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Abd-Hamid NA, Ismail I. An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling. JOURNAL OF PLANT PHYSIOLOGY 2024; 300:154299. [PMID: 38936241 DOI: 10.1016/j.jplph.2024.154299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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2
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Wu R, Song K, Jing R, Du L. The de-ubiquitinase UBQUITIN SPECIFIC PROTEASE 15 (UBP15) interacts with the SCF E3 complex adaptor ARABIDOPSIS SKP1 HOMOLOGUE 1 (ASK1) to regulate petal size and fertility in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112112. [PMID: 38750799 DOI: 10.1016/j.plantsci.2024.112112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/14/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Ubiquitination is a pivotal type of post-translational modification, which plays a far-reaching role in plant growth and development, as well as in the response of plants to stress. Just like the two sides of a coin, de-ubiquitination also plays an important role in plant life, which has been gradually discovered in recent years. Here, we demonstrate that the UBQUITIN SPECIFIC PROTEASE 15 (UBP15), which is a UBP-type de-ubiquitinase, interacts with the SCF E3 complex adaptor ARABIDOPSIS SKP1 HOMOLOGUE 1 (ASK1) and influences its protein stability to regulate plant fertility and petal size. The UBP15 is associated with the ASK1 physically, as verified by yeast-two-hybrid (Y2H) and protein pull-down in vitro assays. Disruption of ASK1 by a T-DNA insertion generates some abnormal phenotypes, such as low fertility and small petals. Genetic analysis shows that the UBP15 mutation enhances the low-fertility and small-petal phenotypes of ask1 mutant plants. By proteomic analysis, many types of proteins were identified as potential candidate downstream genes associated with the phenotypes of ubp15 ask1 double mutant plants. Taken together, these findings reveal a molecular relationship between ASK1 and UBP15 and their interaction in the regulation of petal size and fertility, which would benefit in-depth research about the ubiquitin-related pathway in plant physiological processes in the future.
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Affiliation(s)
- Ruihua Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Kaixuan Song
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Ruotong Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China.
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Yang K, Tang Y, Li Y, Guo W, Hu Z, Wang X, Berger F, Li J. Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm. J Genet Genomics 2024; 51:855-865. [PMID: 38599515 DOI: 10.1016/j.jgg.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
The early development of the endosperm is crucial for balancing the allocation of maternal nutrients to offspring. This process is believed to be evolutionarily associated with genomic imprinting, resulting in parentally biased allelic gene expression. Beyond FertilizationIndependentSeed (FIS) genes, the number of imprinted genes involved in early endosperm development and seed size determination remains limited. This study introduces early endosperm-expressed HAIKU (IKU) downstream Candidate F-box 1 (ICF1) and ICF2 as maternally expressed imprinted genes (MEGs) in Arabidopsis thaliana. Although these genes are also demethylated by DEMETER (DME) in the central cell, their activation differs from the direct DME-mediated activation seen in classical MEGs such as the FIS genes. Instead, ICF maternal alleles carry pre-established hypomethylation in their promoters, priming them for activation by the WRKY10 transcription factor in the endosperm. On the contrary, paternal alleles are predominantly suppressed by CG methylation. Furthermore, we find that ICF genes partially contribute to the small seed size observed in iku mutants. Our discovery reveals a two-step regulatory mechanism that highlights the important role of conventional transcription factors in the activation of imprinted genes, which was previously not fully recognized. Therefore, the mechanism provides a new dimension to understand the transcriptional regulation of imprinting in plant reproduction and development.
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Affiliation(s)
- Ke Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yuling Tang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yue Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenbin Guo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhengdao Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xuanpeng Wang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Jing Li
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China.
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4
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Collins E, Shou H, Mao C, Whelan J, Jost R. Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level. Biochem J 2024; 481:363-385. [PMID: 38421035 DOI: 10.1042/bcj20230163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.
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Affiliation(s)
- Emma Collins
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- Hainan Institute, Zhejiang University, Sanya 572025, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
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5
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Wolf ESA, Vela S, Cuevas HE, Vermerris W. A Sorghum F-Box Protein Induces an Oxidative Burst in the Defense Against Colletotrichum sublineola. PHYTOPATHOLOGY 2024; 114:405-417. [PMID: 37717251 DOI: 10.1094/phyto-06-23-0184-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The hemibiotrophic fungal pathogen Colletotrichum sublineola is the causal agent of anthracnose in sorghum (Sorghum bicolor), resulting in leaf blight, stalk rot, and head blight in susceptible genotypes, with yield losses of up to 50%. The development of anthracnose-resistant cultivars can reduce reliance on fungicides and provide a more sustainable and economical means for disease management. A previous genome-wide association study of the sorghum association panel identified the candidate resistance gene Sobic.005G172300 encoding an F-box protein. To better understand the role of this gene in the defense against C. sublineola, gene expression following infection with C. sublineola was monitored by RNA sequencing in seedlings of sorghum accession SC110, which harbored the resistance allele, and three accessions that harbored a susceptible allele. Only in SC110 did the expression of Sobic.005G172300 increase during the biotrophic phase of infection. Subsequent transcriptome analysis, gene co-expression networks, and gene regulatory networks of inoculated and mock-inoculated seedlings of resistant and susceptible accessions suggest that the increase in expression of Sobic.005G172300 induces an oxidative burst by lowering the concentration of ascorbic acid during the biotrophic phase of infection. Based on gene regulatory network analysis, the protein encoded by Sobic.005G172300 is proposed to target proteins involved in the biosynthesis of ascorbic acid for polyubiquitination through the SCF E3 ubiquitin ligase, causing their degradation via the proteasome.
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Affiliation(s)
- Emily S A Wolf
- Plant Molecular & Cellular Biology graduate program, University of Florida, Gainesville, FL 32611
| | - Saddie Vela
- Plant Molecular & Cellular Biology graduate program, University of Florida, Gainesville, FL 32611
| | - Hugo E Cuevas
- U.S. Department of Agriculture-Agricultural Research Service, Tropical Agriculture Research Station, Mayagüez, PR 00680
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science, University of Florida, Gainesville, FL 32611
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611
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6
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Lu K, Gong H, Yang D, Ye M, Fang Q, Zhang XY, Wu R. Genome-Wide Network Analysis of Above- and Below-Ground Co-growth in Populus euphratica. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0131. [PMID: 38188223 PMCID: PMC10769449 DOI: 10.34133/plantphenomics.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024]
Abstract
Tree growth is the consequence of developmental interactions between above- and below-ground compartments. However, a comprehensive view of the genetic architecture of growth as a cohesive whole is poorly understood. We propose a systems biology approach for mapping growth trajectories in genome-wide association studies viewing growth as a complex (phenotypic) system in which above- and below-ground components (or traits) interact with each other to mediate systems behavior. We further assume that trait-trait interactions are controlled by a genetic system composed of many different interactive genes and integrate the Lotka-Volterra predator-prey model to dissect phenotypic and genetic systems into pleiotropic and epistatic interaction components by which the detailed genetic mechanism of above- and below-ground co-growth can be charted. We apply the approach to analyze linkage mapping data of Populus euphratica, which is the only tree species that can grow in the desert, and characterize several loci that govern how above- and below-ground growth is cooperated or competed over development. We reconstruct multilayer and multiplex genetic interactome networks for the developmental trajectories of each trait and their developmental covariation. Many significant loci and epistatic effects detected can be annotated to candidate genes for growth and developmental processes. The results from our model may potentially be useful for marker-assisted selection and genetic editing in applied tree breeding programs. The model provides a general tool to characterize a complete picture of pleiotropic and epistatic genetic architecture in growth traits in forest trees and any other organisms.
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Affiliation(s)
- Kaiyan Lu
- College of Science,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Huiying Gong
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Dengcheng Yang
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Qing Fang
- Faculty of Science,
Yamagata University, Yamagata 990, Japan
| | - Xiao-Yu Zhang
- College of Science,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Rongling Wu
- Yanqi Lake BeijingInstitute of Mathematical Sciences and Applications, Beijing 101408, China
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
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7
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Hina A, Khan N, Kong K, Lv W, Karikari B, Abbasi A, Zhao T. Exploring the role of FBXL fbxl gene family in Soybean: Implications for plant height and seed size regulation. PHYSIOLOGIA PLANTARUM 2024; 176:e14191. [PMID: 38351287 DOI: 10.1111/ppl.14191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/16/2023] [Accepted: 01/01/2024] [Indexed: 02/16/2024]
Abstract
F-box proteins constitute a significant family in eukaryotes and, as a component of the Skp1p-cullin-F-box complex, are considered critical for cellular protein degradation and other biological processes in plants. Despite their importance, the functions of F-box proteins, particularly those with C-terminal leucine-rich repeat (LRR) domains, remain largely unknown in plants. Therefore, the present study conducted genome-wide identification and in silico characterization of F-BOX proteins with C-terminal LRR domains in soybean (Glycine max L.) (GmFBXLs). A total of 45 GmFBXLs were identified. The phylogenetic analysis showed that GmFBXLs could be subdivided into ten subgroups and exhibited a close relationship with those from Arabidopsis thaliana, Cicer aretineum, and Medicago trunculata. It was observed that most cis-regulatory elements in the promoter regions of GmFBXLs are involved in hormone signalling, stress responses, and developmental stages. In silico transcriptome data illustrated diverse expression patterns of the identified GmFBXLs across various tissues, such as shoot apical meristem, flower, green pods, leaves, nodules, and roots. Overexpressing (OE) GmFBXL12 in Tianlong No.1 cultivar resulted in a significant difference in seed size, number of pods, and number of seeds per plant, indicated a potential increase in yield compared to wild type. This study offers valuable perspectives into the role of FBXLs in soybean, serving as a foundation for future research. Additionally, the identified OE lines represent valuable genetic resources for enhancing seed-related traits in soybean.
