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Wu R, Jia Q, Guo Y, Lin Y, Liu J, Chen J, Yan Q, Yuan N, Xue C, Chen X, Yuan X. Characterization of TBP and TAFs in Mungbean ( Vigna radiata L.) and Their Potential Involvement in Abiotic Stress Response. Int J Mol Sci 2024; 25:9558. [PMID: 39273505 PMCID: PMC11394781 DOI: 10.3390/ijms25179558] [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: 08/02/2024] [Revised: 08/31/2024] [Accepted: 09/01/2024] [Indexed: 09/15/2024] Open
Abstract
The TATA-box binding protein (TBP) and TBP-associated factors (TAFs) constitute the transcription factor IID (TFIID), a crucial component of RNA polymerase II, essential for transcription initiation and regulation. Several TFIID subunits are shared with the Spt-Ada-Gcn5-acetyltransferase (SAGA) coactivator complex. Recent research has revealed the roles of TBP and TAFs in organogenesis and stress adaptation. In this study, we identified 1 TBP and 21 putative TAFs in the mungbean genome, among which VrTAF5, VrTAF6, VrTAF8, VrTAF9, VrTAF14, and VrTAF15 have paralogous genes. Their potential involvement in abiotic stress responses was also investigated here, including high salinity, water deficit, heat, and cold. The findings indicated that distinct genes exerted predominant influences in the response to different abiotic stresses through potentially unique mechanisms. Specifically, under salt stress, VrTBP, VrTAF2, and VrTAF15-1 were strongly induced, while VrTAF10, VrTAF11, and VrTAF13 acted as negative regulators. In the case of water-deficit stress, it was likely that VrTAF1, VrTAF2, VrTAF5-2, VrTAF9, and VrTAF15-1 were primarily involved. Additionally, in response to changes in ambient temperature, it was possible that genes such as VrTAF5-1, VrTAF6-1, VrTAF9-2, VrTAF10, VrTAF13, VrTAF14b-2, and VrTAF15-1 might play a dominant role. This comprehensive exploration of VrTBP and VrTAFs can offer a new perspective on understanding plant stress responses and provide valuable insights into breeding improvement.
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Affiliation(s)
- Ranran Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Qiyuan Jia
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingjian Guo
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Jinyang Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Qiang Yan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Na Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Chenchen Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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Yu R, Xiong Z, Zhu X, Feng P, Hu Z, Fang R, Zhang Y, Liu Q. RcSPL1-RcTAF15b regulates the flowering time of rose ( Rosa chinensis). HORTICULTURE RESEARCH 2023; 10:uhad083. [PMID: 37323236 PMCID: PMC10266950 DOI: 10.1093/hr/uhad083] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Rose (Rosa chinensis), which is an economically valuable floral species worldwide, has three types, namely once-flowering (OF), occasional or re-blooming (OR), and recurrent or continuous flowering (CF). However, the mechanism underlying the effect of the age pathway on the duration of the CF or OF juvenile phase is largely unknown. In this study, we observed that the RcSPL1 transcript levels were substantially upregulated during the floral development period in CF and OF plants. Additionally, accumulation of RcSPL1 protein was controlled by rch-miR156. The ectopic expression of RcSPL1 in Arabidopsis thaliana accelerated the vegetative phase transition and flowering. Furthermore, the transient overexpression of RcSPL1 in rose plants accelerated flowering, whereas silencing of RcSPL1 had the opposite phenotype. Accordingly, the transcription levels of floral meristem identity genes (APETALA1, FRUITFULL, and LEAFY) were significantly affected by the changes in RcSPL1 expression. RcTAF15b protein, which is an autonomous pathway protein, was revealed to interact with RcSPL1. The silencing and overexpression of RcTAF15b in rose plants led to delayed and accelerated flowering, respectively. Collectively, the study findings imply that RcSPL1-RcTAF15b modulates the flowering time of rose plants.
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Affiliation(s)
- Rui Yu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhiying Xiong
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xinhui Zhu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Panpan Feng
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ziyi Hu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Rongxiang Fang
- National Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
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Zentella R, Wang Y, Zahn E, Hu J, Jiang L, Shabanowitz J, Hunt DF, Sun TP. SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants. PLANT PHYSIOLOGY 2023; 191:1546-1560. [PMID: 36740243 PMCID: PMC10022643 DOI: 10.1093/plphys/kiad011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/12/2022] [Indexed: 05/28/2023]
Abstract
SPINDLY (SPY) is a novel nucleocytoplasmic protein O-fucosyltransferase that regulates target protein activity or stability via O-fucosylation of specific Ser/Thr residues. Previous genetic studies indicate that AtSPY regulates plant development during vegetative and reproductive growth by modulating gibberellin and cytokinin responses. AtSPY also regulates the circadian clock and plant responses to biotic and abiotic stresses. The pleiotropic phenotypes of spy mutants point to the likely role of AtSPY in regulating key proteins functioning in diverse cellular pathways. However, very few AtSPY targets are known. Here, we identified 88 SPY targets from Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana via the purification of O-fucosylated peptides using Aleuria aurantia lectin followed by electron transfer dissociation-MS/MS analysis. Most AtSPY targets were nuclear proteins that function in DNA repair, transcription, RNA splicing, and nucleocytoplasmic transport. Cytoplasmic AtSPY targets were involved in microtubule-mediated cell division/growth and protein folding. A comparison with the published O-linked-N-acetylglucosamine (O-GlcNAc) proteome revealed that 30% of AtSPY targets were also O-GlcNAcylated, indicating that these distinct glycosylations could co-regulate many protein functions. This study unveiled the roles of O-fucosylation in modulating many key nuclear and cytoplasmic proteins and provided a valuable resource for elucidating the regulatory mechanisms involved.
