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Guo H, Wang J, Yao D, Yu L, Jiang W, Xie L, Lv S, Zhang X, Wang Y, Wang C, Ji W, Zhang H. Identification of nuclear membrane SUN proteins and components associated with wheat fungal stress responses. STRESS BIOLOGY 2024; 4:29. [PMID: 38861095 PMCID: PMC11166608 DOI: 10.1007/s44154-024-00163-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/21/2024] [Indexed: 06/12/2024]
Abstract
In eukaryotes, the nuclear membrane that encapsulates genomic DNA is composed of an inner nuclear membrane (INM), an outer nuclear membrane (ONM), and a perinuclear space. SUN proteins located in the INM and KASH proteins in the ONM form the SUN-KASH NM-bridge, which functions as the junction of the nucleocytoplasmic complex junction. Proteins containing the SUN domain showed the highest correlation with differentially accumulated proteins (DAPs) in the wheat response to fungal stress. To understand the characteristics of SUN and its associated proteins in wheat responding to pathogen stress, here we investigated and comprehensive analyzed SUN- and KASH-related proteins among the DAPs under fungi infection based on their conserved motifs. In total, four SUN proteins, one WPP domain-interacting protein (WIP), four WPP domain-interacting tail-anchored proteins (WIT), two WPP proteins and one Ran GTPase activating protein (RanGAP) were identified. Following transient expression of Nicotiana benthamiana, TaSUN2, TaRanGAP2, TaWIT1 and TaWIP1 were identified as nuclear membrane proteins, while TaWPP1 and TaWPP2 were expressed in both the nucleus and cell membrane. RT-qPCR analysis demonstrated that the transcription of TaSUN2, TaRanGAP2 and TaWPP1 were strongly upregulated in response to fungal infection. Furthermore, using the bimolecular fluorescence complementation, the luciferase complementation and a nuclear and split-ubiquitin-based membrane yeast two-hybrid systems, we substantiated the interaction between TaSUN2 and TaWIP1, as well as TaWIP1/WIT1 and TaWPP1/WPP2. Silencing of TaSUN2, TaRanGAP2 and TaWPP1 in wheat leaves promoted powdery mildew infection and hyphal growth, and reduced the expression of TaBRI1, TaBAK1 and Ta14-3-3, indicating that these NM proteins play a positive role in resistance to fungal stress. Our study reveals the characteristics of NM proteins and propose the preliminary construction of SUN-WIP-WPP-RanGAP complex in wheat, which represents a foundation for detail elucidating their functions in wheat in future.
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Affiliation(s)
- Huan Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Jianfeng Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Di Yao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Ligang Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Wenting Jiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Lincai Xie
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Shikai Lv
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiangyu Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Yajuan Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Changyou Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Wanquan Ji
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Hong Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China.
- Engineering Research Center of Wheat Breeding, Ministry of Education, Yangling, Shaanxi, 712100, China.
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Roychowdhury T, Chattopadhyay S. Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation. Front Cell Dev Biol 2020; 8:602994. [PMID: 33409278 PMCID: PMC7779526 DOI: 10.3389/fcell.2020.602994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023] Open
Abstract
Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.
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Affiliation(s)
- Tanaya Roychowdhury
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, India.,Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Samit Chattopadhyay
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, India.,Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
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Aizat WM, Ibrahim S, Rahnamaie-Tajadod R, Loke KK, Goh HH, Noor NM. Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation. PeerJ 2018; 6:e5525. [PMID: 30186693 PMCID: PMC6118203 DOI: 10.7717/peerj.5525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Jasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, Persicaria minor, which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like P. minor is unknown. METHOD In this study, P. minor plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression. RESULTS From this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson's r = 0.677) while a weak correlation was observed for downregulated proteins (r = 0.147). DISCUSSION MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak (r = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.
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Affiliation(s)
- Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Sarah Ibrahim
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | | | - Kok-Keong Loke
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Lai MW, Liou RF. Two genes encoding GH10 xylanases are essential for the virulence of the oomycete plant pathogen Phytophthora parasitica. Curr Genet 2018; 64:931-943. [PMID: 29470644 DOI: 10.1007/s00294-018-0814-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/29/2022]
Abstract
Plant cell walls are pivotal battlegrounds between microbial pathogens and their hosts. To penetrate the cell wall and thereby to facilitate infection, microbial pathogens are equipped with a wide array of cell wall-degrading enzymes to depolymerize the polysaccharides in the cell wall. However, many of these enzymes and their role in the pathogenesis of microbial pathogens are not characterized, especially those from Oomycetes. In this study, we analyzed the function of four putative endo-beta-1,4-xylanase-encoding genes (ppxyn1-ppxyn4) from Phytophthora parasitica, an oomycete plant pathogen known to cause severe disease in a wide variety of plant species. All four genes belong to the glycoside hydrolase family 10 (GH10). Recombinant proteins of ppxyn1, ppxyn2, and ppxyn4 obtained from the yeast Pichia pastoris showed degrading activities toward birch wood xylan, but they behaved differently in terms of the conditions for optimal activity, thermostability, and durability. Quantitative RT-PCR revealed upregulated expression of all four genes, especially ppxyn1 and ppxyn2, during plant infection. In contrast, ppxyn3 was highly expressed in cysts and its close homolog, ppxyn4, in germinating cysts. To uncover the role of ppxyn1 and ppxyn2 in the pathogenesis of P. parasitica, we generated silencing transformants for these two genes by double-stranded RNA-mediated gene silencing. Silencing ppxyn1 and ppxyn2 reduced the virulence of P. parasitica toward tobacco (Nicotiana benthamiana) and tomato plants. These results demonstrate the crucial role of xylanase-encoding ppxyn1 and ppxyn2 in the infection process of P. parasitica.