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Affiliation(s)
- Aiman Hina
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Nadeem Khan
- Global Institute for Food Security, Saskatoon, SK, Canada
| | - Keke Kong
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Wenhuan Lv
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Benjamin Karikari
- Département de phytologie, Université Laval, QC, Québec, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University Murree, Pakistan
| | - Tuanjie Zhao
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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8
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Shao M, Wang P, Gou H, Ma Z, Chen B, Mao J. Identification and Expression Analysis of the SKP1-Like Gene Family under Phytohormone and Abiotic Stresses in Apple ( Malus domestica). Int J Mol Sci 2023; 24:16414. [PMID: 38003604 PMCID: PMC10671573 DOI: 10.3390/ijms242216414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Ubiquitination participates in plant hormone signaling and stress response to adversity. SKP1-Like, a core component of the SCF (Skp1-Cullin-F-box) complex, is the final step in catalyzing the ubiquitin-mediated protein degradation pathway. However, the SKP1-Like gene family has not been well characterized in response to apple abiotic stresses and hormonal treatments. This study revealed that 17 MdSKP1-Like gene family members with the conserved domain of SKP1 were identified in apples and were unevenly distributed on eight chromosomes. The MdSKP1-Like genes located on chromosomes 1, 10, and 15 were highly homologous. The MdSKP1-like genes were divided into three subfamilies according to the evolutionary affinities of monocotyledons and dicotyledons. MdSKP1-like members of the same group or subfamily show some similarity in gene structure and conserved motifs. The predicted results of protein interactions showed that members of the MdSKP1-like family have strong interactions with members of the F-Box family of proteins. A selection pressure analysis showed that MdSKP1-Like genes were in purifying selection. A chip data analysis showed that MdSKP1-like14 and MdSKP1-like15 were higher in flowers, whereas MdSKP1-like3 was higher in fruits. The upstream cis-elements of MdSKP1-Like genes contained a variety of elements related to light regulation, drought, low temperature, and many hormone response elements, etc. Meanwhile, qRT-PCR also confirmed that the MdSKP1-Like gene is indeed involved in the response of the apple to hormonal and abiotic stress treatments. This research provides evidence for regulating MdSKP1-Like gene expression in response to hormonal and abiotic stresses to improve apple stress resistance.
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Affiliation(s)
| | | | | | | | | | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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Xia H, Hao Z, Shen Y, Tu Z, Yang L, Zong Y, Li H. Genome-wide association study of multiyear dynamic growth traits in hybrid Liriodendron identifies robust genetic loci associated with growth trajectories. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1544-1563. [PMID: 37272730 DOI: 10.1111/tpj.16337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/30/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
The genetic factors underlying growth traits differ over time points or stages. However, most current studies of phenotypes at single time points do not capture all loci or explain the genetic differences underlying growth trajectories. Hybrid Liriodendron exhibits obvious heterosis and is widely cultivated, although its complex genetic mechanism underlying growth traits remains unknown. A genome-wide association study (GWAS) is an effective method for elucidating the genetic architecture by identifying genetic loci underlying complex quantitative traits. In the present study, using a GWAS, we identified robust loci associated with growth trajectories in hybrid Liriodendron populations. We selected 233 hybrid progenies derived from 25 crosses for resequencing, and measured their tree height (H) and diameter at breast height (DBH) for 11 consecutive years; 192 972 high-quality single nucleotide polymorphisms (SNPs) were obtained. The dynamics of the multiyear single-trait GWAS showed that year-specific SNPs predominated, and only five robust SNPs for DBH were identified in at least three different years. Multitrait GWAS analysis with model parameters as latent variables also revealed 62 SNPs for H and 52 for DBH associated with the growth trajectory, displaying different biomass accumulation patterns, among which four SNPs exerted pleiotropic effects. All identified SNPs also exhibited temporal variations in effect sizes and inheritance patterns potentially related to different growth and developmental stages. The haplotypes resulting from these significant SNPs might pyramid favorable loci, benefitting the selection of superior genotypes. The present study provides insights into the genetic architecture of dynamic growth traits and lays a basis for future molecular-assisted breeding.
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Affiliation(s)
- Hui Xia
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziyuan Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yufang Shen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhonghua Tu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Lichun Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yaxian Zong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Huogen Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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10
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Bressendorff S, Kausika S, Sjøgaard IMZ, Oksbjerg ED, Michels A, Poulsen C, Brodersen P. The N-coil and the globular N-terminal domain of plant ARGONAUTE1 are interaction hubs for regulatory factors. Biochem J 2023; 480:957-974. [PMID: 37278687 DOI: 10.1042/bcj20230025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/07/2023]
Abstract
The effector complex of RNA interference (RNAi) contains at its core an ARGONAUTE (AGO) protein bound to a small guide RNA. AGO proteins adopt a two-lobed structure in which the N-terminal (N) and Piwi-Argonaute-Zwille (PAZ) domains make up one lobe, while the middle (MID) and Piwi domains make up the other. Specific biochemical functions of PAZ, MID and Piwi domains of eukaryotic AGO proteins have been described, but the functions of the N domain remain less clear. Here, we use yeast two-hybrid screening with the N domain of the founding member of the AGO protein family, Arabidopsis AGO1, to reveal that it interacts with many factors involved in regulated proteolysis. Interaction with a large group of proteins, including the autophagy cargo receptors ATI1 and ATI2, requires residues in a short, linear region, the N-coil, that joins the MID-Piwi lobe in the three-dimensional structure of AGO. In contrast, the F-box protein AUF1 interacts with AGO1 independently of the N-coil and requires distinct residues in the globular N domain itself. Mutation of AGO1 residues necessary for interaction with protein degradation factors in yeast stabilizes reporters fused to the AGO1 N domain in plants, supporting their in vivo relevance. Our results define distinct regions of the N domain implicated in protein-protein interaction, and point to a particular importance of the AGO1 N-coil as a site of interaction with regulatory factors.
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Affiliation(s)
- Simon Bressendorff
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Swathi Kausika
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Ida Marie Zobbe Sjøgaard
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Emilie Duus Oksbjerg
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Alec Michels
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Christian Poulsen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter Brodersen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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11
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Jain N, Khurana P, Khurana JP. Overexpression of a rice Tubby-like protein-encoding gene, OsFBT4, confers tolerance to abiotic stresses. PROTOPLASMA 2023; 260:1063-1079. [PMID: 36539640 DOI: 10.1007/s00709-022-01831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/05/2022] [Indexed: 06/07/2023]
Abstract
The OsFBT4 belongs to a small sub-class of rice F-box proteins called TLPs (Tubby-like proteins) containing the conserved N-terminal F-box domain and a C-terminal Tubby domain. These proteins have largely been implicated in both abiotic and biotic stress responses, besides developmental roles in plants. Here, we investigated the role of OsFBT4 in abiotic stress signalling. The OsFBT4 transcript was strongly upregulated in response to different abiotic stresses in rice, including exogenous ABA. When ectopically expressed, in Arabidopsis, under a constitutive CaMV 35S promoter, the overexpression (OE) caused hypersensitivity to most abiotic stresses, including ABA, during seed germination and early seedling growth. At the 5-day-old seedling growth stage, the OE conferred tolerance to all abiotic stresses. The OE lines displayed significant tolerance to salinity and water deficit at the mature growth stage. The stomatal size and density were seen to be altered in the OE lines, accompanied by hypersensitivity to ABA and hydrogen peroxide (H2O2) and a reduced water loss rate. Overexpression of OsFBT4 caused upregulation of several ABA-regulated/independent stress-responsive genes at more advanced stages of growth, showing wide and intricate roles played by OsFBT4 in stress signalling. The OsFBT4 showed interaction with several OSKs (Oryza SKP1 proteins) and localized to the plasma membrane (PM). The protein translocates to the nucleus, in response to oxidative and osmotic stresses, but failed to show transactivation activity in the yeast system. The OE lines also displayed morphological deviations from the wild-type (WT) plants, suggesting a role of the gene also in plant development.
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Affiliation(s)
- Nitin Jain
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
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12
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Jain N, Khurana P, Khurana JP. AtTLP2, a Tubby-like protein, plays intricate roles in abiotic stress signalling. PLANT CELL REPORTS 2023; 42:235-252. [PMID: 36437308 DOI: 10.1007/s00299-022-02953-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
The Arabidopsis Tubby-like protein (TLP) encoding gene, AtTLP2, plays intricate roles during ABA-dependent abiotic stress signalling, particularly salt and dehydration stress responses. TLPs (Tubby-like proteins) are a small group of eukaryotic proteins characterized by the presence of a Tubby domain. The plant TLPs have been widely shown to play important roles during abiotic stress signaling. In this study, we investigated the role of an Arabidopsis TLP, AtTLP2, in mediating abiotic stress responses. Both attlp2 null mutant and overexpression (OE) lines, in Arabidopsis, were studied which indicated the role of the gene also in development. The attlp2 mutant showed an overall dwarfism, while its overexpression caused enhanced growth. AtTLP2 localized to the plasma membrane (PM) and showed nuclear translocation in response to dehydration stress. The protein interacted with ASK1 and ASK2, but failed to show transactivation activity in yeast. AtTLP2 was transcriptionally induced by stress, caused by salt, dehydration and ABA. The attlp2 mutant was insensitive to ABA, but hypersensitive to oxidative stress at all stages of growth. ABA insensitivity conferred tolerance to salt and osmotic stresses at the germination and early seedling growth stages, but caused hypersensitivity to salt and drought stresses at advanced stages of growth. The OE lines were more sensitive to ABA, causing increased sensitivity to most stresses at the seed germination stage, but conferring tolerance to salt and osmotic stresses at more advanced stages of development. The stomata of the attlp2 mutant were less responsive to ABA and H2O2, while that of the OE lines exhibited greater sensitivity. Several ABA-regulated stress responsive marker genes were found to be downregulated in the mutant, but upregulated in the OE lines. The study establishes that AtTLP2 plays intricate roles in abiotic stress signaling, and the response may be largely ABA dependent.
