSE, BP 86510, 21065 DIJON Cedex, France
| | - Mónica Fernández-Aparicio
- Institute for Sustainable Agriculture, CSIC, Alameda del Obispo s/n, Apdo. 4084, 14080 Córdoba, Spain
| | - Rafael Susín
- Department of Biochemistry and Molecular Biology, University of Cordoba, Rabanales Campus, Córdoba, Spain
| | - Rubiales Diego
- Institute for Sustainable Agriculture, CSIC, Alameda del Obispo s/n, Apdo. 4084, 14080 Córdoba, Spain
| | - Jesús V Jorrín
- Department of Biochemistry and Molecular Biology, University of Cordoba, Rabanales Campus, Córdoba, Spain
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Kato K, Gális I, Suzuki S, Araki S, Demura T, Criqui MC, Potuschak T, Genschik P, Fukuda H, Matsuoka K, Ito M. Preferential up-regulation of G2/M phase-specific genes by overexpression of the hyperactive form of NtmybA2 lacking its negative regulation domain in tobacco BY-2 cells. PLANT PHYSIOLOGY 2009; 149:1945-57. [PMID: 19244455 PMCID: PMC2663760 DOI: 10.1104/pp.109.135582] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 02/18/2009] [Indexed: 05/19/2023]
Abstract
Many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. Here, we examined the genome-wide effects of NtmybA2 overexpression, one of the R1R2R3-Myb transcription factors in tobacco (Nicotiana tabacum). We used a custom-made 16-K cDNA microarray for comparative transcriptome analysis of transgenic tobacco BY-2 cell lines that overexpress NtmybA2 or its truncated hyperactive form. The microarray was also used to determine the transcript profile during the cell cycle in synchronized cultures of BY-2 cells. Combined microarray data from transgenic lines and synchronized cells revealed that overexpression of the truncated hyperactive form of NtmybA2, but not its full-length form, preferentially up-regulated many G2/M phase-specific genes in BY-2 cells. We determined promoter sequences of several such up-regulated genes and showed that all contain MSA-like motifs in the proximal regions of their promoters. One of the up-regulated genes, NtE2C, encoding for cyclin-specific ubiquitin carrier proteins, contained a single functional MSA-like motif, which specifically controlled the expression of a reporter gene in the G2/M phase in BY-2 cells. Furthermore, a genomic footprint experiment showed that the MSA element in the NtE2C promoter interacted with nuclear proteins in vivo. Therefore, we propose that the transcription of many G2/M phase-specific genes in tobacco is positively regulated by NtmybA2, in most cases through direct binding to the MSA elements.
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Affiliation(s)
- Kiichi Kato
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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28
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Marrocco K, Thomann A, Parmentier Y, Genschik P, Criqui MC. The APC/C E3 ligase remains active in most post-mitotic Arabidopsis cells and is required for proper vasculature development and organization. Development 2009; 136:1475-85. [PMID: 19336465 DOI: 10.1242/dev.035535] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Selective protein degradation via the ubiquitin-26S proteasome is a major mechanism underlying DNA replication and cell division in all eukaryotes. In particular, the APC/C (anaphase promoting complex or cyclosome) is a master ubiquitin protein ligase (E3) that targets PDS1/SECURIN and cyclin B for degradation allowing sister chromatid separation and exit from mitosis, respectively. Interestingly, it has been found that the APC/C remains active in differentiated neurons in which the E3 ligase regulates axon growth, neuronal survival and synaptic functions. However, despite these recent findings, the role of APC/C in differentiated cells and the regulation of its activity beyond cell division is still poorly understood. Here, we investigate the activity and function of APC/C in the model plant Arabidopsis thaliana. We used cyclin reporter constructs to follow APC/C activity during plant development and found that this E3 ligase remains active in most post-mitotic plant cells. Strikingly, hypomorphic mutant lines, in which the APC/C activity is reduced, exhibited several developmental abnormalities, including defects in cotyledon vein patterning and internode elongation leading to a characteristic broomhead-like phenotype. Histological analyses revealed an increased amount of vascular tissue, most notably xylem and lignified sclerenchyma, indicating a role for APC/C in plant vasculature development and organization.