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Affiliation(s)
- Ming-Wei Lai
- Department of Plant Pathology and Microbiology, National Taiwan University, #1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan
| | - Ruey-Fen Liou
- Department of Plant Pathology and Microbiology, National Taiwan University, #1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
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Park C, Lim CW, Baek W, Kim JH, Lim S, Kim SH, Kim KN, Lee SC. The Pepper WPP Domain Protein, CaWDP1, Acts as a Novel Negative Regulator of Drought Stress via ABA Signaling. PLANT & CELL PHYSIOLOGY 2017; 58:779-788. [PMID: 28339719 DOI: 10.1093/pcp/pcx017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/22/2017] [Indexed: 05/05/2023]
Abstract
Plants are constantly challenged by various environmental stresses, including high salinity and drought, and they have evolved defense mechanisms to counteract the deleterious effects of these stresses. The plant hormone ABA regulates plant growth and developmental processes and mediates abiotic stress responses. Here, we report the identification and characterization of a novel CaWDP1 (Capsicum annuum) protein. The expression of CaWDP1 in pepper leaves was induced by ABA, drought and NaCl treatments, suggesting its role in the abiotic stress response. CaWDP1 proteins show conserved sequence homology with other known WDP1 proteins, and they are localized in the nucleus and cytoplasm. We generated CaWDP1-silenced peppers via virus-induced gene silencing (VIGS). We evaluated the responses of these CaWDP1-silenced pepper plants and CaWDP1-overexpressing (OX) transgenic Arabidopsis plants to ABA and drought. CaWDP1-silenced pepper plants displayed enhanced tolerance to drought stress, and this was characterized by low levels of leaf water loss in the drought-treated leaves. In contrast to CaWDP1-silenced plants, CaWDP1-OX plants exhibited an ABA-hyposensitive and drought-susceptible phenotype, which was accompanied by high levels of leaf water loss, low leaf temperatures, increased stomatal pore size and low expression levels of stress-responsive genes. Our results indicate that CaWDP1, a novel pepper negative regulator of ABA, regulates the ABA-mediated defense response to drought stress.
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Affiliation(s)
- Chanmi Park
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
- These authors contributed equally to this work
| | - Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
- These authors contributed equally to this work
| | - Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
- These authors contributed equally to this work
| | - Jung-Hyun Kim
- Department of Physical Education, Chung-Ang University, Seoul 06911, Korea
- These authors contributed equally to this work
| | - Sohee Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Sang Hyon Kim
- Department of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeonggi-Do17058, Korea
| | - Kyung-Nam Kim
- Department of Molecular Biology, PERI, Sejong University, Seoul 05000, Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
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Petrovská B, Šebela M, Doležel J. Inside a plant nucleus: discovering the proteins. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1627-40. [PMID: 25697798 DOI: 10.1093/jxb/erv041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nuclear proteins are a vital component of eukaryotic cell nuclei and have a profound effect on the way in which genetic information is stored, expressed, replicated, repaired, and transmitted to daughter cells and progeny. Because of the plethora of functions, nuclear proteins represent the most abundant components of cell nuclei in all eukaryotes. However, while the plant genome is well understood at the DNA level, information on plant nuclear proteins remains scarce, perhaps with the exception of histones and a few other proteins. This lack of knowledge hampers efforts to understand how the plant genome is organized in the nucleus and how it functions. This review focuses on the current state of the art of the analysis of the plant nuclear proteome. Previous proteome studies have generally been designed to search for proteins involved in plant response to various forms of stress or to identify rather a modest number of proteins. Thus, there is a need for more comprehensive and systematic studies of proteins in the nuclei obtained at individual phases of the cell cycle, or isolated from various tissue types and stages of cell and tissue differentiation. All this in combination with protein structure, predicted function, and physical localization in 3D nuclear space could provide much needed progress in our understanding of the plant nuclear proteome and its role in plant genome organization and function.
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Affiliation(s)
- Beáta Petrovská
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 783 71 Olomouc, Czech Republic Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 783 71 Olomouc, Czech Republic
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Verma JK, Gayali S, Dass S, Kumar A, Parveen S, Chakraborty S, Chakraborty N. OsAlba1, a dehydration-responsive nuclear protein of rice (Oryza sativa L. ssp. indica), participates in stress adaptation. PHYTOCHEMISTRY 2014; 100:16-25. [PMID: 24534105 DOI: 10.1016/j.phytochem.2014.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 01/16/2014] [Accepted: 01/22/2014] [Indexed: 05/13/2023]
Abstract
Alba proteins have exhibited great functional plasticity through the course of evolution and constitute a superfamily that spans across three domains of life. Earlier, we had developed the dehydration-responsive nuclear proteome of an indica rice cultivar, screening of which led to the identification of an Alba protein. Here we describe, for the first time, the complete sequence of the candidate gene OsAlba1, its genomic organization, and possible function/s in plant. Phylogenetic analysis showed its close proximity to other monocots as compared to dicot Alba proteins. Protein-DNA interaction prediction indicates a DNA-binding property for OsAlba1. Confocal microscopy showed the localization of OsAlba1-GFP fusion protein to the nucleus, and also sparsely to the cytoplasm. Water-deficit conditions triggered OsAlba1 expression suggesting its function in dehydration stress, possibly through an ABA-dependent pathway. Functional complementation of the yeast mutant ΔPop6 established that OsAlba1 also functions in oxidative stress tolerance. The preferential expression of OsAlba1 in the flag leaves implies its role in grain filling. Our findings suggest that the Alba components such as OsAlba1, especially from a plant where there is no evidence for a major chromosomal role, might play important function in stress adaptation.