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Affiliation(s)
- Nitin Jain
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
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13
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Li Y, Jin F, Wu X, Teixeira da Silva JA, Xiong Y, Zhang X, Ma G. Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153866. [PMID: 36399836 DOI: 10.1016/j.jplph.2022.153866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.
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Affiliation(s)
- Yuan Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Feng Jin
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Xiuju Wu
- College of Life Science, Northeast Agricultural University, Harbin, 150040, China.
| | | | - Yuping Xiong
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Xinhua Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Guohua Ma
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
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14
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Sarikaya Bayram Ö, Bayram Ö, Karahoda B, Meister C, Köhler AM, Thieme S, Elramli N, Frawley D, McGowan J, Fitzpatrick DA, Schmitt K, de Assis LJ, Valerius O, Goldman GH, Braus GH. F-box receptor mediated control of substrate stability and subcellular location organizes cellular development of Aspergillus nidulans. PLoS Genet 2022; 18:e1010502. [PMID: 36508464 PMCID: PMC9744329 DOI: 10.1371/journal.pgen.1010502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/31/2022] [Indexed: 12/14/2022] Open
Abstract
Fungal growth and development are coordinated with specific secondary metabolism. This coordination requires 8 of 74 F-box proteins of the filamentous fungus Aspergillus nidulans. F-box proteins recognize primed substrates for ubiquitination by Skp1-Cul1-Fbx (SCF) E3 ubiquitin RING ligases and degradation by the 26S proteasome. 24 F-box proteins are found in the nuclear fraction as part of SCFs during vegetative growth. 43 F-box proteins interact with SCF proteins during growth, development or stress. 45 F-box proteins are associated with more than 700 proteins that have mainly regulatory roles. This corroborates that accurate surveillance of protein stability is prerequisite for organizing multicellular fungal development. Fbx23 combines subcellular location and protein stability control, illustrating the complexity of F-box mediated regulation during fungal development. Fbx23 interacts with epigenetic methyltransferase VipC which interacts with fungal NF-κB-like velvet domain regulator VeA that coordinates fungal development with secondary metabolism. Fbx23 prevents nuclear accumulation of methyltransferase VipC during early development. These results suggest that in addition to their role in protein degradation, F-box proteins also control subcellular accumulations of key regulatory proteins for fungal development.
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Affiliation(s)
| | - Özgür Bayram
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
- * E-mail: (ÖB); (GHB)
| | - Betim Karahoda
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Cindy Meister
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Anna M. Köhler
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Sabine Thieme
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Nadia Elramli
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Dean Frawley
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Jamie McGowan
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Leandro Jose de Assis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail: (ÖB); (GHB)
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15
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Kanapin A, Rozhmina T, Bankin M, Surkova S, Duk M, Osyagina E, Samsonova M. Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration. Int J Mol Sci 2022; 23:ijms232314536. [PMID: 36498863 PMCID: PMC9738745 DOI: 10.3390/ijms232314536] [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: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection.
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Affiliation(s)
- Alexander Kanapin
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Tatyana Rozhmina
- Laboratory of Breeding Technologies, Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Mikhail Bankin
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Svetlana Surkova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Duk
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Ekaterina Osyagina
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-812-290-9645
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16
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Wan S, Yang M, Ni F, Chen W, Wang Y, Chu P, Guan R. A small chromosomal inversion mediated by MITE transposons confers cleistogamy in Brassica napus. PLANT PHYSIOLOGY 2022; 190:1841-1853. [PMID: 36005931 PMCID: PMC9614453 DOI: 10.1093/plphys/kiac395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Cleistogamy, self-pollination within closed flowers, can help maintain seed purity, accelerate breeding speed, and aid in the development of ornamental flowers. However, the mechanism underlying petal closing/opening behavior remains elusive. Here, we found that a Brassica napus petal closing/opening behavior was inherited in a Mendelian manner. Fine mapping and positional cloning experiments revealed that the Mendelian factor originated from a short (29.8 kb) inversion mediated by BnDTH9 miniature inverted-repeat transposable elements (MITEs) on chromosome C03. This inversion led to tissue-specific gene promoter exchange between BnaC03.FBA (BnaC03G0156800ZS encoding an F-Box-associated domain-containing protein) and BnaC03.EFO1 (BnaC03G0157400ZS encoding an EARLY FLOWERING BY OVEREXPRESSION 1 protein) positioned near the respective inversion breakpoints. Our genetic transformation work demonstrated that the cleistogamy originated from high tissue-specific expression of the BnaC03.FBA gene caused by promoter changes due to the MITE-mediated inversion. BnaC03.FBA is involved in the formation of an SCF (Skp1-Cullin-F-box) complex, which participates in ubiquitin-mediated protein targeting for degradation through the ubiquitin 26S-proteasome system. Our results shed light on a molecular model of petal-closing behavior.
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Affiliation(s)
- Shubei Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mao Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Ni
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Pu Chu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongzhan Guan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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17
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Sabharwal T, Lu Z, Slocum RD, Kang S, Wang H, Jiang HW, Veerappa R, Romanovicz D, Nam JC, Birk S, Clark G, Roux SJ. Constitutive expression of a pea apyrase, psNTP9, increases seed yield in field-grown soybean. Sci Rep 2022; 12:10870. [PMID: 35760854 PMCID: PMC9237067 DOI: 10.1038/s41598-022-14821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
To address the demand for food by a rapidly growing human population, agricultural scientists have carried out both plant breeding and genetic engineering research. Previously, we reported that the constitutive expression of a pea apyrase (Nucleoside triphosphate, diphosphohydrolase) gene, psNTP9, under the control of the CaMV35S promoter, resulted in soybean plants with an expanded root system architecture, enhanced drought resistance and increased seed yield when they are grown in greenhouses under controlled conditions. Here, we report that psNTP9-expressing soybean lines also show significantly enhanced seed yields when grown in multiple different field conditions at multiple field sites, including when the gene is introgressed into elite germplasm. The transgenic lines have higher leaf chlorophyll and soluble protein contents and decreased stomatal density and cuticle permeability, traits that increase water use efficiency and likely contribute to the increased seed yields of field-grown plants. These altered properties are explained, in part, by genome-wide gene expression changes induced by the transgene.
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Affiliation(s)
- Tanya Sabharwal
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Robert D Slocum
- Program in Biological Sciences, Goucher College, Towson, MD, 21204, USA
| | - Seongjoon Kang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Huan Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Han-Wei Jiang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Roopadarshini Veerappa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Dwight Romanovicz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ji Chul Nam
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Simon Birk
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Greg Clark
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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18
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Zheng H, Hou L, Xie J, Cao F, Wei R, Yang M, Qi Z, Zhu R, Zhang Z, Xin D, Li C, Liu C, Jiang H, Chen Q. Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:869455. [PMID: 35783974 PMCID: PMC9247457 DOI: 10.3389/fpls.2022.869455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.
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Affiliation(s)
| | - Lilong Hou
- Northeast Agricultural University, Harbin, China
| | - Jianguo Xie
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
| | - Fubin Cao
- Northeast Agricultural University, Harbin, China
| | - Ruru Wei
- Northeast Agricultural University, Harbin, China
| | | | - Zhaoming Qi
- Northeast Agricultural University, Harbin, China
| | | | | | - Dawei Xin
- Northeast Agricultural University, Harbin, China
| | - Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Chunyan Liu
- Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
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19
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Amoanimaa-Dede H, Shao Z, Su C, Yeboah A, Zhu H. Genome-wide identification and characterization of F-box family proteins in sweet potato and its expression analysis under abiotic stress. Gene 2022; 817:146191. [PMID: 35026290 DOI: 10.1016/j.gene.2022.146191] [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: 05/05/2021] [Revised: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/04/2022]
Abstract
In this study, genome-wide characterization of F-box proteins in sweet potato yielded 243 IbFBX genes, unevenly distributed on the 15 chromosomes of sweet potato. Gene duplication analysis suggested segmental duplication as the principal factor influencing the expansive evolution of IbFBX genes in sweet potato. Phylogenetic analysis clustered F-box proteins in sweet potato, Arabidopsis, and rice into six clades (I-VI). Gene structure analysis of the IbFBX genes revealed that most of the genes within the same clade were highly conserved. Expression profiles of IbFBX family genes in 9 different tissues and under stress conditions revealed that the IbFBXs were highly upregulated or downregulated in response to salt and drought stress, suggesting their significant roles in abiotic stress response and adaptation. Knowledge of the diverse functions and expression patterns of IbFBXs presents a solid theoretical basis for annotating the functions of IbFBXs and further facilitate the molecular breeding of sweet potato.
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Affiliation(s)
- Hanna Amoanimaa-Dede
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Zhengwei Shao
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Chuntao Su
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Akwasi Yeboah
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Hongbo Zhu
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China.
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20
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Benincore-Flórez E, El-Azaz J, Solarte GA, Rodríguez A, Reyes LH, Alméciga-Díaz CJ, Cardona C. Iduronate-2-sulfatase interactome: Validation by Yeast Two-Hybrid Assay. Heliyon 2022; 8:e09031. [PMID: 35284671 PMCID: PMC8913312 DOI: 10.1016/j.heliyon.2022.e09031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 11/25/2022] Open
Abstract
Mucopolysaccharidosis type II (MPS II), also known as Hunter syndrome, is a rare X-linked recessive disease caused by a deficiency of the lysosomal enzyme iduronate-2-sulfatase (IDS), which activates intracellular accumulation of nonmetabolized glycosaminoglycans such as heparan sulfate and dermatan sulfate. This accumulation causes severe damage to several tissues, principally the central nervous system. Previously, we identified 187 IDS-protein interactions in the mouse brain. To validate a subset of these interactions, we selected and cloned the coding regions of 10 candidate genes to perform a targeted yeast two-hybrid assay. The results allowed the identification of the physical interaction of IDS with LSAMP and SYT1. Although the physiological relevance of these complexes is unknown, recent advances allow us to point out that these interactions could be involved in vesicular trafficking of IDS through the interaction with SYT1, as well as to the ability to form a transcytosis module between the cellular components of the blood-brain-barrier (BBB) through its interaction with LSAMP. These results may shed light on the role of IDS on cellular homeostasis and may also contribute to the understanding of MPS II physiopathology and the development of novel therapeutic strategies to transport recombinant IDS through the brain endothelial cells toward the brain parenchyma.