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Affiliation(s)
- Katia Marrocco
- Institut de Biologie Moléculaire des Plantes du CNRS, 67084 Strasbourg Cedex, France
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29
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Biochemical function of typical and variant Arabidopsis thaliana U-box E3 ubiquitin-protein ligases. Biochem J 2008; 413:447-57. [PMID: 18393940 DOI: 10.1042/bj20071568] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The variance of the U-box domain in 64 Arabidopsis thaliana (thale cress) E3s (ubiquitin-protein ligases) was used to examine the interactions between E3s and E2s (ubiquitin-conjugating enzymes). E2s and E3s are components of the ubiquitin protein degradation pathway. Seven U-box proteins were analysed for their ability to ubiquitinate proteins in vitro in co-operation with different E2s. All U-box domains exhibited ubiquitination activity and interacted productively with UBC4/5-type E2s. Three and four of the U-box domains mediated ubiquitin addition in the presence of UBC13 and UBC7 E2s respectively, but no productive interaction was observed with the UBC15 E2 tested. The activity of AtPUB54 [Arabidopsis thaliana (thale cress) plant U-box 54 protein] was dependent on Trp(266) in the E2-binding cleft, and the E2 selectivity was changed by substitution of this position. The function of the distant U-box protein, AtPUB49, representing a large family of eukaryotic proteins containing a U-box linked to a cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, was characterized biochemically. AtPUB49 functioned both as a prolyl isomerase and a chaperone by catalysing cis-trans isomerization of peptidyl-prolyl bonds and dissolving protein aggregates. In conclusion, both typical and atypical Arabidopsis U-box proteins were active E3s. The overlap in the E3/E2 selectivity suggests that in vivo specificity is not determined only by the E3-E2 interactions, but also by other parameters, e.g. co-existence or interactions with additional domains. The biochemical functions of AtPUB49 suggest that the protein can be involved in folding or degradation of protein substrates. Similar functions can also be retained within a protein complex with separate chaperone and U-box proteins.
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Curto M, Camafeita E, Lopez JA, Maldonado AM, Rubiales D, Jorrín JV. A proteomic approach to study pea (Pisum sativum) responses to powdery mildew (Erysiphe pisi). Proteomics 2006; 6 Suppl 1:S163-74. [PMID: 16511815 DOI: 10.1002/pmic.200500396] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
As a global approach to gain a better understanding of the mechanisms involved in pea resistance to Erysiphe pisi, changes in the leaf proteome of two pea genotypes differing in their resistance phenotype were analyzed by a combination of 2-DE and MALDI-TOF/TOF MS. Leaf proteins from control non-inoculated and inoculated susceptible (Messire) and resistant (JI2480) plants were resolved by 2-DE, with IEF in the 5-8 pH range and SDS-PAGE on 12% gels. CBB-stained gels revealed the existence of quantitative and qualitative differences between extracts from: (i) non-inoculated leaves of both genotypes (77 spots); (ii) inoculated and non-inoculated Messire leaves (19 spots); and (iii) inoculated and non-inoculated JI2480 leaves (12 spots). Some of the differential spots have been identified, after MALDI-TOF/TOF analysis and database searching, as proteins belonging to several functional categories, including photosynthesis and carbon metabolism, energy production, stress and defense, protein synthesis and degradation and signal transduction. Results are discussed in terms of constitutive and induced elements involved in pea resistance against Erysiphe pisi.