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Affiliation(s)
- Jitendra Kumar Verma
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Suchismita Dass
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Amit Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shaista Parveen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Ji L, Xu R, Lu L, Zhang J, Yang G, Huang J, Wu C, Zheng C. TM6, a novel nuclear matrix attachment region, enhances its flanking gene expression through influencing their chromatin structure. Mol Cells 2013; 36:127-37. [PMID: 23852133 PMCID: PMC3887953 DOI: 10.1007/s10059-013-0092-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/21/2013] [Accepted: 05/28/2013] [Indexed: 01/16/2023] Open
Abstract
Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.
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Affiliation(s)
- Lusha Ji
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
- Present address: College of Life Sciences, Liaocheng University, Liaocheng, Shandong 252059,
P.R. China
| | - Rui Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Longtao Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
- Present address: Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong 261061,
P.R.China
| | - Jiedao Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
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Ueda K, Xu ZJ, Miyagi N, Ono M, Wabiko H, Masuda K, Inoue M. Isolation and characterization of a carrot nucleolar protein with structural and sequence similarity to the vertebrate PESCADILLO protein. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 208:83-92. [PMID: 23683933 DOI: 10.1016/j.plantsci.2013.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 03/29/2013] [Accepted: 04/03/2013] [Indexed: 06/02/2023]
Abstract
The nuclear matrix is involved in many nuclear events, but its protein architecture in plants is still not fully understood. A cDNA clone was isolated by immunoscreening with a monoclonal antibody raised against nuclear matrix proteins of Daucus carota L. Its deduced amino acid sequence showed about 40% identity with the PESCADILLO protein of zebrafish and humans. Primary structure analysis of the protein revealed a Pescadillo N-terminus domain, a single breast cancer C-terminal domain, two nuclear localization signals, and a potential coiled-coil region as also found in animal PESCADILLO proteins. Therefore, we designated this gene DcPES1. Although DcPES1 mRNA was detected in all tissues examined, its levels were highest in tissues with proliferating cells. Immunofluorescence using specific antiserum against the recombinant protein revealed that DcPES1 localized exclusively in the nucleolus. Examination of fusion proteins with green fluorescent protein revealed that the N-terminal portion was important for localization to the nucleoli of tobacco and onion cells. Moreover, when the nuclear matrix of carrot cells was immunostained with an anti-DcPES1 serum, the signal was detected in the nucleolus. Therefore, the DcPES1 protein appears to be a component of or tightly bound to components of the nuclear matrix.
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Affiliation(s)
- Kenji Ueda
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan.
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Sakamoto Y, Takagi S. LITTLE NUCLEI 1 and 4 regulate nuclear morphology in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2013; 54:622-33. [PMID: 23396599 DOI: 10.1093/pcp/pct031] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The morphology of plant nuclei varies among different species, organs, tissues and cell types. However, mechanisms and factors involved in the maintenance of nuclear morphology are poorly understood. Because nuclei retain their shapes even after cytoskeletal inhibitor treatments both in vivo and in vitro, we assumed involvement of the nuclear lamina, which plays a critical role in the regulation of nuclear morphology in animals. The crude nuclear lamina fraction isolated from Arabidopsis thaliana leaves was analyzed by mass spectrometry, and putative nuclear lamina proteins were identified. Among their T-DNA insertion lines, nuclei of little nuclei1 (linc1) and linc4 disruptants were more spherical than those of wild-type plants. Because A. thaliana harbors four LINC genes, we prepared all single and linc1/4 and linc2/3 double disruptants. In leaf epidermal cells, the circularity index of the nucleus in all linc disruptants except linc3 was significantly higher than that in the wild-type plants. The extent of the effects of LINC1 and/or LINC4 disruption was significantly higher than that of the effects of LINC2 disruption. The nuclear area was significantly smaller in the linc1, linc4 and linc1/4 disruptants than in the wild-type plants. Regardless of the defects in nuclear morphology, all linc disruptants exhibited a normal ploidy level. In interphase cells, LINC1 and LINC4 were mainly localized to the nuclear periphery, whereas LINC2 was in the nucleoplasm and LINC3 was detected in both regions. From prometaphase to anaphase in mitotic root tip cells, LINC1 was co-localized with chromosomes, whereas other LINCs were dispersed in the cytoplasm.
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Affiliation(s)
- Yuki Sakamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043 Japan.
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Wozny M, Schattat MH, Mathur N, Barton K, Mathur J. Color recovery after photoconversion of H2B::mEosFP allows detection of increased nuclear DNA content in developing plant cells. PLANT PHYSIOLOGY 2012; 158:95-106. [PMID: 22108524 PMCID: PMC3252088 DOI: 10.1104/pp.111.187062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/21/2011] [Indexed: 05/10/2023]
Abstract
Many higher plants are polysomatic whereby different cells possess variable amounts of nuclear DNA. The conditional triggering of endocycles results in higher nuclear DNA content (C value) that in some cases has been correlated to increased cell size. While numerous multicolored fluorescent protein (FP) probes have revealed the general behavior of the nucleus and intranuclear components, direct visualization and estimation of changes in nuclear-DNA content in live cells during their development has not been possible. Recently, monomeric Eos fluorescent protein (mEosFP) has emerged as a useful photoconvertible protein whose color changes irreversibly from a green to a red fluorescent form upon exposure to violet-blue light. The stability and irreversibility of red fluorescent mEosFP suggests that detection of green color recovery would be possible as fresh mEosFP is produced after photoconversion. Thus a ratiometric evaluation of the red and green forms of mEosFP following photoconversion could be used to estimate production of a core histone such as H2B during its concomitant synthesis with DNA in the synthesis phase of the cell cycle. Here we present proof of concept observations on transgenic tobacco (Nicotiana tabacum) Bright Yellow 2 cells and Arabidopsis (Arabidopsis thaliana) plants stably expressing H2B::mEosFP. In Arabidopsis seedlings an increase in green fluorescence is observed specifically in cells known to undergo endoreduplication. The detection of changes in nuclear DNA content by correlating color recovery of H2B::mEosFP after photoconversion is a novel approach involving a single FP. The method has potential for facilitating detailed investigations on conditions that favor increased cell size and the development of polysomaty in plants.