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Iantcheva A, Zhiponova M, Revalska M, Heyman J, Dincheva I, Badjakov I, De Geyter N, Boycheva I, Goormachtig S, De Veylder L. A common F-box gene regulates the leucine homeostasis of Medicago truncatula and Arabidopsis thaliana. PROTOPLASMA 2022; 259:277-290. [PMID: 33973099 DOI: 10.1007/s00709-021-01662-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The F-box domain is a conserved structural protein motif that most frequently interacts with the SKP1 protein, the core of the SCFs (SKP1-CULLIN-F-box protein ligase) E3 ubiquitin protein ligases. As part of the SCF complexes, the various F-box proteins recruit substrates for degradation through ubiquitination. In this study, we functionally characterized an F-box gene (MtF-box) identified earlier in a population of Tnt1 retrotransposon-tagged mutants of Medicago truncatula and its Arabidopsis thaliana homolog (AtF-box) using gain- and loss-of-function plants. We highlighted the importance of MtF-box in leaf development of M. truncatula. Protein-protein interaction analyses revealed the 2-isopropylmalate synthase (IPMS) protein as a common interactor partner of MtF-box and AtF-box, being a key enzyme in the biosynthesis pathway of the branched-chain amino acid leucine. For further detailed analysis, we focused on AtF-box and its role during the cell division cycle. Based on this work, we suggest a mechanism for the role of the studied F-box gene in regulation of leucine homeostasis, which is important for growth.
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Affiliation(s)
- Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria.
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov blvd., 1164, Sofia, Bulgaria
| | - Miglena Revalska
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Ivayla Dincheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Ilian Badjakov
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Nathan De Geyter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Irina Boycheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
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22
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Interactome of Arabidopsis Thaliana. PLANTS 2022; 11:plants11030350. [PMID: 35161331 PMCID: PMC8838453 DOI: 10.3390/plants11030350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/24/2023]
Abstract
More than 95,000 protein–protein interactions of Arabidopsis thaliana have been published and deposited in databases. This dataset was supplemented by approximately 900 additional interactions, which were identified in the literature from the years 2002–2021. These protein–protein interactions were used as the basis for a Cytoscape network and were supplemented with data on subcellular localization, gene ontologies, biochemical properties and co-expression. The resulting network has been exemplarily applied in unraveling the PPI-network of the plant vacuolar proton-translocating ATPase (V-ATPase), which was selected due to its central importance for the plant cell. In particular, it is involved in cellular pH homeostasis, providing proton motive force necessary for transport processes, trafficking of proteins and, thereby, cell wall synthesis. The data points to regulation taking place on multiple levels: (a) a phosphorylation-dependent regulation by 14-3-3 proteins and by kinases such as WNK8 and NDPK1a, (b) an energy-dependent regulation via HXK1 and the glucose receptor RGS1 and (c) a Ca2+-dependent regulation by SOS2 and IDQ6. The known importance of V-ATPase for cell wall synthesis is supported by its interactions with several proteins involved in cell wall synthesis. The resulting network was further analyzed for (experimental) biases and was found to be enriched in nuclear, cytosolic and plasma membrane proteins but depleted in extracellular and mitochondrial proteins, in comparison to the entity of protein-coding genes. Among the processes and functions, proteins involved in transcription were highly abundant in the network. Subnetworks were extracted for organelles, processes and protein families. The degree of representation of organelles and processes reveals limitations and advantages in the current knowledge of protein–protein interactions, which have been mainly caused by a high number of database entries being contributed by only a few publications with highly specific motivations and methodologies that favor, for instance, interactions in the cytosol and the nucleus.
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23
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Xu H, Wang C, Shao G, Wu S, Liu P, Cao P, Jiang P, Wang S, Zhu H, Lin X, Tauqeer A, Lin Y, Chen W, Huang W, Wen Q, Chang J, Zhong F, Wu S. The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption. HORTICULTURE RESEARCH 2022; 9:uhac123. [PMID: 35949690 PMCID: PMC9358696 DOI: 10.1093/hr/uhac123] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/17/2022] [Indexed: 05/20/2023]
Abstract
Brassica rapa includes various vegetables with high economic value. Among them, green petiole type pakchoi (B. rapa ssp. chinensis) is one of the major vegetables grown in southern China. Compared with other B. rapa varieties, green petiole type pakchoi shows a higher level of heat resistance, which is partially derived from the rich epicuticular wax. Here we sequence a high-quality genome of green petiole type pakchoi, which has been widely used as the parent in breeding. Our results reveal that long terminal repeat retrotransposon insertion plays critical roles in promoting the genome expansion and transcriptional diversity of pakchoi genes through preferential insertions, particularly in cuticle biosynthetic genes. After whole-genome triplication, over-retained pakchoi genes escape stringent selection pressure, and among them a set of cuticle-related genes are retained. Using bulked-segregant analysis of a heat-resistant pakchoi cultivar, we identify a frame-shift deletion across the third exon and the subsequent intron of BrcCER1 in candidate regions. Using Nanopore long-read sequencing, we analyze the full-length transcriptome of two pakchoi cultivars with opposite sensitivity to high temperature. We find that the heat-resistant pakchoi cultivar can mitigate heat-caused leaf damage by activating an unfolded protein response, as well as by inhibiting chloroplast development and energy metabolism, which are presumably mediated by both transcriptional regulation and splicing factors. Our study provides valuable resources for Brassica functional genomics and breeding research, and deepens our understanding of plant stress resistance.
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Affiliation(s)
| | | | | | - Shasha Wu
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Liu
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ping Cao
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Peng Jiang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shubin Wang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Zhu
- Fujian Seed Chief Station, Fuzhou 350003, China
| | - Xiao Lin
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Arfa Tauqeer
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yizhang Lin
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Wei Chen
- Fujian Seed Chief Station, Fuzhou 350003, China
| | | | - Qingfang Wen
- Crop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Jiang Chang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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24
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Sepulveda-Garcia E, Fulton EC, Parlan EV, O’Connor LE, Fleming AA, Replogle AJ, Rocha-Sosa M, Gendron JM, Thines B. Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2021; 10:2228. [PMID: 34686037 PMCID: PMC8537223 DOI: 10.3390/plants10102228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022]
Abstract
SCF-type E3 ubiquitin ligases provide specificity to numerous selective protein degradation events in plants, including those that enable survival under environmental stress. SCF complexes use F-box (FBX) proteins as interchangeable substrate adaptors to recruit protein targets for ubiquitylation. FBX proteins almost universally have structure with two domains: A conserved N-terminal F-box domain interacts with a SKP protein and connects the FBX protein to the core SCF complex, while a C-terminal domain interacts with the protein target and facilitates recruitment. The F-BOX STRESS INDUCED (FBS) subfamily of plant FBX proteins has an atypical structure, however, with a centrally located F-box domain and additional conserved regions at both the N- and C-termini. FBS proteins have been linked to environmental stress networks, but no ubiquitylation target(s) or biological function has been established for this subfamily. We have identified two WD40 repeat-like proteins in Arabidopsis that are highly conserved in plants and interact with FBS proteins, which we have named FBS INTERACTING PROTEINs (FBIPs). FBIPs interact exclusively with the N-terminus of FBS proteins, and this interaction occurs in the nucleus. FBS1 destabilizes FBIP1, consistent with FBIPs being ubiquitylation targets SCFFBS1 complexes. This work indicates that FBS proteins may function in stress-responsive nuclear events, and it identifies two WD40 repeat-like proteins as new tools with which to probe how an atypical SCF complex, SCFFBS, functions via FBX protein N-terminal interaction events.
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Affiliation(s)
- Edgar Sepulveda-Garcia
- Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Mexico;
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico;
| | - Elena C. Fulton
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Emily V. Parlan
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Lily E. O’Connor
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Anneke A. Fleming
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Amy J. Replogle
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Mario Rocha-Sosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico;
| | - Joshua M. Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA;
| | - Bryan Thines
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
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25
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Jost R. How sensing arsenite helps plants survive on toxic soils. MOLECULAR PLANT 2021; 14:1424-1426. [PMID: 34216832 DOI: 10.1016/j.molp.2021.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Ricarda Jost
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, Australian Research HUB for Medicinal Agriculture, La Trobe Institute for Agriculture and Food (LIAF), La Trobe University, Bundoora, VIC, Australia.