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Affiliation(s)
- Rodolfo Zentella
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Yan Wang
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Emily Zahn
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Jianhong Hu
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Liang Jiang
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia 22903, USA
| | - Tai-ping Sun
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
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Savinkova LK, Sharypova EB, Kolchanov NA. On the Role of TATA Boxes and TATA-Binding Protein in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1000. [PMID: 36903861 PMCID: PMC10005294 DOI: 10.3390/plants12051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
For transcription initiation by RNA polymerase II (Pol II), all eukaryotes require assembly of basal transcription machinery on the core promoter, a region located approximately in the locus spanning a transcription start site (-50; +50 bp). Although Pol II is a complex multi-subunit enzyme conserved among all eukaryotes, it cannot initiate transcription without the participation of many other proteins. Transcription initiation on TATA-containing promoters requires the assembly of the preinitiation complex; this process is triggered by an interaction of TATA-binding protein (TBP, a component of the general transcription factor TFIID (transcription factor II D)) with a TATA box. The interaction of TBP with various TATA boxes in plants, in particular Arabidopsis thaliana, has hardly been investigated, except for a few early studies that addressed the role of a TATA box and substitutions in it in plant transcription systems. This is despite the fact that the interaction of TBP with TATA boxes and their variants can be used to regulate transcription. In this review, we examine the roles of some general transcription factors in the assembly of the basal transcription complex, as well as functions of TATA boxes of the model plant A. thaliana. We review examples showing not only the involvement of TATA boxes in the initiation of transcription machinery assembly but also their indirect participation in plant adaptation to environmental conditions in responses to light and other phenomena. Examples of an influence of the expression levels of A. thaliana TBP1 and TBP2 on morphological traits of the plants are also examined. We summarize available functional data on these two early players that trigger the assembly of transcription machinery. This information will deepen the understanding of the mechanisms underlying transcription by Pol II in plants and will help to utilize the functions of the interaction of TBP with TATA boxes in practice.
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Friis Theisen F, Salladini E, Davidsen R, Jo Rasmussen C, Staby L, Kragelund BB, Skriver K. αα-hub coregulator structure and flexibility determine transcription factor binding and selection in regulatory interactomes. J Biol Chem 2022; 298:101963. [PMID: 35452682 PMCID: PMC9127584 DOI: 10.1016/j.jbc.2022.101963] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
Formation of transcription factor (TF)-coregulator complexes is a key step in transcriptional regulation, with coregulators having essential functions as hub nodes in molecular networks. How specificity and selectivity are maintained in these nodes remain open questions. In this work, we addressed specificity in transcriptional networks using complexes formed between TFs and αα-hubs, which are defined by a common αα-hairpin secondary structure motif, as a model. Using NMR spectroscopy and binding thermodynamics, we analyzed the structure, dynamics, stability, and ligand-binding properties of the Arabidopsis thaliana RST domains from TAF4 and known binding partner RCD1, and the TAFH domain from human TAF4, allowing comparison across species, functions, and architectural contexts. While these αα-hubs shared the αα-hairpin motif, they differed in length and orientation of accessory helices as well as in their thermodynamic profiles of ligand binding. Whereas biologically relevant RCD1-ligand pairs displayed high affinity driven by enthalpy, TAF4-ligand interactions were entropy driven and exhibited less binding-induced structuring. We in addition identified a thermal unfolding state with a structured core for all three domains, although the temperature sensitivity differed. Thermal stability studies suggested that initial unfolding of the RCD1-RST domain localized around helix 1, lending this region structural malleability, while effects in TAF4-RST were more stochastic, suggesting variability in structural adaptability upon binding. Collectively, our results support a model in which hub structure, flexibility, and binding thermodynamics contribute to αα-hub-TF binding specificity, a finding of general relevance to the understanding of coregulator-ligand interactions and interactome sizes.
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Affiliation(s)
- Frederik Friis Theisen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Davidsen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christina Jo Rasmussen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Zhang L, Wang R, Xing Y, Xu Y, Xiong D, Wang Y, Yao S. Separable regulation of POW1 in grain size and leaf angle development in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2517-2531. [PMID: 34343399 PMCID: PMC8633490 DOI: 10.1111/pbi.13677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/27/2023]
Abstract
Leaf angle is one of the key factors that determines rice plant architecture. However, the improvement of leaf angle erectness is often accompanied by unfavourable changes in other traits, especially grain size reduction. In this study, we identified the pow1 (put on weight 1) mutant that leads to increased grain size and leaf angle, typical brassinosteroid (BR)-related phenotypes caused by excessive cell proliferation and cell expansion. We show that modulation of the BR biosynthesis genes OsDWARF4 (D4) and D11 and the BR signalling gene D61 could rescue the phenotype of leaf angle but not grain size in the pow1 mutant. We further demonstrated that POW1 functions in grain size regulation by repressing the transactivation activity of the interacting protein TAF2, a highly conserved member of the TFIID transcription initiation complex. Down-regulation of TAF2 rescued the enlarged grain size of pow1 but had little effect on the increased leaf angle phenotype of the mutant. The separable functions of the POW1-TAF2 and POW1-BR modules in grain size and leaf angle control provide a promising strategy for designing varieties with compact plant architecture and increased grain size, thus promoting high-yield breeding in rice.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Ruci Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Yide Xing
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yufang Xu
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
- College of Life ScienceHenan Agricultural UniversityZhengzhouChina
| | - Dunping Xiong
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yueming Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Shanguo Yao
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
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Gipson AB, Giloteaux L, Hanson MR, Bentolila S. Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PLANTS 2020; 9:plants9030307. [PMID: 32121603 PMCID: PMC7154859 DOI: 10.3390/plants9030307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
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Xuan L, Yan T, Lu L, Zhao X, Wu D, Hua S, Jiang L. Genome-wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.). PLANT, CELL & ENVIRONMENT 2020; 43:675-691. [PMID: 31889328 DOI: 10.1111/pce.13694] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 05/18/2023]
Abstract
Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, we demonstrated that hairy leaves were less attractive to Plutella xylostella larvae than glabrous leaves. We established a core germplasm collection with 290 accessions for a genome-wide association study (GWAS) of the leaf trichome trait in oilseed rape. We compared the transcriptomes of the shoot apical meristem (SAM) between hairy- and glabrous-leaf genotypes to narrow down the candidate genes identified by GWAS. The single nucleotide polymorphisms and the different transcript levels of BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b corresponded to the divergence of the hairy- and glabrous-leaf phenotypes, indicating the role of sugar and/or auxin signalling in leaf trichome initiation. The hairy-leaf SAMs had lower glucose and sucrose contents but higher expression of putative auxin responsive factors than the glabrous-leaf SAMs. Spraying of exogenous auxin (8 μm) increased leaf trichome number in certain genotypes, whereas spraying of sucrose (1%) plus glucose (6%) slightly repressed leaf trichome initiation. These data contribute to the existing knowledge about the genetic control of leaf trichomes and would assist breeding towards the desired leaf surface type in oilseed rape.