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Affiliation(s)
| | | | | | | | - Jaideep Mathur
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G2W1
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12
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Bazargani MM, Sarhadi E, Bushehri AAS, Matros A, Mock HP, Naghavi MR, Hajihoseini V, Mardi M, Hajirezaei MR, Moradi F, Ehdaie B, Salekdeh GH. A proteomics view on the role of drought-induced senescence and oxidative stress defense in enhanced stem reserves remobilization in wheat. J Proteomics 2011; 74:1959-73. [PMID: 21621021 DOI: 10.1016/j.jprot.2011.05.015] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 05/06/2011] [Accepted: 05/09/2011] [Indexed: 01/04/2023]
Abstract
Drought is one of the major factors limiting the yield of wheat (Triticum aestivum L.) particularly during grain filling. Under terminal drought condition, remobilization of pre-stored carbohydrates in wheat stem to grain has a major contribution in yield. To determine the molecular mechanism of stem reserve utilization under drought condition, we compared stem proteome patterns of two contrasting wheat landraces (N49 and N14) under a progressive post-anthesis drought stress, during which period N49 peduncle showed remarkably higher stem reserves remobilization efficiency compared to N14. Out of 830 protein spots reproducibly detected and analyzed on two-dimensional electrophoresis gels, 135 spots showed significant changes in at least one landrace. The highest number of differentially expressed proteins was observed in landrace N49 at 20days after anthesis when active remobilization of dry matter was observed, suggesting a possible involvement of these proteins in effective stem reserve remobilization of N49. The identification of 82 of differentially expressed proteins using mass spectrometry revealed a coordinated expression of proteins involved in leaf senescence, oxidative stress defense, signal transduction, metabolisms and photosynthesis which might enable N49 to efficiently remobilized its stem reserves compared to N14. The up-regulation of several senescence-associated proteins and breakdown of photosynthetic proteins in N49 might reflect the fact that N49 increased carbon remobilization from the stem to the grains by enhancing senescence. Furthermore, the up-regulation of several oxidative stress defense proteins in N49 might suggest a more effective protection against oxidative stress during senescence in order to protect stem cells from premature cell death. Our results suggest that wheat plant might response to soil drying by efficiently remobilize assimilates from stem to grain through coordinated gene expression.
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13
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Wang T, Hou G, Wang Y, Xue L. Characterization and heterologous expression of a new matrix attachment region binding protein from the unicellular green alga Dunaliella salina. J Biochem 2010; 148:651-8. [PMID: 20926505 DOI: 10.1093/jb/mvq100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although interactions between the nuclear matrix and special regions of chromosomal DNA called matrix attachment regions (MARs) are implicated in various nuclear functions, the understanding of the regulatory mechanism of MARs is still poor. A few MAR-binding proteins (MARBP) have been isolated from some plants and animals, but not from the unicellular algae. Here, we identify a novel MAR-binding protein, namely DMBP-1, from the halotolerant alga Dunaliella salina. The cDNA of DMBP-1 is 2322-bp long and contains a 1626 bp of an open reading frame encoding a polypeptide of 542 amino acids (59 kDa). The DMBP-1 expressed in Escherichia coli specifically binds A/T-rich MAR DNA. The DMBP-1 fused to green fluorescent protein appears only inside the nuclei of Chinese hamster ovarian cells transfected with the pEGFP-MBP, indicating that the protein is located in the nuclei. The findings mentioned above may contribute to better understanding of the nuclear matrix-MAR interactions.
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Affiliation(s)
- Tianyun Wang
- Laboratory for Cell Biology, The First Affiliated Hospital, Zhengzhou University, 40 Daxue Road, Henan, China
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14
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Chi W, Mao J, Li Q, Ji D, Zou M, Lu C, Zhang L. Interaction of the pentatricopeptide-repeat protein DELAYED GREENING 1 with sigma factor SIG6 in the regulation of chloroplast gene expression in Arabidopsis cotyledons. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:14-25. [PMID: 20626654 DOI: 10.1111/j.1365-313x.2010.04304.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The pentatricopeptide-repeat (PPR) protein DELAYED GREENING 1 (DG1) has been shown to be involved in the regulation of early chloroplast development and chloroplast gene expression in Arabidopsis. To gain insight into the mode of DG1 action, we used a yeast two-hybrid screening approach and identified a partner, SIG6, which is a chloroplast sigma factor responsible for the transcription of plastid-encoded RNA polymerase (PEP)-dependent chloroplast genes in cotyledons. Further analysis showed that the C-terminal region of DG1 and the N-terminal region of SIG6 are responsible for such interactions. High-level expression of a truncated C-terminal DG1 in wild-type Arabidopsis caused a dominant-negative phenotype. The sig6 dg1 double mutant displayed a more severe chlorotic phenotype, and the PEP-dependent chloroplast gene transcripts were greatly reduced compared with transcript levels in the single mutants. Overexpression of SIG6 rescued the chlorophyll deficiency in dg1 cotyledons but not in young leaves. In addition, increased SIG6 promoted PEP-dependent chloroplast gene transcript accumulation in the dg1 mutant background. These results suggest that the interaction of DG1 and SIG6 is functionally significant in the regulation of PEP-dependent chloroplast gene transcription in Arabidopsis cotyledons.