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Affiliation(s)
- Miguel Curto
- Agricultural and Plant Biochemistry Research Group, Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
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Kraft E, Stone SL, Ma L, Su N, Gao Y, Lau OS, Deng XW, Callis J. Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis. PLANT PHYSIOLOGY 2005; 139:1597-611. [PMID: 16339806 PMCID: PMC1310545 DOI: 10.1104/pp.105.067983] [Citation(s) in RCA: 289] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Attachment of ubiquitin to substrate proteins is catalyzed by the three enzymes E1, E2 (ubiquitin conjugating [UBC]), and E3 (ubiquitin ligase). Forty-one functional proteins with a UBC domain and active-site cysteine are predicted in the Arabidopsis (Arabidopsis thaliana) genome, which includes four that are predicted or shown to function with ubiquitin-like proteins. Only nine were previously characterized biochemically as ubiquitin E2s. We obtained soluble protein for 22 of the 28 uncharacterized UBCs after expression in Escherichia coli and demonstrated that 16 function as ubiquitin E2s. Twelve, plus three previously characterized ubiquitin E2s, were also tested for the ability to catalyze ubiquitination in vitro in the presence of one of 65 really interesting new gene (RING) E3 ligases. UBC22, UBC19-20, and UBC1-6 had variable levels of E3-independent activity. Six UBCs were inactive with all RINGs tested. Closely related UBC8, 10, 11, and 28 were active with the largest number of RING E3s and with all RING types. Expression analysis was performed to determine whether E2s or E3s were expressed in specific organs or under specific environmental conditions. Closely related E2s show unique patterns of expression and most express ubiquitously. Some RING E3s are also ubiquitously expressed; however, others show organ-specific expression. Of all the organs tested, RING mRNAs are most abundant in floral organs. This study demonstrates that E2 diversity includes examples with broad and narrow specificity toward RINGs, and that most ubiquitin E2s are broadly expressed with each having a unique spatial and developmental pattern of expression.
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Affiliation(s)
- Edward Kraft
- Section of Molecular and Cellular Biology, Division of Biological Sciences , University of California, Davis, California 95616, USA
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Fong CJ, Burgoon LD, Zacharewski TR. Comparative microarray analysis of basal gene expression in mouse Hepa-1c1c7 wild-type and mutant cell lines. Toxicol Sci 2005; 86:342-53. [PMID: 15888666 DOI: 10.1093/toxsci/kfi194] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Hepa-1c1c7 wild-type and benzo[a]pyrene-resistant derived mutant cell lines have been used to elucidate pathways and mechanisms involving the aryl hydrocarbon receptor (AhR). However, there has been little focus on other biological processes which may differ between the isolated lines. In this study, mouse cDNA microarrays representing 4858 genes were used to examine differences in basal gene expression between mouse Hepa-1c1c7 wild-type and c1 (truncated Cyp1a1 protein), c4 (AhR nuclear translocator, ARNT, deficient), and c12 (low AhR levels) mutant cell lines. Surprisingly, c1 mutants exhibited the greatest number of gene expression changes compared to wild-type cells, followed by c4 and c12 lines, respectively. Differences in basal gene expression were consistent with cell line specific variations in morphology, mitochondrial activity, and proliferation rate. MTT and direct cell count assays indicate both c4 and c12 mutants exhibit increased proliferative activity when compared to wild-type cells, while the c1 mutants exhibited decreased activity. This study further characterizes Hepa-1c1c7 wild-type and mutant cells and identifies significant differences in biological processes that should be considered when conducting comparative mechanistic studies with these lines.
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Affiliation(s)
- C J Fong
- Department of Biochemistry and Molecular Biology, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, USA
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Abstract
Much of plant physiology, growth, and development is controlled by the selective removal of short-lived regulatory proteins. One important proteolytic pathway involves the small protein ubiquitin (Ub) and the 26S proteasome, a 2-MDa protease complex. In this pathway, Ub is attached to proteins destined for degradation; the resulting Ub-protein conjugates are then recognized and catabolized by the 26S proteasome. This review describes our current understanding of the pathway in plants at the biochemical, genomic, and genetic levels, using Arabidopsis thaliana as the model. Collectively, these analyses show that the Ub/26S proteasome pathway is one of the most elaborate regulatory mechanisms in plants. The genome of Arabidopsis encodes more than 1400 (or >5% of the proteome) pathway components that can be connected to almost all aspects of its biology. Most pathway components participate in the Ub-ligation reactions that choose with exquisite specificity which proteins should be ubiquitinated. What remains to be determined is the identity of the targets, which may number in the thousands in plants.
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Affiliation(s)
- Jan Smalle
- Department of Genetics, 445 Henry Mall, University of Wisconsin-Madison, Madison, Wisconsin 53706-1574, USA
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