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Affiliation(s)
- Lijie Xuan
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Tao Yan
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Lingzhi Lu
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Xinze Zhao
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Dezhi Wu
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lixi Jiang
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
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Gura MA, Mikedis MM, Seymour KA, de Rooij DG, Page DC, Freiman RN. Dynamic and regulated TAF gene expression during mouse embryonic germ cell development. PLoS Genet 2020; 16:e1008515. [PMID: 31914128 PMCID: PMC7010400 DOI: 10.1371/journal.pgen.1008515] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 02/10/2020] [Accepted: 11/11/2019] [Indexed: 12/02/2022] Open
Abstract
Germ cells undergo many developmental transitions before ultimately becoming either eggs or sperm, and during embryonic development these transitions include epigenetic reprogramming, quiescence, and meiosis. To begin understanding the transcriptional regulation underlying these complex processes, we examined the spatial and temporal expression of TAF4b, a variant TFIID subunit required for fertility, during embryonic germ cell development. By analyzing published datasets and using our own experimental system to validate these expression studies, we determined that both Taf4b mRNA and protein are highly germ cell-enriched and that Taf4b mRNA levels dramatically increase from embryonic day 12.5–18.5. Surprisingly, additional mRNAs encoding other TFIID subunits are coordinately upregulated through this time course, including Taf7l and Taf9b. The expression of several of these germ cell-enriched TFIID genes is dependent upon Dazl and/or Stra8, known regulators of germ cell development and meiosis. Together, these data suggest that germ cells employ a highly specialized and dynamic form of TFIID to drive the transcriptional programs that underlie mammalian germ cell development. Assisted reproductive therapy and fertility preservation are increasingly used to improve human reproduction across the world, yet there are still many unanswered questions regarding what factors govern the development of eggs and sperm and how these factors work together. We previously identified a subunit of the general transcription factor TFIID, TAF4b, that is essential for fertility. However, many basic characteristics of how Taf4b and its associated TFIID family members contribute to the formation of healthy sperm and eggs in mice and humans remain unknown. In this study, we find that mouse Taf4b and several closely related TFIID subunits become highly abundant during mouse embryonic gonad development, specifically in the cells that ultimately become eggs and sperm. Here, we analyzed data from public repositories and isolated these developing cells to examine their gene expression patterns throughout embryonic development. Together these data suggest that the dynamic expression of Taf4b and other TFIID family members are dependent on the well-established reproductive cell regulators Dazl and Stra8. This understanding of Taf4b gene expression and regulation in mouse reproductive cell development is likely conserved during development of human cells and offers novel insights into the interconnectedness of the factors that govern the formation of healthy eggs and sperm.
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Affiliation(s)
- Megan A. Gura
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
| | | | - Kimberly A. Seymour
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
| | | | - David C. Page
- Whitehead Institute, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, United States of America
| | - Richard N. Freiman
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
- * E-mail:
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10
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Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Curr Biol 2019; 29:2676-2686.e3. [PMID: 31378616 DOI: 10.1016/j.cub.2019.06.084] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Abstract
Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.
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Affiliation(s)
- Emma J Lawrence
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Hongbo Gao
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Andrew J Tock
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Christophe Lambing
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Alexander R Blackwell
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
| | - Ian R Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK.
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Parvathi MS, Nataraja KN, Reddy YAN, Naika MBN, Gowda MVC. Transcriptome analysis of finger millet (Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes. J Genet 2019. [DOI: 10.1007/s12041-019-1087-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Eom H, Park SJ, Kim MK, Kim H, Kang H, Lee I. TAF15b, involved in the autonomous pathway for flowering, represses transcription of FLOWERING LOCUS C. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:79-91. [PMID: 29086456 DOI: 10.1111/tpj.13758] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/26/2017] [Accepted: 10/25/2017] [Indexed: 05/03/2023]
Abstract
TATA-binding protein-associated factors (TAFs) are general transcription factors within the transcription factor IID (TFIID) complex, which recognizes the core promoter of genes. In addition to their biochemical function, it is known that several TAFs are involved in the regulation of developmental processes. In this study, we found that TAF15b affects flowering time, especially through the autonomous pathway (AP) in Arabidopsis. The mutant taf15b shows late flowering compared with the wild type plant during both long and short days, and vernalization accelerates the flowering time of taf15b. In addition, taf15b shows strong upregulation of FLOWERING LOCUS C (FLC), a flowering repressor in Arabidopsis, and the flc taf15b double mutant completely offsets the late flowering of taf15b, indicating that TAF15b is a typical AP gene. The taf15b mutant also shows increased transcript levels of COOLAIR, an antisense transcript of FLC. Consistently, chromatin immunoprecipitation (ChIP) analyses showed that the TAF15b protein is enriched around both sense and antisense transcription start sites of the FLC locus. In addition, co-immunoprecipitation showed that TAF15b interacts with RNA polymerase II (Pol II), while ChIP showed increased enrichment of the phosphorylated forms, both serine 2 (Ser2) and Ser5, of the C-terminal domain of Pol II at the FLC locus, which is indicative of transcriptional elongation. Finally, taf15b showed higher enrichment of the active histone marker, H3K4me3, on FLC chromatin. Taken together, our results suggest that TAF15b affects flowering time through transcriptional repression of FLC in Arabidopsis.
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Affiliation(s)
- Hyunjoo Eom
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea
| | - Su Jung Park
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Min Kyung Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Hoyeun Kim
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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Chong X, Zhang F, Wu Y, Yang X, Zhao N, Wang H, Guan Z, Fang W, Chen F. A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the Identification of Candidate Genes in Chrysanthemum. Genome Biol Evol 2017; 8:3661-3671. [PMID: 28082602 PMCID: PMC5521737 DOI: 10.1093/gbe/evw270] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2016] [Indexed: 12/11/2022] Open
Abstract
Varieties of the economically important ornamental species chrysanthemum have been bred to fit a number of market niches, but the genetic basis and evolutionary relationships among various cultivated types are poorly understood. Here, a DNA marker-based analysis of 199 chrysanthemum entries representing each of the five cultivated types is presented. A set of >90,000 single nucleotide polymorphisms (SNPs) associated with a minor allele frequency of at least 5% was defined, and used to perform a phylogenetic analysis which corresponded well with the phenotypic classification. The analysis revealed that the small-flowered types, spray cut chrysanthemum (SCC) and potted and ground chrysanthemum (PGC), are more closely related to the wild progenitor species (WC) than are the large-flowered ones, disbud cut chrysanthemum (DCC) and traditional chrysanthemum (TC); and the PGC type was closest. Some 550 genetic regions appeared to have experienced selection in the separation of potted and ground-cover types from disbud cut types, and that between potted and ground-cover types from traditional types. A genome-wide association analysis revealed that seven SNPs lying within six genes were predictive of three important traits (ray floret type, cultivated type and flower shape), but no association with flower color was detected. The study has provided a number of novel insights into evolutionary relationships, the population structure and the genetic basis of some key ornamental traits.