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26
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Tian W, Wang R, Bo C, Yu Y, Zhang Y, Shin GI, Kim WY, Wang L. SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis. Nucleic Acids Res 2021; 49:3764-3780. [PMID: 33675668 PMCID: PMC8053106 DOI: 10.1093/nar/gkab128] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
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Affiliation(s)
- Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ruyi Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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27
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Mo F, Li H, Li Y, Chen X, Wang M, Li Z, Deng N, Yang Y, Huang X, Zhang R, Deng W. Physiological, biochemical, and transcriptional regulation in a leguminous forage Trifolium pratense L. responding to silver ions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:531-546. [PMID: 33773229 DOI: 10.1016/j.plaphy.2021.02.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Trifolium pratense L. (red clover) is an important leguminous crop with great potential for Ag-contaminated environment remediation. Whereas, the molecular mechanisms of Ag tolerance in red clover are largely unknown. Red clover seedlings were used for physiological and transcriptomic investigation under 0, 20, 50, and 100 mg/L Ag+ stress in our research to reveal potential molecular resistance mechanism. Research showed that red clover possessed fairly strong Ag absorbance capacity, the Ag level reached 0.14 and 2.35 mg/g·FW in the leaves and roots under 100 mg/L AgNO3 stress condition. Root fresh weight, root dry weight, root water content, and photosynthetic pigments contents were significantly decreased with elevating AgNO3 concentration. Obvious withered plant tissue, microstructure disorder, and disrupted organelles were observed. In vitro evaluations (e.g., PI and DCFH-DA staining) represented that AgNO3 at high concentration (100 mg/L) exhibited obvious inhibition on cell viability, which was due possibly to the induction of reactive oxygen species (ROS) accumulation. A total of 44643 differentially expressed genes (DEGs) were identified under Ag stress, covering 27155 upregulated and 17488 downregulated genes. 12 stress-responsive DEGs was authenticated utilizing real-time quantitative PCR (qRT-PCR). Gene ontology (GO) analysis revealed that the DEGs were mostly related to metal ion binding (molecular function), nucleus (cellular component), and defense response (biological process). Involved DEGs in sequence-specific DNA binding transcription factor activity, response to various hormones (e.g., abscisic acid, IAA/Auxin, salicylic acid, and etc), calcium signal transduction, and protein ubiquitination were concluded to play crucial roles in Ag tolerance of red clover. On the other hand, Kyoto Encyclopedia of Genes and Genomes (KEGG) database annotated several stress responsive pathways such as plant-pathogen interaction, phenylpropanoid biosynthesis, ubiquitin mediated proteolysis, hormone signal transduction, and autophagy. Several down-regulated genes (e.g., RSF2, RCD1, DOX1, and etc) were identified indicating possible metabolic disturbance. Besides, protein-protein interaction network (PPI) identified several pivotal genes such as ribosomal proteins, TIR, and ZAT.
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Affiliation(s)
- Fan Mo
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Haibo Li
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Yinghua Li
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Xi Chen
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Mingshuai Wang
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Zhe Li
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Ningcan Deng
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Yue Yang
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Xin Huang
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Ran Zhang
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
| | - Wenhe Deng
- School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China.
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28
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Cheng T, Zhao P, Ren Y, Zou J, Sun MX. AtMIF1 increases seed oil content by attenuating GL2 inhibition. THE NEW PHYTOLOGIST 2021; 229:2152-2162. [PMID: 33098089 DOI: 10.1111/nph.17016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/30/2020] [Indexed: 05/22/2023]
Abstract
Vegetable oil is a major edible oil and an important industrial raw material. However, breeders have found it challenging to improve the oil content of crop seeds, and little is known about regulators with the potential to increase oil content via molecular engineering in modern oil crop breeding. We reported an F-box protein, Arabidopsis thaliana MYB Interaction Factor 1 (AtMIF1), which is a member of the ubiquitin-protein ligase E3 complex involved in the 26S proteasome protein degradation pathway. AtMIF1 physically interacts with MYB domain protein 5 (MYB5), which results in MYB5 degradation, so that transcriptional activation of the MYB/bHLH/WD-repeat (MBW) complex does not occur normally and GLABRA2 (GL2), encoding an inhibitor of oil content and functioning as a direct downstream gene of MBW, is not properly transcribed. AtMIF1 functioned as a positive regulator that increases oil content by attenuating GL2 inhibition. We overexpressed AtMIF1 and obtained transgenic plants with significantly higher seed oil contents. Importantly, both vegetative and reproductive growth of the transgenic plants appeared normal. In summary, this work reveals a novel regulator, AtMIF1, and a new regulatory pathway, 26S proteasome-AtMIF1-MYB5, for increasing the oil content of seeds without affecting plant growth, thus facilitating oil crop breeding.
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Affiliation(s)
- Tianhe Cheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanru Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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29
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Yapa MM, Yu P, Liao F, Moore AG, Hua Z. Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF-mediated intracellular functions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:493-509. [PMID: 33543567 DOI: 10.1111/tpj.14939] [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: 06/24/2019] [Accepted: 07/09/2020] [Indexed: 06/12/2023]
Abstract
Many eukaryotic intracellular processes employ protein ubiquitylation by ubiquitin E3 ligases for functional regulation or protein quality control. In plants, the multi-subunit Skp1-Cullin1-F-box (SCF) complexes compose the largest group of E3 ligases whose specificity is determined by a diverse array of F-box proteins. Although both sequence divergence and polymorphism of F-box genes well support a broad spectrum of SCF functions, experimental evidence is scarce due to the low number of identified SCF substrates. Taking advantage of the bridge role of Skp1 between F-box and Cullin1 in the complex, we systematically analyzed the functional influence of a well-characterized Arabidopsis Skp1-Like1 (ASK1) Ds insertion allele, ask1, in different Arabidopsis accessions. Through 10 generations of backcrossing with Columbia-0 (Col-0), we partially rescued the fertility of this otherwise sterile ask1 allele in Landsberg erecta, thus providing experimental evidence showing the polymorphic roles of SCF complexes. This ask1 mutant produces twisted rosette leaves, a reduced number of petals, fewer viable pollen grains, and larger embryos and seeds compared to Col-0. RNA-Seq-based transcriptome analysis of ask1 uncovered a large spectrum of SCF functions, which is greater than a 10-fold increase compared with previous studies. We also identified its hyposensitive responses to auxin and abscisic acid treatments and enhanced far-red light/phyA-mediated photomorphogenesis. Such diverse roles are consistent with the 20-30% reduction of ubiquitylation events in ask1 estimated by immunoblotting analysis in this work. Collectively, we conclude that ASK1 is a predominant Skp1 protein in Arabidopsis and that the fertile ask1 mutant allowed us to uncover a comprehensive set of SCF functions.
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Affiliation(s)
- Madhura M Yapa
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
| | - Peifeng Yu
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio, 45701, USA
| | - Fanglei Liao
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
| | - Abigail G Moore
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio, 45701, USA
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30
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Weng ST, Kuo YW, King YC, Lin HH, Tu PY, Tung KS, Jeng ST. Regulation of micoRNA2111 and its target IbFBK in sweet potato on wounding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110391. [PMID: 32005396 DOI: 10.1016/j.plantsci.2019.110391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 05/14/2023]
Abstract
Plant microRNAs (miRNAs) are non-coding RNAs, which are composed of 20-24 nucleotides. MiRNAs play important roles in plant growth and responses to biotic and abiotic stresses. Wounding is one of the most serious stresses for plants; however, the regulation of miRNAs in plants upon wounding is not well studied. In this study, miR2111, a wound-repressed miRNA, identified previously in sweet potato (Ipomoea batatas cv Tainung 57) by small RNA deep sequencing was chosen for further analysis. Based on sweet potato transcriptome database, F-box/kelch repeat protein (IbFBK), a target gene of miR2111, was identified. IbFBK is a wound-inducible gene, and the miR2111-induced cleavage site in IbFBK mRNA is between the 10th and 11th nucleotides of miR2111. IbFBK is a component of the E3 ligase SCF (SKP1-Cullin-F-box) complex participating in protein ubiquitination and degradation. The results of yeast two-hybrid and bimolecular fluorescence complementation assays demonstrate that IbFBK was conjugated with IbSKP1 through the F-box domain in IbFBK N-terminus to form SCF complex, and interacted with IbCNR8 through the kelch-repeat domain in IbFBK C-terminus. The interaction of IbFBK and IbCNR8 may lead to the ubiquitination and degradation of IbCNR8. In conclusion, the suppression of miR2111 resulted in the increase of IbFBK, and may regulate protein degradation of IbCNR8 in sweet potato responding to wounding.
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Affiliation(s)
- Shiau-Ting Weng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; Academy of Agricultural Sciences, Sanming 365000, Fujian, China.
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pin-Yang Tu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Kuei-Shu Tung
- Institute of Molecular and Cellular Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
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Abd-Hamid NA, Ahmad-Fauzi MI, Zainal Z, Ismail I. Diverse and dynamic roles of F-box proteins in plant biology. PLANTA 2020; 251:68. [PMID: 32072251 DOI: 10.1007/s00425-020-03356-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Muhammad-Izzat Ahmad-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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32
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Hwang JE, Hwang SG, Jung IJ, Han SM, Ahn JW, Kim JB. Overexpression of rice F-box protein OsFBX322 confers increased sensitivity to gamma irradiation in Arabidopsis. Genet Mol Biol 2019; 43:e20180273. [PMID: 31479093 PMCID: PMC7251472 DOI: 10.1590/1678-4685-gmb-2018-0273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 03/25/2019] [Indexed: 11/30/2022] Open
Abstract
Ionizing radiation has a substantial effect on physiological and biochemical
processes in plants via induction of transcriptional changes and diverse genetic
alterations. Previous microarray analysis showed that rice
OsFBX322, which encodes a rice F-box protein, was
downregulated in response to three types of ionizing radiation: gamma
irradiation, ion beams, and cosmic rays. In order to characterize the
radiation-responsive genes in rice, OsFBX322 was selected for
further analysis. OsFBX322 expression patterns in response to
radiation were confirmed using quantitative RT-PCR. Transient expression of a
GFP-OsFBX322 fusion protein in tobacco leaf epidermis indicated that OsFBX322 is
localized to the nucleus. To determine the effect of OsFBX322
expression on radiation response, OsFBX322 was overexpressed in
Arabidopsis. Transgenic overexpression lines were more
sensitive to gamma irradiation than control plants. These results suggest that
OsFBX322 plays a negative role in the defense response to
radiation in plants. In addition, we obtained four co-expression genes of
OsFBX322 by specific co-expression networks using the
ARANCE. Quantitative RT-PCR showed that the four genes were also downregulated
after exposure to the three types of radiation. These results imply that the
co-expressed genes may serve as key regulators in the radiation response pathway
in plants.