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Affiliation(s)
- Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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15
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Wei PC, Tan F, Gao XQ, Zhang XQ, Wang GQ, Xu H, Li LJ, Chen J, Wang XC. Overexpression of AtDOF4.7, an Arabidopsis DOF family transcription factor, induces floral organ abscission deficiency in Arabidopsis. PLANT PHYSIOLOGY 2010; 153:1031-45. [PMID: 20466844 PMCID: PMC2899910 DOI: 10.1104/pp.110.153247] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 05/12/2010] [Indexed: 05/18/2023]
Abstract
After flower pollination, a programmed process called abscission occurs in which unwanted floral organs are actively shed from the main plant body. We found that a member of the DOF (for DNA binding with one finger) transcription factor family, Arabidopsis (Arabidopsis thaliana) DOF4.7, was expressed robustly in the abscission zone. The Arabidopsis 35S::AtDOF4.7 lines with constitutive expression of AtDOF4.7 exhibited an ethylene-independent floral organ abscission deficiency. In these lines, anatomical analyses showed that the formation of the abscission zone was normal. However, dissolution of the middle lamella failed to separate between the cell walls. AtDOF4.7 was identified as a nucleus-localized transcription factor. This protein had both in vitro and in vivo binding activity to typical DOF cis-elements in the promoter of an abscission-related polygalacturonase (PG) gene, PGAZAT. Overexpression of AtDOF4.7 resulted in down-regulation of PGAZAT. AtDOF4.7 interacted with another abscission-related transcription factor, Arabidopsis ZINC FINGER PROTEIN2. Taken together, our results suggest that AtDOF4.7 participates in the control of abscission as part of the transcription complex that directly regulates the expression of cell wall hydrolysis enzymes.
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Abstract
The nuclear envelope and the nuclear pore are important structures that both separate and selectively connect the nucleoplasm and the cytoplasm. The requirements for specific targeting of proteins to the plant nuclear envelope and nuclear pore are poorly understood. How are transmembrane-domain proteins sorted to the nuclear envelope and nuclear pore membranes? What protein–protein interactions are involved in associating other proteins to the nuclear pore? Are there plant-specific aspects to these processes? We are using the case of the nuclear pore-associated Ran-cycle component RanGAP (Ran GTPase-activating protein) to address these fundamental questions. Plant RanGAP is targeted to the nuclear pore by a plant-specific mechanism involving two families of nuclear pore-associated proteins [WIP (WPP-domain-interacting protein) and WIT (WPP-domain-interacting tail-anchored protein)] not found outside the land plant lineage. One protein family (WIP or WIT) is sufficient for RanGAP targeting in differentiated root cells, whereas both families are necessary in meristematic cells. A C-terminal predicted transmembrane domain is sufficient for targeting WIP proteins to the nuclear envelope. Nuclear-envelope targeting of WIT proteins requires a coiled-coil domain and is facilitated by HSC70 (heat-shock cognate 70 stress protein) chaperones and a class of plant-specific proteins resembling the RanGAP-targeting domain (WPP proteins). Taken together, this sheds the first light on the requirements and interdependences of nuclear envelope and nuclear pore targeting in land plants.
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17
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Siaud N, Dubois E, Massot S, Richaud A, Dray E, Collier J, Doutriaux MP. The SOS screen in Arabidopsis: a search for functions involved in DNA metabolism. DNA Repair (Amst) 2010; 9:567-78. [PMID: 20227352 DOI: 10.1016/j.dnarep.2010.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/08/2010] [Accepted: 02/10/2010] [Indexed: 11/19/2022]
Abstract
The SOS screen, as originally described by Perkins et al. (1999) [7], was setup with the aim of identifying Arabidopsis functions that might potentially be involved in the DNA metabolism. Such functions, when expressed in bacteria, are prone to disturb replication and thus trigger the SOS response. Consistently, expression of AtRAD51 and AtDMC1 induced the SOS response in bacteria, even affecting E. coli viability. 100 SOS-inducing cDNAs were isolated from a cDNA library constructed from an Arabidopsis cell suspension that was found to highly express meiotic genes. A large proportion of these SOS(+) candidates are clearly related to the DNA metabolism, others could be involved in the RNA metabolism, while the remaining cDNAs encode either totally unknown proteins or proteins that were considered as irrelevant. Seven SOS(+) candidate genes are induced following gamma irradiation. The in planta function of several of the SOS-inducing clones was investigated using T-DNA insertional mutants or RNA interference. Only one SOS(+) candidate, among those examined, exhibited a defined phenotype: silenced plants for DUT1 were sensitive to 5-fluoro-uracil (5FU), as is the case of the leaky dut-1 mutant in E. coli that are affected in dUTPase activity. dUTPase is essential to prevent uracil incorporation in the course of DNA replication.
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Affiliation(s)
- Nicolas Siaud
- Institut de Biologie des Plantes, CNRS UMR8618, Bâtiment 630, Université Paris Sud 11, 91405 Orsay Cedex, France.
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18
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Wang TY, Han ZM, Chai YR, Zhang JH. A mini review of MAR-binding proteins. Mol Biol Rep 2010; 37:3553-60. [PMID: 20174991 DOI: 10.1007/s11033-010-0003-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 02/08/2010] [Indexed: 02/08/2023]
Abstract
Genomic DNA encompasses several levels of organization, the nuclear matrix mediates the formation of DNA loop domains that are anchored to matrix attachment regions (MARs). By means of specific interaction with MAR binding proteins (MARBPs), MAR plays an important regulation role in enhancing transgene expression, decreasing expression variation among individuals of different transformants and serving as the replication origin. Through these years, some MARBPs have been identified and characterized from humans, plants, animals and algae so far and the list is growing. Most of MARBPs exist in a co-repressor/co-activator complex and involve in chromosome folding, regulation of gene expression, influencing cell development and inducing cell apoptosis. This review covers recent advances that have contributed to our understanding of MARBPs.