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Affiliation(s)
- Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yangyang Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaodong Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Nan Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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14
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Sinha I, Kumar S, Poonia P, Sawhney S, Natarajan K. Functional specialization of two paralogous TAF12 variants by their selective association with SAGA and TFIID transcriptional regulatory complexes. J Biol Chem 2017; 292:6047-6055. [PMID: 28275052 PMCID: PMC5391738 DOI: 10.1074/jbc.c116.768549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/16/2017] [Indexed: 01/08/2023] Open
Abstract
TATA box-binding protein (TBP)-associated factors (TAFs), evolutionarily conserved from yeast to humans, play a central role during transcription initiation. A subset of TAF proteins is shared in transcription factor II D (TFIID) and SAGA transcription regulatory complexes. Although higher eukaryotes contain multiple TAF variants that specify tissue- and developmental stage-specific organization of TFIID or SAGA complexes, in unicellular genomes, however, each TAF is encoded by a single gene. Surprisingly, we found that the genome of Candida albicans, the predominant human fungal pathogen, contains two paralogous TAF12 genes, CaTAF12L and CaTAF12, encoding H2B-like histone-fold domain-containing variants. Of the available fungal genome sequences, only seven other closely related diploid pathogenic Candida genomes encode the two TAF12 paralogs. Using affinity purifications from C. albicans cell extracts, we demonstrate that CaTAF12L uniquely associates with the SAGA complex and CaTAF12 associates with the TFIID complex. We further show that CaTAF12, but not CaTAF12L, is essential for C. albicans growth. Conditional depletion of the two TAF12 variant proteins caused distinct cellular and colony phenotypes. Together our results define a specialized organization of the TAF12 variants and non-redundant roles for the two TAF12 variants in the unicellular C. albicans genome.
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Affiliation(s)
- Ishani Sinha
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shambhu Kumar
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Poonia
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sonal Sawhney
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Krishnamurthy Natarajan
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Fina JP, Masotti F, Rius SP, Crevacuore F, Casati P. HAC1 and HAF1 Histone Acetyltransferases Have Different Roles in UV-B Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:1179. [PMID: 28740501 PMCID: PMC5502275 DOI: 10.3389/fpls.2017.01179] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/20/2017] [Indexed: 05/17/2023]
Abstract
Arabidopsis has 12 histone acetyltransferases grouped in four families: the GNAT/HAG, the MYST/HAM, the p300/CBP/HAC and the TAFII250/HAF families. We previously showed that ham1 and ham2 mutants accumulated higher damaged DNA after UV-B exposure than WT plants. In contrast, hag3 RNA interference transgenic plants showed less DNA damage and lower inhibition of plant growth by UV-B, and increased levels of UV-B-absorbing compounds. These results demonstrated that HAM1, HAM2, and HAG3 participate in UV-B-induced DNA damage repair and signaling. In this work, to further explore the role of histone acetylation in UV-B responses, a putative function of other acetyltransferases of the HAC and the HAF families was analyzed. Neither HAC nor HAF acetyltrasferases participate in DNA damage and repair after UV-B radiation in Arabidopsis. Despite this, haf1 mutants presented lower inhibition of leaf and root growth by UV-B, with altered expression of E2F transcription factors. On the other hand, hac1 plants showed a delay in flowering time after UV-B exposure and changes in FLC and SOC1 expression patterns. Our data indicate that HAC1 and HAF1 have crucial roles for in UV-B signaling, confirming that, directly or indirectly, both enzymes also have a role in UV-B responses.
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16
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Dong OX, Meteignier LV, Plourde MB, Ahmed B, Wang M, Jensen C, Jin H, Moffett P, Li X, Germain H. Arabidopsis TAF15b Localizes to RNA Processing Bodies and Contributes to snc1-Mediated Autoimmunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:247-57. [PMID: 26713351 DOI: 10.1094/mpmi-11-15-0246-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In both animals and plants, messenger (m)RNA export has been shown to contribute to immune response regulation. The Arabidopsis nuclear protein MOS11, along with the nucleoporins MOS3/Nup96/SAR3 and Nup160/SAR1 are components of the mRNA export machinery and contribute to immunity mediated by nucleotide binding leucine-rich repeat immune receptors (NLR). The human MOS11 ortholog CIP29 is part of a small protein complex with three additional members: the RNA helicase DDX39, ALY, and TAF15b. We systematically assessed the biological roles of the Arabidopsis homologs of these proteins in toll interleukin 1 receptor-type NLR (TNL)-mediated immunity using reverse genetics. Although mutations in ALY and DDX39 did not result in obvious defects, taf15b mutation partially suppressed the autoimmune phenotypes of a gain-of-function TNL mutant, snc1. An additive effect on snc1 suppression was observed in mos11-1 taf15b snc1 triple mutant plants, suggesting that MOS11 and TAF15b have independent functions. TAF15b-GFP fusion protein, which fully complemented taf15b mutant phenotypes, localized to nuclei similarly to MOS11. However, it was also targeted to cytosolic granules identified as processing bodies. In addition, we observed no change in SNC1 mRNA levels, whereas less SNC1 protein accumulated in taf15b mutant, suggesting that TAF15b contributes to SNC1 homeostasis through posttranscriptional mechanisms. In summary, this study highlights the importance of posttranscriptional RNA processing mediated by TAF15b in the regulation of TNL-mediated immunity.