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Affiliation(s)
- Jung Eun Hwang
- National Institute of Ecology, Research Center for Endangered Species, Division of Restoration Research, Yeongyang, Republic of Korea
| | - Sun-Goo Hwang
- Kangwon Natl University, Department of Applied Plant Sciences, Plant Genomics Lab, Chuncheon, Republic of Korea
| | - In Jung Jung
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
| | - Sung Min Han
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
| | - Joon-Woo Ahn
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
| | - Jin-Baek Kim
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
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Williams C, Fernández-Calvo P, Colinas M, Pauwels L, Goossens A. Jasmonate and auxin perception: how plants keep F-boxes in check. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3401-3414. [PMID: 31173086 DOI: 10.1093/jxb/erz272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/29/2019] [Indexed: 05/24/2023]
Abstract
Phytohormones regulate the plasticity of plant growth and development, and responses to biotic and abiotic stresses. Many hormone signal transduction cascades involve ubiquitination and subsequent degradation of proteins by the 26S proteasome. The conjugation of ubiquitin to a substrate is facilitated by the E1 activating, E2 conjugating, and the substrate-specifying E3 ligating enzymes. The most prevalent type of E3 ligase in plants is the Cullin-RING ligase (CRL)-type, with F-box proteins (FBPs) as the substrate recognition component. The activity of these SKP-Cullin-F-box (SCF) complexes needs to be tightly regulated in time and place. Here, we review the regulation of SCF function in plants on multiple levels, with a focus on the auxin and jasmonate SCF-type receptor complexes. We discuss in particular the relevance of protein-protein interactions and post-translational modifications as mechanisms to keep SCF functioning under control. Additionally, we highlight the unique property of SCFTIR1/AFB and SCFCOI1 to recognize substrates by forming co-receptor complexes. Finally, we explore how engineered selective agonists can be used to study and uncouple the outcomes of the complex auxin and jasmonate signaling networks that are governed by these FBPs.
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Affiliation(s)
- Clara Williams
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Patricia Fernández-Calvo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Centre for Plant Biotechnology and Genomics, Parque Cientifico y Tecnologico, UPM Campus de Montegancedo, Madrid, Spain
| | - Maite Colinas
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Lama S, Broda M, Abbas Z, Vaneechoutte D, Belt K, Säll T, Vandepoele K, Van Aken O. Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants. Mol Biol Evol 2019; 36:974-989. [PMID: 30938771 PMCID: PMC6501883 DOI: 10.1093/molbev/msz031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Because of their symbiotic origin, many mitochondrial proteins are well conserved across eukaryotic kingdoms. It is however less obvious how specific lineages have obtained novel nuclear-encoded mitochondrial proteins. Here, we report a case of mitochondrial neofunctionalization in plants. Phylogenetic analysis of genes containing the Domain of Unknown Function 295 (DUF295) revealed that the domain likely originated in Angiosperms. The C-terminal DUF295 domain is usually accompanied by an N-terminal F-box domain, involved in ubiquitin ligation via binding with ASK1/SKP1-type proteins. Due to gene duplication, the gene family has expanded rapidly, with 94 DUF295-related genes in Arabidopsis thaliana alone. Two DUF295 family subgroups have uniquely evolved and quickly expanded within Brassicaceae. One of these subgroups has completely lost the F-box, but instead obtained strongly predicted mitochondrial targeting peptides. We show that several representatives of this DUF295 Organellar group are effectively targeted to plant mitochondria and chloroplasts. Furthermore, many DUF295 Organellar genes are induced by mitochondrial dysfunction, whereas F-Box DUF295 genes are not. In agreement, several Brassicaceae-specific DUF295 Organellar genes were incorporated in the evolutionary much older ANAC017-dependent mitochondrial retrograde signaling pathway. Finally, a representative set of DUF295 T-DNA insertion mutants was created. No obvious aberrant phenotypes during normal growth and mitochondrial dysfunction were observed, most likely due to the large extent of gene duplication and redundancy. Overall, this study provides insight into how novel mitochondrial proteins can be created via “intercompartmental” gene duplication events. Moreover, our analysis shows that these newly evolved genes can then be specifically integrated into relevant, pre-existing coexpression networks.
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Affiliation(s)
- Sbatie Lama
- Department of Biology, Lund University, Lund, Sweden
| | - Martyna Broda
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Zahra Abbas
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Katharina Belt
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia.,CSIRO, Floreat, WA, Australia
| | - Torbjörn Säll
- Department of Biology, Lund University, Lund, Sweden
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
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35
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Hua Z, Gao Z. Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana. PeerJ 2019; 7:e6740. [PMID: 30997292 PMCID: PMC6463862 DOI: 10.7717/peerj.6740] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/07/2019] [Indexed: 11/20/2022] Open
Abstract
Genome sequencing has uncovered tremendous sequence variation within and between species. In plants, in addition to large variations in genome size, a great deal of sequence polymorphism is also evident in several large multi-gene families, including those involved in the ubiquitin-26S proteasome protein degradation system. However, the biological function of this sequence variation is yet not clear. In this work, we explicitly demonstrated a single origin of retroposed Arabidopsis Skp1-Like (ASK) genes using an improved phylogenetic analysis. Taking advantage of the 1,001 genomes project, we here provide several lines of polymorphism evidence showing both adaptive and degenerative evolutionary processes in ASK genes. Yeast two-hybrid quantitative interaction assays further suggested that recent neutral changes in the ASK2 coding sequence weakened its interactions with some F-box proteins. The trend that highly polymorphic upstream regions of ASK1 yield high levels of expression implied negative expression regulation of ASK1 by an as-yet-unknown transcriptional suppression mechanism, which may contribute to the polymorphic roles of Skp1-CUL1-F-box complexes. Taken together, this study provides new evolutionary evidence to guide future functional genomic studies of SCF-mediated protein ubiquitylation.
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Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology and Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, USA
| | - Zhenyu Gao
- Department of Environmental and Plant Biology and Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, USA
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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36
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Yoshida Y, Mizushima T, Tanaka K. Sugar-Recognizing Ubiquitin Ligases: Action Mechanisms and Physiology. Front Physiol 2019; 10:104. [PMID: 30837888 PMCID: PMC6389600 DOI: 10.3389/fphys.2019.00104] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022] Open
Abstract
F-box proteins, the substrate recognition subunits of SKP1–CUL1–F-box protein (SCF) E3 ubiquitin ligase complexes, play crucial roles in various cellular events mediated by ubiquitination. Several sugar-recognizing F-box proteins exist in both mammalian and plant cells. Although glycoproteins generally reside outside of cells, or in organelles of the secretory pathway, these lectin-type F-box proteins reside in the nucleocytoplasmic compartment. Mammalian sugar-recognizing F-box proteins commonly bind to the innermost position of N-glycans through a unique small hydrophobic pocket in their loops. Two cytosolic F-box proteins, Fbs1 and Fbs2, recognize high-mannose glycans synthesized in the ER, and SCFFbs1 and SCFFbs2 ubiquitinate excess unassembled or misfolded glycoproteins in the ERAD pathway by recognizing the innermost glycans, which serve as signals for aberrant proteins. On the other hand, endomembrane-bound Fbs3 recognizes complex glycans as well as high-mannose glycans, and SCFFbs3 ubiquitinates exposed glycoproteins in damaged lysosomes fated for elimination by selective autophagy. Plants express stress-inducible lectin-type F-box proteins recognizing a wider range of N- and O-glycans, suggesting that the roles of mammalian and plant lectin-type F-box proteins have diverged over the course of evolution to recognize species-specific targets with distinct functions. These sugar-recognizing F-box proteins interpret glycans in the cytosol as markers of unwanted proteins and organelles, and degrade them via the proteasome or autophagy.
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Affiliation(s)
- Yukiko Yoshida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tsunehiro Mizushima
- Graduate School of Life Science, Picobiology Institute, University of Hyogo, Kobe, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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37
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Klepikova AV, Kulakovskiy IV, Kasianov AS, Logacheva MD, Penin AA. An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana. BMC PLANT BIOLOGY 2019; 19:49. [PMID: 30813912 PMCID: PMC6393959 DOI: 10.1186/s12870-019-1636-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress .
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Affiliation(s)
- Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
| | - Ivan V. Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991 Russia
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, Pushchino, Moscow Region, 142290 Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991 Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
- Moscow State University, Leninskye gory, build 1, Moscow, 119992 Russia
- Skolkovo Institute of Science and Technology, Nobelya Ulitsa 3, Moscow, 121205 Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
- Moscow State University, Leninskye gory, build 1, Moscow, 119992 Russia
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38
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Rao V, Petla BP, Verma P, Salvi P, Kamble NU, Ghosh S, Kaur H, Saxena SC, Majee M. Arabidopsis SKP1-like protein13 (ASK13) positively regulates seed germination and seedling growth under abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3899-3915. [PMID: 29788274 PMCID: PMC6054272 DOI: 10.1093/jxb/ery191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/15/2018] [Indexed: 05/03/2023]
Abstract
SKP1 (S-phase kinase-associated protein1) proteins are key members of the SCF (SKP-cullin-F-box protein) E3 ligase complexes that ubiquitinate target proteins and play diverse roles in plant biology. However, in comparison with other members of the SCF complex, knowledge of SKP1-like proteins is very limited in plants. In the present work, we report that Arabidopsis SKP1-like protein13 (ASK13) is differentially regulated in different organs during seed development and germination and is up-regulated in response to abiotic stress. Yeast two-hybrid library screening and subsequent assessment of in vivo interactions through bimolecular fluorescence complementation analysis revealed that ASK13 not only interacts with F-box proteins but also with other proteins that are not components of SCF complexes. Biochemical analysis demonstrated that ASK13 not only exists as a monomer but also as a homo-oligomer or heteromer with other ASK proteins. Functional analysis using ASK13 overexpression and knockdown lines showed that ASK13 positively influences seed germination and seedling growth, particularly under abiotic stress. Taken together, our data strongly suggest that apart from participation to form SCF complexes, ASK13 interacts with several other proteins and is implicated in different cellular processes distinct from protein degradation.