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Affiliation(s)
- Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Jinsui Road, Xinxiang, Henan, 453003, People's Republic of China.
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19
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Meier I, Brkljacic J. The Arabidopsis nuclear pore and nuclear envelope. THE ARABIDOPSIS BOOK 2010; 8:e0139. [PMID: 22303264 PMCID: PMC3244964 DOI: 10.1199/tab.0139] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The nuclear envelope is a double membrane structure that separates the eukaryotic cytoplasm from the nucleoplasm. The nuclear pores embedded in the nuclear envelope are the sole gateways for macromolecular trafficking in and out of the nucleus. The nuclear pore complexes assembled at the nuclear pores are large protein conglomerates composed of multiple units of about 30 different nucleoporins. Proteins and RNAs traffic through the nuclear pore complexes, enabled by the interacting activities of nuclear transport receptors, nucleoporins, and elements of the Ran GTPase cycle. In addition to directional and possibly selective protein and RNA nuclear import and export, the nuclear pore gains increasing prominence as a spatial organizer of cellular processes, such as sumoylation and desumoylation. Individual nucleoporins and whole nuclear pore subcomplexes traffic to specific mitotic locations and have mitotic functions, for example at the kinetochores, in spindle assembly, and in conjunction with the checkpoints. Mutants of nucleoporin genes and genes of nuclear transport components lead to a wide array of defects from human diseases to compromised plant defense responses. The nuclear envelope acts as a repository of calcium, and its inner membrane is populated by functionally unique proteins connected to both chromatin and-through the nuclear envelope lumen-the cytoplasmic cytoskeleton. Plant nuclear pore and nuclear envelope research-predominantly focusing on Arabidopsis as a model-is discovering both similarities and surprisingly unique aspects compared to the more mature model systems. This chapter gives an overview of our current knowledge in the field and of exciting areas awaiting further exploration.
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Affiliation(s)
- Iris Meier
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, 520 Aronoff Laboratory, 318 W 12th Avenue, Columbus, OH 43210
- Address correspondence to
| | - Jelena Brkljacic
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, 520 Aronoff Laboratory, 318 W 12th Avenue, Columbus, OH 43210
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20
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Seltzer V, Janski N, Canaday J, Herzog E, Erhardt M, Evrard JL, Schmit AC. Arabidopsis GCP2 and GCP3 are part of a soluble gamma-tubulin complex and have nuclear envelope targeting domains. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:322-31. [PMID: 17714428 DOI: 10.1111/j.1365-313x.2007.03240.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In higher plants, microtubules (MTs) are assembled in distinctive arrays in the absence of a defined organizing center. Three MT nucleation sites have been described: the nuclear surface, the cell cortex and cortical MT branch points. The Arabidopsis thaliana (At) genome contains putative orthologues encoding all the components of characterized mammalian nucleation complexes: gamma-tubulin and gamma-tubulin complex proteins GCP2 to GCP6. We have cloned the cDNA encoding AtGCP2, and show that gamma-tubulin, AtGCP2 and AtGCP3 are part of the same tandem affinity-purified complex and are present in a large membrane-associated complex. In addition, small soluble gamma-tubulin complexes of the size expected for a gamma-tubulin core complex are recruited to isolated nuclei. Using immunogold labelling, AtGCP3 is localized to both the nuclear envelope (NE) and the plasma membrane. To identify domains that could play a role in targeting complexes to these nucleation sites, truncated AtGCP2- and AtGCP3-green fluorescent protein fusion proteins were expressed in BY-2 cells. Several domains from AtGCP2 and AtGCP3 are capable of targeting fusions to the NE. We propose that regulated recruitment of soluble gamma-tubulin-containing complexes is responsible for nucleation at dispersed sites in plant cells and contributes to the formation and organization of the various MT arrays.
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Affiliation(s)
- Virginie Seltzer
- Institut de Biologie Moléculaire des Plantes, UPR2357-CNRS, Université Louis Pasteur, 12 rue du Général Zimmer, 67084 Strasbourg cedex, France
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21
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22
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Vyetrogon K, Tebbji F, Olson DJH, Ross ARS, Matton DP. A comparative proteome and phosphoproteome analysis of differentially regulated proteins during fertilization in the self-incompatible speciesSolanum chacoense Bitt. Proteomics 2007; 7:232-47. [PMID: 17205606 DOI: 10.1002/pmic.200600399] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have used 2-DE for a time-course study of the changes in protein and phosphoprotein expression that occur immediately after fertilization in Solanum chacoense. The phosphorylation status of the detected proteins was determined with three methods: in vivo labeling, immunodetection, and phosphoprotein-specific staining. Using a pI range of 4-7, 262 phosphorylated proteins could be mapped to the 619 proteins detected by Sypro Ruby staining, representing 42% of the total proteins. Among these phosphoproteins, antibodies detected 184 proteins from which 78 were also detected with either of the other two methods (42%). Pro-Q Diamond phosphoprotein stain detected 111 proteins, of which 76 were also detected with either of the other two methods (68%). The 32P in vivo labeling method detected 90 spots from which 78 were also detected with either of other two methods (87%). On comparing before and after fertilization profiles, 38 proteins and phosphoproteins presented a reproducible change in their accumulation profiles. Among these, 24 spots were selected and analyzed by LC-MS/MS using a hybrid quadrupole-TOF (Q-TOF) instrument. Peptide data were searched against publicly available protein and EST databases, and the putative roles of the identified proteins in early fertilization events are discussed.