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Affiliation(s)
- Oliver X Dong
- 1 Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- 2 Michael Smith Laboratories, University of British Columbia
| | | | - Melodie B Plourde
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
| | - Bulbul Ahmed
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
| | - Ming Wang
- 6 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, U.S.A
| | | | - Hailing Jin
- 6 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, U.S.A
| | - Peter Moffett
- 3 Department of Biology, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Xin Li
- 1 Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- 2 Michael Smith Laboratories, University of British Columbia
| | - Hugo Germain
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
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17
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Waterworth WM, Drury GE, Blundell-Hunter G, West CE. Arabidopsis TAF1 is an MRE11-interacting protein required for resistance to genotoxic stress and viability of the male gametophyte. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:545-57. [PMID: 26358508 PMCID: PMC4949998 DOI: 10.1111/tpj.13020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 05/07/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) by recombination pathways is essential for plant growth and fertility. The recombination endonuclease MRE11 plays important roles in sensing and repair of DNA DSBs. Here we demonstrate protein interaction between Arabidopsis MRE11 and the histone acetyltransferase TAF1, a TATA-binding protein Associated Factor (TAF) of the RNA polymerase II transcription initiation factor complex TFIID. Arabidopsis has two TAF1 homologues termed TAF1 and TAF1b and mutant taf1b lines are viable and fertile. In contrast, taf1 null mutations are lethal, demonstrating that TAF1 is an essential gene. Heterozygous taf1+/- plants display abnormal segregation of the mutant allele resulting from defects in pollen tube development, indicating that TAF1 is important for gamete viability. Characterization of an allelic series of taf1 lines revealed that hypomorphic mutants are viable but display developmental defects and reduced plant fertility. Hypersensitivity of taf1 mutants lacking the C-terminal bromodomain to X-rays and mitomycin C, but not to other forms of abiotic stress, established a specific role for TAF1 in plant DNA repair processes. Collectively these studies reveal a function for TAF1 in plant resistance to genotoxic stress, providing further insight into the molecular mechanisms of the DNA damage response in plants.
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Affiliation(s)
- Wanda M Waterworth
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Georgina E Drury
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | | | - Christopher E West
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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18
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Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination. PLoS One 2015; 10:e0134709. [PMID: 26263547 PMCID: PMC4532415 DOI: 10.1371/journal.pone.0134709] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 07/13/2015] [Indexed: 01/17/2023] Open
Abstract
The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.
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19
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Krishnamurthy P, Kim JA, Jeong MJ, Kang CH, Lee SI. Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes. Mol Genet Genomics 2015; 290:2279-95. [PMID: 26123085 DOI: 10.1007/s00438-015-1080-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
RNA-binding glycine-rich (RBG) proteins play diverse roles in plant growth, development, protection and genome organization. An overly broad definition for class IV glycine-rich proteins (GRPs), namely RNA-binding activity and a glycine-rich C-terminus, has resulted in many distantly related and/or non-related proteins being grouped into this class of RBGs. This definition has hampered the study of RBG evolution. In this study, we used a comparative genomic approach consisting of ortholog, homolog, synteny and phylogenetic analyses to legitimately exclude all distantly/non-related proteins from class IV GRPs and to identify 15, 22, 12 and 18 RBG proteins in Arabidopsis, Chinese cabbage, rice and maize genomes, respectively. All identified RBGs could be divided into three subclasses, namely RBGA, RBGB and RBGD, which may be derived from a common ancestor. We assigned RBGs excluded from class IV GRPs to a separate RBG superfamily. RBGs have evolved and diversified in different species via different mechanisms; segmental duplication and recombination have had major effects, with tandem duplication, intron addition/deletion and domain recombination/deletion playing minor roles. Loss and retention of duplicated RBGs after polyploidization has been species and subclass specific. For example, following recent whole-genome duplication and triplication in maize and Chinese cabbage, respectively, most duplicated copies of RBGA have been lost in maize while RBGD duplicates have been retained; in Chinese cabbage, in contrast, RBGA duplicates have been retained while RBGD duplicates have been lost. Our findings reveal fundamental information and shed new light on the structural characteristics and evolutionary dynamics of RBGs.
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Affiliation(s)
- Panneerselvam Krishnamurthy
- Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), Jeonju, 560-500, Korea
| | - Jin A Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), Jeonju, 560-500, Korea
| | - Mi-Jeong Jeong
- Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), Jeonju, 560-500, Korea
| | - Chang Ho Kang
- Division of Applied Life Science and PMBBRC, Gyeongsang National University, Jinju, 660-701, Korea
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), Jeonju, 560-500, Korea.
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20
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Moraga F, Aquea F. Composition of the SAGA complex in plants and its role in controlling gene expression in response to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2015; 6:865. [PMID: 26528322 PMCID: PMC4604261 DOI: 10.3389/fpls.2015.00865] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/30/2015] [Indexed: 05/07/2023]
Abstract
Protein complexes involved in epigenetic regulation of transcription have evolved as molecular strategies to face environmental stress in plants. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is a transcriptional co-activator complex that regulates numerous cellular processes through the coordination of multiple post-translational histone modifications, including acetylation, deubiquitination, and chromatin recognition. The diverse functions of the SAGA complex involve distinct modules that are highly conserved between yeast, flies, and mammals. In this review, the composition of the SAGA complex in plants is described and its role in gene expression regulation under stress conditions summarized. Some of these proteins are likely involved in the regulation of the inducible expression of genes under light, cold, drought, salt, and iron stress, although the functions of several of its components remain unknown.
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Affiliation(s)
- Felipe Moraga
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
| | - Felipe Aquea
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
- Center for Applied Ecology and SustainabilitySantiago, Chile
- *Correspondence: Felipe Aquea
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21
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Lindner M, Simonini S, Kooiker M, Gagliardini V, Somssich M, Hohenstatt M, Simon R, Grossniklaus U, Kater MM. TAF13 interacts with PRC2 members and is essential for Arabidopsis seed development. Dev Biol 2013; 379:28-37. [PMID: 23506837 DOI: 10.1016/j.ydbio.2013.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 11/24/2022]
Abstract
TBP-Associated Factors (TAFs) are components of complexes like TFIID, TFTC, SAGA/STAGA and SMAT that are important for the activation of transcription, either by establishing the basic transcription machinery or by facilitating histone acetylation. However, in Drosophila embryos several TAFs were shown to be associated with the Polycomb Repressive Complex 1 (PRC1), even though the role of this interaction remains unclear. Here we show that in Arabidopsis TAF13 interacts with MEDEA and SWINGER, both members of a plant variant of Polycomb Repressive Complex 2 (PRC2). PRC2 variants play important roles during the plant life cycle, including seed development. The taf13 mutation causes seed defects, showing embryo arrest at the 8-16 cell stage and over-proliferation of the endosperm in the chalazal region, which is typical for Arabidopsis PRC2 mutants. Our data suggest that TAF13 functions together with PRC2 in transcriptional regulation during seed development.