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Affiliation(s)
- Venkateswara Rao
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Bhanu Prakash Petla
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Pooja Verma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Prafull Salvi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Nitin Uttam Kamble
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shraboni Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Harmeet Kaur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Saurabh C Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Manoj Majee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
- Correspondence:
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39
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Regulation of SCF TIR1/AFBs E3 ligase assembly by S-nitrosylation of Arabidopsis SKP1-like1 impacts on auxin signaling. Redox Biol 2018; 18:200-210. [PMID: 30031268 PMCID: PMC6076216 DOI: 10.1016/j.redox.2018.07.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/26/2018] [Accepted: 07/05/2018] [Indexed: 12/22/2022] Open
Abstract
The F-box proteins (FBPs) TIR1/AFBs are the substrate recognition subunits of SKP1–cullin–F-box (SCF) ubiquitin ligase complexes and together with Aux/IAAs form the auxin co-receptor. Although tremendous knowledge on auxin perception and signaling has been gained in the last years, SCFTIR1/AFBs complex assembly and stabilization are emerging as new layers of regulation. Here, we investigated how nitric oxide (NO), through S-nitrosylation of ASK1 is involved in SCFTIR1/AFBs assembly. We demonstrate that ASK1 is S-nitrosylated and S-glutathionylated in cysteine (Cys) 37 and Cys118 residues in vitro. Both, in vitro and in vivo protein-protein interaction assays show that NO enhances ASK1 binding to CUL1 and TIR1/AFB2, required for SCFTIR1/AFB2 assembly. In addition, we demonstrate that Cys37 and Cys118 are essential residues for proper activation of auxin signaling pathway in planta. Phylogenetic analysis revealed that Cys37 residue is only conserved in SKP proteins in Angiosperms, suggesting that S-nitrosylation on Cys37 could represent an evolutionary adaption for SKP1 function in flowering plants. Collectively, these findings indicate that multiple events of redox modifications might be part of a fine-tuning regulation of SCFTIR1/AFBs for proper auxin signal transduction. ASK1 adaptor protein of the SCFTIR1/AFB E3 ligase complex is redox regulated. NO regulates ASK1 function by S-nitrosylation in Cys37 and Cys118 residues. NO enhances ASK1-CUL1 and ASK1-TIR1/AFB2 protein-protein interactions required for SCFTIR1/AFB2 assembly in vitro and in vivo. S-nitrosylated residues in ASK1 are essential for activation of auxin signaling pathway in plants.
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40
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Chen Y, Chi Y, Meng Q, Wang X, Yu D. GmSK1, an SKP1 homologue in soybean, is involved in the tolerance to salt and drought. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:25-31. [PMID: 29544210 DOI: 10.1016/j.plaphy.2018.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 02/26/2018] [Accepted: 03/06/2018] [Indexed: 05/20/2023]
Abstract
In plants, various proteins are regulated by the ubiquitin-mediated system in response to different environmental stresses, such as drought, cold and heat. The Skp1-Cullin-F-box (SCF) complex, one of the multisubunit E3 ligases, has been shown to be involved in abiotic response pathways. In this study, Glycine max SKP1-like 1 (GmSK1), which had the typical characteristics of an SKP1 protein, with an alpha/beta structure, targeted to the cytoplasm and nucleus, was isolated from soybean [Glycine max (L.)]. GmSK1 was constitutively expressed in all the tested tissues, especially in the roots. Furthermore, the expression of GmSK1 was simultaneously induced by abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), NaCl, low temperatures and drought, which suggests important roles for GmSK1 in plant responses to hormone treatments and abiotic stress. GmSK1-overexpressing transgenic tobacco (Nicotiana tobacum cv. Samsun) plants showed enhanced tolerance to high salinity and drought stress; exhibited significantly reduced inhibition of growth, greenness and water loss; and exhibited increased MDA accumulation compared with wild-type controls. Our results suggest that GmSK1 might play a role in the crosstalk between ubiquitination and abiotic stress responses in plants.
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Affiliation(s)
- Yanping Chen
- College of Life Sciences/National Center for Soybean Improvement/Nanjing Agricultural University, Nanjing, 210095, China; Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yingjun Chi
- College of Life Sciences/National Center for Soybean Improvement/Nanjing Agricultural University, Nanjing, 210095, China; College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qingchang Meng
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xiaolin Wang
- College of Life Sciences/National Center for Soybean Improvement/Nanjing Agricultural University, Nanjing, 210095, China
| | - Deyue Yu
- College of Life Sciences/National Center for Soybean Improvement/Nanjing Agricultural University, Nanjing, 210095, China.
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41
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Li H, Yao R, Ma S, Hu S, Li S, Wang Y, Yan C, Xie D, Yan J. Efficient ASK-assisted system for expression and purification of plant F-box proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:736-743. [PMID: 28985004 DOI: 10.1111/tpj.13708] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Ubiquitin-mediated protein degradation plays an essential role in plant growth and development as well as responses to environmental and endogenous signals. F-box protein is one of the key components of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which recruit specific substrate proteins for subsequent ubiquitination and 26S proteasome-mediated degradation to regulate developmental processes and signaling networks. However, it is not easy to obtain purified F-box proteins with high activity due to their unstable protein structures. Here, we found that Arabidopsis SKP-like proteins (ASKs) can significantly improve soluble expression of F-box proteins and maintain their bioactivity. We established an efficient ASK-assisted method to express and purify plant F-box proteins. The method meets a broad range of criteria required for the biochemical analysis or protein crystallization of plant F-box proteins.
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Affiliation(s)
- Haiou Li
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Ruifeng Yao
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Sui Ma
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shuai Hu
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Suhua Li
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yupei Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chun Yan
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Daoxin Xie
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jianbin Yan
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
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He R, Li X, Zhong M, Yan J, Ji R, Li X, Wang Q, Wu D, Sun M, Tang D, Lin J, Li H, Liu B, Liu H, Liu X, Zhao X, Lin C. A photo-responsive F-box protein FOF2 regulates floral initiation by promoting FLC expression in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:788-801. [PMID: 28608936 DOI: 10.1111/tpj.13607] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/08/2017] [Accepted: 05/13/2017] [Indexed: 05/09/2023]
Abstract
Floral initiation is regulated by various genetic pathways in response to light, temperature, hormones and developmental status; however, the molecular mechanisms underlying the interactions between different genetic pathways are not fully understood. Here, we show that the photoresponsive gene FOF2 (F-box of flowering 2) negatively regulates flowering. FOF2 encodes a putative F-box protein that interacts specifically with ASK14, and its overexpression results in later flowering under both long-day and short-day photoperiods. Conversely, transgenic plants expressing the F-box domain deletion mutant of FOF2 (FOF2ΔF), or double loss of function mutant of FOF2 and FOL1 (FOF2-LIKE 1) present early flowering phenotypes. The late flowering phenotype of the FOF2 overexpression lines is suppressed by the flc-3 loss-of-function mutation. Furthermore, FOF2 mRNA expression is regulated by autonomous pathway gene FCA, and the repressive effect of FOF2 in flowering can be overcome by vernalization. Interestingly, FOF2 expression is regulated by light. The protein level of FOF2 accumulates in response to light, whereas it is degraded under dark conditions via the 26S proteasome pathway. Our findings suggest a possible mechanistic link between light conditions and the autonomous floral promotion pathway in Arabidopsis.
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Affiliation(s)
- Reqing He
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Xinmei Li
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Ming Zhong
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Jindong Yan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Ronghuan Ji
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qin Wang
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Dan Wu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Mengsi Sun
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Dongying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Jianzhong Lin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Hongyu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaoying Zhao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA
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43
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Gonzalez LE, Keller K, Chan KX, Gessel MM, Thines BC. Transcriptome analysis uncovers Arabidopsis F-BOX STRESS INDUCED 1 as a regulator of jasmonic acid and abscisic acid stress gene expression. BMC Genomics 2017; 18:533. [PMID: 28716048 PMCID: PMC5512810 DOI: 10.1186/s12864-017-3864-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 06/15/2017] [Indexed: 01/14/2023] Open
Abstract
Background The ubiquitin 26S proteasome system (UPS) selectively degrades cellular proteins, which results in physiological changes to eukaryotic cells. F-box proteins are substrate adaptors within the UPS and are responsible for the diversity of potential protein targets. Plant genomes are enriched in F-box genes, but the vast majority of these have unknown roles. This work investigated the Arabidopsis F-box gene F-BOX STRESS INDUCED 1 (FBS1) for its effects on gene expression in order elucidate its previously unknown biological function. Results Using publically available Affymetrix ATH1 microarray data, we show that FBS1 is significantly co-expressed in abiotic stresses with other well-characterized stress response genes, including important stress-related transcriptional regulators. This gene suite is most highly expressed in roots under cold and salt stresses. Transcriptome analysis of fbs1–1 knock-out plants grown at a chilling temperature shows that hundreds of genes require FBS1 for appropriate expression, and that these genes are enriched in those having roles in both abiotic and biotic stress responses. Based on both this genome-wide expression data set and quantitative real-time PCR (qPCR) analysis, it is apparent that FBS1 is required for elevated expression of many jasmonic acid (JA) genes that have established roles in combatting environmental stresses, and that it also controls a subset of JA biosynthesis genes. FBS1 also significantly impacts abscisic acid (ABA) regulated genes, but this interaction is more complex, as FBS1 has both positive and negative effects on ABA-inducible and ABA-repressible gene modules. One noteworthy effect of FBS1 on ABA-related stress processes, however, is the restraint it imposes on the expression of multiple class I LIPID TRANSFER PROTEIN (LTP) gene family members that have demonstrated protective effects in water deficit-related stresses. Conclusion FBS1 impacts plant stress responses by regulating hundreds of genes that respond to the plant stress hormones JA and ABA. The positive effect that FBS1 has on JA processes and the negative effect it has on at least some ABA processes indicates that it in part regulates cellular responses balanced between these two important stress hormones. More broadly then, FBS1 may aid plant cells in switching between certain biotic (JA) and abiotic (ABA) stress responses. Finally, because FBS1 regulates a subset of JA biosynthesis and response genes, we conclude that it might have a role in tuning hormone responses to particular circumstances at the transcriptional level. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3864-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lauren E Gonzalez
- Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA.,Present address: Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Kristen Keller
- Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA.,Present address: Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, CA, 90095, USA
| | - Karen X Chan
- Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Megan M Gessel
- Chemistry Department, University of Puget Sound, Tacoma, WA, 98416, USA
| | - Bryan C Thines
- Biology Department, University of Puget Sound, Tacoma, WA, 98416, USA.