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Affiliation(s)
- Kateryna Vyetrogon
- Institut de Recherche en Biologie Végétale (IRBV), Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
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23
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Pandey A, Choudhary MK, Bhushan D, Chattopadhyay A, Chakraborty S, Datta A, Chakraborty N. The Nuclear Proteome of Chickpea (Cicer arietinumL.) Reveals Predicted and Unexpected Proteins. J Proteome Res 2006; 5:3301-11. [PMID: 17137331 DOI: 10.1021/pr060147a] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear proteins constitute a highly organized, complex network that plays diverse roles during cellular development and other physiological processes. The yeast nuclear proteome corresponds to about one-fourth of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. In an attempt to understand the complexity of plant nuclear proteins, we have developed a proteome reference map of a legume, chickpea, using two-dimensional gel electrophoresis (2-DE). Approximately, 600 protein spots were detected, and LC-ESI-MS/MS analyses led to the identification of 150 proteins that have been implicated in a variety of cellular functions. The largest percentage of the identified proteins was involved in signaling and gene regulation (36%), while 17% were involved in DNA replication and transcription. The chickpea nuclear proteome indicates the presence of few new nuclear proteins of unknown functions vis-à-vis many known resident proteins. To the best of our knowledge, this is the first report of a nuclear proteome of an unsequenced genome.
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Affiliation(s)
- Aarti Pandey
- National Centre for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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24
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Marty AJ, Thompson JK, Duffy MF, Voss TS, Cowman AF, Crabb BS. Evidence that Plasmodium falciparum chromosome end clusters are cross-linked by protein and are the sites of both virulence gene silencing and activation. Mol Microbiol 2006; 62:72-83. [PMID: 16942599 DOI: 10.1111/j.1365-2958.2006.05364.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The malaria parasite Plasmodium falciparum undergoes antigenic variation through allelic exclusion and variant expression of surface proteins encoded by the var gene family. Regulation of var genes is under epigenetic control and involves reversible silencing and activation that requires the physical repositioning of a var locus into a transcriptionally permissive zone of the nuclear periphery. P. falciparum chromosome ends appear to aggregate into large perinuclear clusters which house both subtelomeric and chromosome central var genes. In this study we further define the composition of telomeric clusters using fluorescent in situ hybridization, and provide evidence that chromosome end clusters are formed by cross-linking protein. In addition, we demonstrate that a subtelomeric reporter gene and a var gene remain within clusters regardless of their transcriptional status. Our findings support a model whereby a highly localized structure dedicated to the activation of a single var gene can be housed within a gene dense chromosome end cluster that is otherwise transcriptionally silent.
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Affiliation(s)
- Allison J Marty
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
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25
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Ding YH, Liu NY, Tang ZS, Liu J, Yang WC. Arabidopsis GLUTAMINE-RICH PROTEIN23 is essential for early embryogenesis and encodes a novel nuclear PPR motif protein that interacts with RNA polymerase II subunit III. THE PLANT CELL 2006; 18:815-30. [PMID: 16489121 PMCID: PMC1425853 DOI: 10.1105/tpc.105.039495] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2005] [Revised: 01/03/2006] [Accepted: 01/26/2006] [Indexed: 05/05/2023]
Abstract
Precise control of gene expression is critical for embryo development in both animals and plants. We report that Arabidopsis thaliana GLUTAMINE-RICH PROTEIN23 (GRP23) is a pentatricopeptide repeat (PPR) protein that functions as a potential regulator of gene expression during early embryogenesis in Arabidopsis. Loss-of-function mutations of GRP23 caused the arrest of early embryo development. The vast majority of the mutant embryos arrested before the 16-cell dermatogen stage, and none of the grp23 embryos reached the heart stage. In addition, 19% of the mutant embryos displayed aberrant cell division patterns. GRP23 encodes a polypeptide with a Leu zipper domain, nine PPRs at the N terminus, and a Gln-rich C-terminal domain with an unusual WQQ repeat. GRP23 is a nuclear protein that physically interacts with RNA polymerase II subunit III in both yeast and plant cells. GRP23 is expressed in developing embryos up to the heart stage, as revealed by beta-glucuronidase reporter gene expression and RNA in situ hybridization. Together, our data suggest that GRP23, by interaction with RNA polymerase II, likely functions as a transcriptional regulator essential for early embryogenesis in Arabidopsis.
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Affiliation(s)
- Yong-He Ding
- Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
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26
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Mahfouz MM, Kim S, Delauney AJ, Verma DPS. Arabidopsis TARGET OF RAPAMYCIN interacts with RAPTOR, which regulates the activity of S6 kinase in response to osmotic stress signals. THE PLANT CELL 2006; 18:477-90. [PMID: 16377759 PMCID: PMC1356553 DOI: 10.1105/tpc.105.035931] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
TARGET OF RAPAMYCIN (TOR) kinase controls many cellular functions in eukaryotic cells in response to stress and nutrient availability and was shown to be essential for embryonic development in Arabidopsis thaliana. We demonstrated that Arabidopsis RAPTOR1 (a TOR regulatory protein) interacts with the HEAT repeats of TOR and that RAPTOR1 regulates the activity of S6 kinase (S6K) in response to osmotic stress. RAPTOR1 also interacts in vivo with Arabidopsis S6K1, a putative substrate for TOR. S6K1 fused to green fluorescent protein and immunoprecipitated from tobacco (Nicotiana tabacum) leaves after transient expression was active in phosphorylating the Arabidopsis ribosomal S6 protein. The catalytic domain of S6K1 could be phosphorylated by Arabidopsis 3-phosphoinositide-dependent protein kinase-1 (PDK1), indicating the involvement of PDK1 in the regulation of S6K. The S6K1 activity was sensitive to osmotic stress, while PDK1 activity was not affected. However, S6K1 sensitivity to osmotic stress was relieved by co-overexpression of RAPTOR1. Overall, these observations demonstrated the existence of a functional TOR kinase pathway in plants. However, Arabidopsis seedlings do not respond to normal physiological levels of rapamycin, which appears to be due its inability to bind to the Arabidopsis homolog of FKBP12, a protein that is essential for the binding of rapamycin with TOR. Replacement of the Arabidopsis FKBP12 with the human FKBP12 allowed rapamycin-dependent interaction with TOR. Since homozygous mutation in TOR is lethal, it suggests that this pathway is essential for integrating the stress signals into the growth regulation.