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Affiliation(s)
- Matias Lindner
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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22
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Hollister JD, Arnold BJ, Svedin E, Xue KS, Dilkes BP, Bomblies K. Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Genet 2012; 8:e1003093. [PMID: 23284289 PMCID: PMC3527224 DOI: 10.1371/journal.pgen.1003093] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 09/27/2012] [Indexed: 11/18/2022] Open
Abstract
Genome duplication, which results in polyploidy, is disruptive to fundamental biological processes. Genome duplications occur spontaneously in a range of taxa and problems such as sterility, aneuploidy, and gene expression aberrations are common in newly formed polyploids. In mammals, genome duplication is associated with cancer and spontaneous abortion of embryos. Nevertheless, stable polyploid species occur in both plants and animals. Understanding how natural selection enabled these species to overcome early challenges can provide important insights into the mechanisms by which core cellular functions can adapt to perturbations of the genomic environment. Arabidopsis arenosa includes stable tetraploid populations and is related to well-characterized diploids A. lyrata and A. thaliana. It thus provides a rare opportunity to leverage genomic tools to investigate the genetic basis of polyploid stabilization. We sequenced the genomes of twelve A. arenosa individuals and found signatures suggestive of recent and ongoing selective sweeps throughout the genome. Many of these are at genes implicated in genome maintenance functions, including chromosome cohesion and segregation, DNA repair, homologous recombination, transcriptional regulation, and chromatin structure. Numerous encoded proteins are predicted to interact with one another. For a critical meiosis gene, ASYNAPSIS1, we identified a non-synonymous mutation that is highly differentiated by cytotype, but present as a rare variant in diploid A. arenosa, indicating selection may have acted on standing variation already present in the diploid. Several genes we identified that are implicated in sister chromatid cohesion and segregation are homologous to genes identified in a yeast mutant screen as necessary for survival of polyploid cells, and also implicated in genome instability in human diseases including cancer. This points to commonalities across kingdoms and supports the hypothesis that selection has acted on genes controlling genome integrity in A. arenosa as an adaptive response to genome doubling.
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Affiliation(s)
- Jesse D. Hollister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Brian J. Arnold
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Elisabeth Svedin
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
- Molecular Evolutionary Genetics, Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana, United States of America
| | - Katherine S. Xue
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Brian P. Dilkes
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
- Molecular Evolutionary Genetics, Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana, United States of America
| | - Kirsten Bomblies
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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23
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Toppino L, Kooiker M, Lindner M, Dreni L, Rotino GL, Kater MM. Reversible male sterility in eggplant (Solanum melongena L.) by artificial microRNA-mediated silencing of general transcription factor genes. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:684-92. [PMID: 20955179 DOI: 10.1111/j.1467-7652.2010.00567.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Since decades, plant male sterility is considered a powerful tool for biological containment to minimize unwanted self-pollination for hybrid seed production. Furthermore, prevention of pollen dispersal also answers to concerns regarding transgene flow via pollen from Genetically Modified (GM) crops to traditional crop fields or wild relatives. We induced male sterility by suppressing endogenous general transcription factor genes, TAFs, using anther-specific promoters combined with artificial microRNA (amiRNA) technology (Schwab et al., 2006). The system was made reversible by the ethanol inducible expression of an amiRNA-insensitive form of the target gene. We provide proof of concept in eggplant, a cultivated crop belonging to the Solanaceae family that includes many important food crops. The transgenic eggplants that we generated are completely male sterile and fertility can be fully restored by short treatments with ethanol, confirming the efficiency but also the reliability of the system in view of open field cultivation. By combining this system with induced parthenocarpy (Rotino et al., 1997), we provide a novel example of complete transgene containment in eggplant, which enables biological mitigation measures for the benefit of coexistence or biosafety purposes for GM crop cultivation.
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Affiliation(s)
- Laura Toppino
- CRA-ORL Agricultural Research Council, Research Unit for Vegetable Crops, Montanaso Lombardo (Lo) Italy DSBB, Department of Biomolecular Sciences and Biotechnology, University of Milano, Milan, Italy
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Jaspers P, Overmyer K, Wrzaczek M, Vainonen JP, Blomster T, Salojärvi J, Reddy RA, Kangasjärvi J. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. BMC Genomics 2010; 11:170. [PMID: 20226034 PMCID: PMC2848248 DOI: 10.1186/1471-2164-11-170] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 03/12/2010] [Indexed: 02/05/2023] Open
Abstract
Background The SROs (SIMILAR TO RCD-ONE) are a group of plant-specific proteins which have important functions in stress adaptation and development. They contain the catalytic core of the poly(ADP-ribose) polymerase (PARP) domain and a C-terminal RST (RCD-SRO-TAF4) domain. In addition to these domains, several, but not all, SROs contain an N-terminal WWE domain. Results SROs are present in all analyzed land plants and sequence analysis differentiates between two structurally distinct groups; cryptogams and monocots possess only group I SROs whereas eudicots also contain group II. Group I SROs possess an N-terminal WWE domain (PS50918) but the WWE domain is lacking in group II SROs. Group I domain structure is widely represented in organisms as distant as humans (for example, HsPARP11). We propose a unified nomenclature for the SRO family. The SROs are able to interact with transcription factors through the C-terminal RST domain but themselves are generally not regulated at the transcriptional level. The most conserved feature of the SROs is the catalytic core of the poly(ADP-ribose) polymerase (PS51059) domain. However, bioinformatic analysis of the SRO PARP domain fold-structure and biochemical assays of AtRCD1 suggested that SROs do not possess ADP-ribosyl transferase activity. Conclusions The SROs are a highly conserved family of plant specific proteins. Sequence analysis of the RST domain implicates a highly preserved protein structure in that region. This might have implications for functional conservation. We suggest that, despite the presence of the catalytic core of the PARP domain, the SROs do not possess ADP-ribosyl transferase activity. Nevertheless, the function of SROs is critical for plants and might be related to transcription factor regulation and complex formation.
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Affiliation(s)
- Pinja Jaspers
- Plant Biology Division, Department of Biosciences, University of Helsinki, Viikinkaari 1, FI-00014 Helsinki, Finland
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25
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Airoldi CA, Rovere FD, Falasca G, Marino G, Kooiker M, Altamura MM, Citterio S, Kater MM. The Arabidopsis BET bromodomain factor GTE4 is involved in maintenance of the mitotic cell cycle during plant development. PLANT PHYSIOLOGY 2010; 152:1320-34. [PMID: 20032077 PMCID: PMC2832235 DOI: 10.1104/pp.109.150631] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bromodomain and Extra Terminal domain (BET) proteins are characterized by the presence of two types of domains, the bromodomain and the extra terminal domain. They bind to acetylated lysines present on histone tails and control gene transcription. They are also well known to play an important role in cell cycle regulation. In Arabidopsis (Arabidopsis thaliana), there are 12 BET genes; however, only two of them, IMBIBITION INDUCIBLE1 and GENERAL TRANSCRIPTION FACTOR GROUP E6 (GTE6), were functionally analyzed. We characterized GTE4 and show that gte4 mutant plants have some characteristic features of cell cycle mutants. Their size is reduced, and they have jagged leaves and a reduced number of cells in most organs. Moreover, cell size is considerably increased in the root, and, interestingly, the root quiescent center identity seems to be partially lost. Cell cycle analyses revealed that there is a delay in activation of the cell cycle during germination and a premature arrest of cell proliferation, with a switch from mitosis to endocycling, leading to a statistically significant increase in ploidy levels in the differentiated organs of gte4 plants. Our results point to a role of GTE4 in cell cycle regulation and specifically in the maintenance of the mitotic cell cycle.