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Eggermont L, Verstraeten B, Van Damme EJM. Genome-Wide Screening for Lectin Motifs in Arabidopsis thaliana. THE PLANT GENOME 2017; 10. [PMID: 28724081 DOI: 10.3835/plantgenome2017.02.0010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
For more than three decades, served as a model for plant biology research. At present only a few protein families have been studied in detail in . This study focused on all sequences with lectin motifs in the genome of . Based on amino acid sequence similarity (BLASTp searches), 217 putative lectin genes were retrieved belonging to 9 out of 12 different lectin families. The domain organization and genomic distribution for each lectin family were analyzed. Domain architecture analysis revealed that most of these lectin gene sequences are linked to other domains, often belonging to protein families with catalytic activity. Many protein domains identified are known to play a role in stress signaling and defense, suggesting a major contribution of the putative lectins in development and plant defense. This genome-wide screen for different lectin motifs will help to unravel the functional characteristics of lectins. In addition, phylogenetic trees and WebLogos were created and showed that most lectin sequences that share the same domain architecture evolved together. Furthermore, the amino acids responsible for carbohydrate binding are largely conserved. Our results provide information about the evolutionary relationships and functional divergence of the lectin motifs in .
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45
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Van Holle S, De Schutter K, Eggermont L, Tsaneva M, Dang L, Van Damme EJM. Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics. Int J Mol Sci 2017; 18:ijms18061136. [PMID: 28587095 PMCID: PMC5485960 DOI: 10.3390/ijms18061136] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 01/07/2023] Open
Abstract
Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsisthaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.
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Affiliation(s)
- Sofie Van Holle
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Kristof De Schutter
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Lore Eggermont
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Mariya Tsaneva
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Liuyi Dang
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Els J M Van Damme
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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46
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Brenner WG, Leuendorf JE, Cortleven A, Martin LBB, Schaller H, Schmülling T. Analysis of CFB, a cytokinin-responsive gene of Arabidopsis thaliana encoding a novel F-box protein regulating sterol biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2769-2785. [PMID: 28505379 PMCID: PMC5853388 DOI: 10.1093/jxb/erx146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 04/06/2017] [Indexed: 05/29/2023]
Abstract
Protein degradation by the ubiquitin-26S proteasome pathway is important for the regulation of cellular processes, but the function of most F-box proteins relevant to substrate recognition is unknown. We describe the analysis of the gene Cytokinin-induced F-box encoding (CFB, AT3G44326), identified in a meta-analysis of cytokinin-related transcriptome studies as one of the most robust cytokinin response genes. F-box domain-dependent interaction with the E3 ubiquitin ligase complex component ASK1 classifies CFB as a functional F-box protein. Apart from F-box and transmembrane domains, CFB contains no known functional domains. CFB is expressed in all plant tissues, predominantly in root tissue. A ProCFB:GFP-GUS fusion gene showed strongest expression in the lateral root cap and during lateral root formation. CFB-GFP fusion proteins were mainly localized in the nucleus and the cytosol but also at the plasma membrane. cfb mutants had no discernible phenotype, but CFB overexpressing plants showed several defects, such as a white upper inflorescence stem, similar to the hypomorphic cycloartenol synthase mutant cas1-1. Both CFB overexpressing plants and cas1-1 mutants accumulated the CAS1 substrate 2,3-oxidosqualene in the white stem tissue, the latter even more after cytokinin treatment, indicating impairment of CAS1 function. This suggests that CFB may link cytokinin and the sterol biosynthesis pathway.
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Affiliation(s)
- Wolfram G Brenner
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
| | - Jan Erik Leuendorf
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
| | - Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
| | - Laetitia B B Martin
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, rue du Général Zimmer, Strasbourg Cedex, France
| | - Hubert Schaller
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, rue du Général Zimmer, Strasbourg Cedex, France
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
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47
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Jia Q, Xiao ZX, Wong FL, Sun S, Liang KJ, Lam HM. Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress. Int J Mol Sci 2017; 18:E818. [PMID: 28417911 PMCID: PMC5412402 DOI: 10.3390/ijms18040818] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
The F-box family is one of the largest gene families in plants that regulate diverse life processes, including salt responses. However, the knowledge of the soybean F-box genes and their roles in salt tolerance remains limited. Here, we conducted a genome-wide survey of the soybean F-box family, and their expression analysis in response to salinity via in silico analysis of online RNA-sequencing (RNA-seq) data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) to predict their potential functions. A total of 725 potential F-box proteins encoded by 509 genes were identified and classified into 9 subfamilies. The gene structures, conserved domains and chromosomal distributions were characterized. There are 76 pairs of duplicate genes identified, including genome-wide segmental and tandem duplication events, which lead to the expansion of the number of F-box genes. The in silico expression analysis showed that these genes would be involved in diverse developmental functions and play an important role in salt response. Our qRT-PCR analysis confirmed 12 salt-responding F-box genes. Overall, our results provide useful information on soybean F-box genes, especially their potential roles in salt tolerance.
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Affiliation(s)
- Qi Jia
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China.
- School of Life Sciences and Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Zhi-Xia Xiao
- School of Life Sciences and Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Fuk-Ling Wong
- School of Life Sciences and Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Song Sun
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China.
| | - Kang-Jing Liang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China.
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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48
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Hong JP, Adams E, Yanagawa Y, Matsui M, Shin R. AtSKIP18 and AtSKIP31, F-box subunits of the SCF E3 ubiquitin ligase complex, mediate the degradation of 14-3-3 proteins in Arabidopsis. Biochem Biophys Res Commun 2017; 485:174-180. [DOI: 10.1016/j.bbrc.2017.02.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
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49
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Naeem-ul-Hassan M, Zainal Z, Kiat CJ, Monfared HH, Ismail I. Arabidopsis thaliana SKP1 interacting protein 11 (At2g02870) negatively regulates the release of green leaf volatiles. RSC Adv 2017. [DOI: 10.1039/c7ra09895b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AtSKIP11, a kelch-repeat containing F-box protein from Arabidopsis thaliana, negatively regulates the HPL pathway and can serve as a potential molecular switch for the biosynthesis of green leaf volatiles.
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Affiliation(s)
- Muhammad Naeem-ul-Hassan
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Malaysia
- Department of Chemistry
| | - Zamri Zainal
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Malaysia
- Institute of Systems Biology (INBIOSIS)
| | - Chew Jin Kiat
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Malaysia
- Institute of Systems Biology (INBIOSIS)
| | - Hossein Hosseini Monfared
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Malaysia
| | - Ismanizan Ismail
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Malaysia
- Institute of Systems Biology (INBIOSIS)
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50
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Hao Q, Ren H, Zhu J, Wang L, Huang S, Liu Z, Gao Z, Shu Q. Overexpression of PSK1, a SKP1-like gene homologue, from Paeonia suffruticosa, confers salinity tolerance in Arabidopsis. PLANT CELL REPORTS 2017; 36:151-162. [PMID: 27787596 DOI: 10.1007/s00299-016-2066-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/18/2016] [Indexed: 05/25/2023]
Abstract
Our study is the first to demonstrate that PSK1 , a SKP1 -like gene homologue, is involved in salinity tolerance. Our functional characterization of PSK1 provides new insights into tree peony development. A homologous gene of S-phase kinase-associated protein1 (SKP1) was cloned from tree peony (Paeonia suffruticosa) and denoted as PSK1. The 462-bp open reading frame of PSK1 was predicted to encode a protein comprising 153 amino acids, with a molecular mass of 17 kDa. The full-length gene was 1,634 bp long and included a large 904-bp intron. PSK1 transcription was detected in all tissues, with the highest level observed in sepals, followed by leaves. Under salinity stress, overexpression of PSK1 in Arabidopsis resulted in increased germination percentages, cotyledon greening, and fresh weights relative to wild-type plants. Furthermore, transgenic Arabidopsis lines containing 35S::PSK1 displayed increased expression of genes that would be essential for reproduction and growth under salinity stress: ASK1, LEAFY, FT, and CO involved in flower development and flowering time as well as P5CS, RAB18, DREB, and SOD1-3 contributing to salinity tolerance. Our functional characterization of PSK1 adds to global knowledge of the multiple functions of previously explored SKP1-like genes in plants and sheds light on the molecular mechanism underlying its role in salinity tolerance. Our findings also provide information on the function and molecular mechanism of PSK1 in tree peony flower development, thereby revealing a theoretical basis for regulation of flowering and conferral of salinity tolerance in tree peony.
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Affiliation(s)
- Qing Hao
- Landscape and Forestry College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hongxu Ren
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin Zhu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangsheng Wang
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shouchen Huang
- Landscape and Forestry College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zheng'an Liu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhimin Gao
- International Center for Bamboo and Rattan, Key Laboratory on the Science and Technology of Bamboo and Rattan, Beijing, 100102, China.
| | - Qingyan Shu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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