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Dynamic networks from hierarchical bayesian graph clustering. PLoS One 2010; 5:e8118. [PMID: 20084108 PMCID: PMC2799515 DOI: 10.1371/journal.pone.0008118] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 09/25/2009] [Indexed: 11/20/2022] Open
Abstract
Biological networks change dynamically as protein components are synthesized and degraded. Understanding the time-dependence and, in a multicellular organism, tissue-dependence of a network leads to insight beyond a view that collapses time-varying interactions into a single static map. Conventional algorithms are limited to analyzing evolving networks by reducing them to a series of unrelated snapshots.Here we introduce an approach that groups proteins according to shared interaction patterns through a dynamical hierarchical stochastic block model. Protein membership in a block is permitted to evolve as interaction patterns shift over time and space, representing the spatial organization of cell types in a multicellular organism. The spatiotemporal evolution of the protein components are inferred from transcript profiles, using Arabidopsis root development (5 tissues, 3 temporal stages) as an example.The new model requires essentially no parameter tuning, out-performs existing snapshot-based methods, identifies protein modules recruited to specific cell types and developmental stages, and could have broad application to social networks and other similar dynamic systems.
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Jaspers P, Blomster T, Brosché M, Salojärvi J, Ahlfors R, Vainonen JP, Reddy RA, Immink R, Angenent G, Turck F, Overmyer K, Kangasjärvi J. Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:268-79. [PMID: 19548978 DOI: 10.1111/j.1365-313x.2009.03951.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RADICAL-INDUCED CELL DEATH1 (RCD1) is an important regulator of stress and hormonal and developmental responses in Arabidopsis thaliana. Together with its closest homolog, SIMILAR TO RCD-ONE1 (SRO1), it is the only Arabidopsis protein containing the WWE domain, which is known to mediate protein-protein interactions in other organisms. Additionally, these two proteins contain the core catalytic region of poly-ADP-ribose transferases and a conserved C-terminal domain. Tissue and subcellular localization data indicate that RCD1 and SRO1 have partially overlapping functions in plant development. In contrast mutant data indicate that rcd1 has defects in plant development, whereas sro1 displays normal development. However, the rcd1 sro1 double mutant has severe growth defects, indicating that RCD1 and SRO1 exemplify an important genetic principle - unequal genetic redundancy. A large pair-wise interaction test against the REGIA transcription factor collection revealed that RCD1 interacts with a large number of transcription factors belonging to several protein families, such as AP2/ERF, NAC and basic helix-loop-helix (bHLH), and that SRO1 interacts with a smaller subset of these. Full genome array analysis indicated that in many cases targets of these transcription factors have altered expression in the rcd1 but not the sro1 mutant. Taken together RCD1 and SRO1 are required for proper plant development.
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Affiliation(s)
- Pinja Jaspers
- Plant Biology, Department of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, Helsinki, Finland
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28
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Freiman RN. Specific variants of general transcription factors regulate germ cell development in diverse organisms. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:161-6. [PMID: 19437618 DOI: 10.1016/j.bbagrm.2009.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Through the reductive divisions of meiosis, sexually reproducing organisms have gained the ability to produce specialized haploid cells called germ cells that fuse to establish the diploid genome of the resulting progeny. The totipotent nature of these germ cells is highlighted by their ability to provide a single fertilized egg cell with all the genetic information necessary to develop the complete repertoire of cell types of the future organism. Thus, the production of these germ cells must be tightly regulated to ensure the continued success of the germ line in future generations. One surprising germ cell development mechanism utilizes variation of the global transcriptional machinery, such as TFIID and TFIIA. Like histone variation, general transcription factor variation serves to produce gonadal-restricted or -enriched expression of selective transcriptional regulatory factors required for establishing and/or maintaining the germ line of diverse organisms. This strategy is observed among invertebrates and vertebrates, and perhaps plants, suggesting that a common theme in germ cell evolution is the diversification of selective promoter initiation factors to regulate critical gonadal-specific programs of gene expression required for sexual reproduction. This review discusses the identification and characterization of a subset of these specialized general transcription factors in diverse organisms that share a common goal of germ line regulation through transcriptional control at its most fundamental level.
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Affiliation(s)
- Richard N Freiman
- Department of Molecular and Cell Biology, Brown University, 70 Ship St., Box G-E4, Providence, RI 02903, USA.
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Lawit SJ, O'Grady K, Gurley WB, Czarnecka-Verner E. Yeast two-hybrid map of Arabidopsis TFIID. PLANT MOLECULAR BIOLOGY 2007; 64:73-87. [PMID: 17340043 DOI: 10.1007/s11103-007-9135-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 01/05/2007] [Indexed: 05/11/2023]
Abstract
General transcription factor IID (TFIID) is a multisubunit protein complex involved in promoter recognition and is fundamental to the nucleation of the RNA polymerase II transcriptional preinitiation complex. TFIID is comprised of the TATA binding protein (TBP) and 12-15 TBP-associated factors (TAFs). While general transcription factors have been extensively studied in metazoans and yeast, little is known about the details of their structure and function in the plant kingdom. This work represents the first attempt to compare the structure of a plant TFIID complex with that determined for other organisms. While no TAF3 homolog has been observed in plants, at least one homolog has been identified for each of the remaining 14 TFIID subunits, including both TAF14 and TAF15 which have previously been shown to be unique to either yeast or humans. The presence of both TAFs 14 and 15 in plants suggests ancient roles for these proteins that were lost in metazoans and fungi, respectively. Yeast two-hybrid interaction assays resulted in a total of 65 binary interactions between putative subunits of Arabidopsis TFIID, including 26 contacts unique to plants. The interaction matrix of Arabidopsis TAFs is largely consistent with the three-lobed topological map for yeast TFIID, which suggests that the structure and composition of TFIID have been highly conserved among eukaryotes.
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Affiliation(s)
- Shai J Lawit
- Pioneer Hi-Bred International, Inc., a DuPont Company, 7300 N.W. 62nd Ave, PO Box 1004, Johnston, IA 50131-1004, USA
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Tamada Y, Nakamori K, Nakatani H, Matsuda K, Hata S, Furumoto T, Izui K. Temporary expression of the TAF10 gene and its requirement for normal development of Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2007; 48:134-46. [PMID: 17148695 DOI: 10.1093/pcp/pcl048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
TAF10 is one of the TATA box-binding protein (TBP)-associated factors (TAFs) which constitute a TFIID with a TBP. Initially most TAFs were thought to be necessary for accurate transcription initiation from a broad group of core promoters. However, it was recently revealed that several TAFs are expressed in limited tissues during animal embryogenesis, and are indispensable for normal development of the tissues. They are called 'selective' TAFs. In plants, however, little is known as to these 'selective' TAFs and their function. Here we isolated the Arabidopsis thaliana TAF10 gene (atTAF10), which is a single gene closely related to the TAF10 genes of other organisms. atTAF10 was expressed transiently during the development of several organs such as lateral roots, rosette leaves and most floral organs. Such an expression pattern was clearly distinct from that of Arabidopsis Rpb1, which encodes a component of RNA polymerase II, suggesting that atTAF10 functions in not only general transcription but also the selective expression of a subset of genes. In a knockdown mutant of atTAF10, we observed several abnormal phenotypes involved in meristem activity and leaf development, suggesting that atTAF10 is concerned in pleiotropic, but selected morphological events in Arabidopsis. These results clearly demonstrate that TAF10 is a 'selective' TAF in plants, providing a new insight into the function of TAFs in plants.
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Affiliation(s)
- Yosuke Tamada
- Laboratory of Plant Physiology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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Gao X, Ren F, Lu YT. The Arabidopsis Mutant stg1 Identifies a Function for TBP-Associated Factor 10 in Plant Osmotic Stress Adaptation. ACTA ACUST UNITED AC 2006; 47:1285-94. [PMID: 16945932 DOI: 10.1093/pcp/pcj099] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plant salt tolerance is a complex trait involving many genes. To identify new salt tolerance determinants during seed germination, we have screened a population of chemically inducible activation-tagged Arabidopsis mutants. A mutant, designated stg1 (salt tolerance during germination 1), was obtained. The stg1 mutant is less sensitive than the wild type to NaCl and osmotic stress inhibition of germination in the presence of the inducer. Germination assays on media containing various salts upon inducer application indicate that the stg1 mutation enhances tolerance to Na(+) and K(+). Under salt stress, stg1 maintains a higher K(+)/Na(+) ratio and accumulates less proline than the wild-type control, suggesting that its salt tolerance mechanisms are mainly involved in the regulation of ion balance. STG1 encodes a putative Arabidopsis TATA box-binding protein (TBP)-associated factor 10 (atTAF10), which constitutes the transcriptional factor IID (TFIID) complex. Overexpression of atTAF10 under the control of the 35S promoter in Arabidopsis improves seed tolerance to salt stress during germination and the knocked-down mutant is more sensitive to salt stress, indicating the transcription initiation factor as a physiological target of salt toxicity in plants.
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Affiliation(s)
- Xiang Gao
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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Gregis V, Sessa A, Colombo L, Kater MM. AGL24, SHORT VEGETATIVE PHASE, and APETALA1 redundantly control AGAMOUS during early stages of flower development in Arabidopsis. THE PLANT CELL 2006; 18:1373-82. [PMID: 16679456 PMCID: PMC1475495 DOI: 10.1105/tpc.106.041798] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Loss-of-function alleles of AGAMOUS-LIKE24 (AGL24) and SHORT VEGETATIVE PHASE (SVP) revealed that these two similar MADS box genes have opposite functions in controlling the floral transition in Arabidopsis thaliana, with AGL24 functioning as a promoter and SVP as a repressor. AGL24 promotes inflorescence identity, and its expression is downregulated by APETALA1 (AP1) and LEAFY to establish floral meristem identity. Here, we combine the two mutants to generate the agl24 svp double mutant. Analysis of flowering time revealed that svp is epistatic to agl24. Furthermore, when grown at 30 degrees C, the double mutant was severely affected in flower development. All four floral whorls showed homeotic conversions due to ectopic expression of class B and C organ identity genes. The observed phenotypes remarkably resembled the leunig (lug) and seuss (seu) mutants. Protein interaction studies showed that dimers composed of AP1-AGL24 and AP1-SVP interact with the LUG-SEU corepressor complex. We provide genetic evidence for the role of AP1 in these interactions by showing that the floral phenotype in the ap1 agl24 svp triple mutant is significantly enhanced. Our data suggest that MADS box proteins are involved in the recruitment of the SEU-LUG repressor complex for the regulation of AGAMOUS.
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Affiliation(s)
- Veronica Gregis
- Dipartimento di Biologia, Università degli Studi di Milano, 20133 Milan, Italy
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Lago C, Clerici E, Dreni L, Horlow C, Caporali E, Colombo L, Kater MM. The Arabidopsis TFIID factor AtTAF6 controls pollen tube growth. Dev Biol 2005; 285:91-100. [PMID: 16039640 DOI: 10.1016/j.ydbio.2005.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Revised: 05/30/2005] [Accepted: 06/08/2005] [Indexed: 10/25/2022]
Abstract
Initiation of transcription mediated by RNA polymerase II requires a number of transcription factors among which TFIID is the major core promoter recognition factor. TFIID is composed of highly conserved factors which include the TATA-binding protein (TBP) and about 14 TBP-associated factors (TAFs). Recently, the complete Arabidopsis TAF family has been identified. To obtain functional information about Arabidopsis TAFs, we analyzed a T-DNA insertion mutant for AtTAF6. Segregation analysis showed that plants homozygous for the mutant allele were never found, indicating that inhibition of the AtTAF6 function is lethal. Genetic experiments also revealed that the male gametophyte was affected by the attaf6 mutation since significant reduced transmission of the mutant allele through the male gametophyte was observed. Detailed histological and morphological analysis showed that the T-DNA insertion in AtTAF6 specifically affects pollen tube growth, indicating that the transcriptional regulation of only a specific subset of genes is controlled by this basal transcription factor.
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Affiliation(s)
- Clara Lago
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli studi di Milano, via Celoria 26, 20133 Milan, Italy
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