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Affiliation(s)
- Magdy M Mahfouz
- Department of Molecular Genetics and Plant Biotechnology Center, The Ohio State University, Columbus, Ohio 43210, USA
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27
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Patel S, Brkljacic J, Gindullis F, Rose A, Meier I. The plant nuclear envelope protein MAF1 has an additional location at the Golgi and binds to a novel Golgi-associated coiled-coil protein. PLANTA 2005; 222:1028-40. [PMID: 16231153 DOI: 10.1007/s00425-005-0076-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Accepted: 06/28/2005] [Indexed: 05/04/2023]
Abstract
Tomato MAF1 (LeMAF1) is a plant-specific, nuclear envelope (NE)-associated protein. It is the founding member of a group of WPP domain-containing, NE-associated proteins. This group includes the Arabidopsis WPP family, which is involved in cell division, as well as plant RanGAPs. In addition to its NE localization, LeMAF1 accumulates in speckles in the cytoplasm. Here, we show that the LeMAF1-containing speckles are components of the Golgi apparatus. A novel tomato coiled-coil protein was identified that specifically binds to LeMAF1. Tomato WPP domain-associated protein (LeWAP) interacts in yeast and in vitro through its coiled-coil domain with several WPP-domain containing proteins, including AtRanGAP1 and the WPP family (LeMAF, WPP1 and WPP2). Like LeMAF1, LeWAP is localized at the Golgi. Moreover, we present data showing that Arabidopsis WAP is necessary for the existence of a multi-protein complex containing WPP2.
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Affiliation(s)
- Shalaka Patel
- Plant Biotechnology Center and Department of Plant Cellular and Molecular Biology, The Ohio State University, 244 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210-1002, USA
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Jeong SY, Rose A, Joseph J, Dasso M, Meier I. Plant-specific mitotic targeting of RanGAP requires a functional WPP domain. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:270-82. [PMID: 15807788 DOI: 10.1111/j.1365-313x.2005.02368.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The small GTPase Ran is involved in nucleocytoplasmic transport, spindle formation, nuclear envelope (NE) formation, and cell-cycle control. In vertebrates, these functions are controlled by a three-dimensional gradient of Ran-GTP to Ran-GDP, established by the spatial separation of Ran GTPase-activating protein (RanGAP) and the Ran guanine nucleotide exchange factor RCC1. While this spatial separation is established by the NE during interphase, it is orchestrated during mitosis by association of RCC1 with the chromosomes and RanGAP with the spindle and kinetochores. SUMOylation of vertebrate RanGAP1 is required for NE, spindle, and centromere association. Arabidopsis RanGAP1 (AtRanGAP1) lacks the SUMOylated C-terminal domain of vertebrate RanGAP, but contains a plant-specific N-terminal domain (WPP domain), which is necessary and sufficient for its targeting to the NE in interphase. Here we show that the human and plant RanGAP-targeting domains are kingdom specific. AtRanGAP1 has a mitotic trafficking pattern uniquely different from that of vertebrate RanGAP, which includes targeting to the outward-growing rim of the cell plate. The WPP domain is necessary and sufficient for this targeting. Point mutations in conserved residues of the WPP domain also abolish targeting to the nuclear rim and the cell plate, suggesting that the same mechanism is involved in both targeting events. These results indicate that plant and animal RanGAPs undergo different migration patterns during cell division, which require their kingdom-specific targeting domains.
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Affiliation(s)
- Sun Yong Jeong
- Plant Biotechnology Center and Department of Plant Cellular and Molecular Biology, The Ohio State University, Columbus, OH 43210, USA
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29
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Moriguchi K, Suzuki T, Ito Y, Yamazaki Y, Niwa Y, Kurata N. Functional isolation of novel nuclear proteins showing a variety of subnuclear localizations. THE PLANT CELL 2005; 17:389-403. [PMID: 15659629 PMCID: PMC548814 DOI: 10.1105/tpc.104.028456] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nuclear proteins play key roles in the fundamental regulation of genome instability, the phases of organ development, and physiological responsiveness through gene expression. Although nuclear proteins have been shown to account for approximately one-fourth of total proteins in yeast, no efficient method to identify novel nuclear proteins has been applied to plants. In this study, a trial to isolate nuclear proteins in rice was attempted, and several novel nuclear proteins showing a variety of subnuclear localizations were identified. The nuclear transportation trap (NTT) system, which is a modified two-hybrid system, isolated many nuclear proteins from rice (Oryza sativa) NTT cDNA libraries. Nuclear localization of the isolated proteins was confirmed by transient introduction of green fluorescent protein fusion constructs for a subset of protein genes into onion (Allium cepa) cells. The majority of these proteins, including novel proteins and proteins initially categorized as cytoplasmic proteins, were revealed to be localized in the nucleus. Detailed characterization of unknown proteins revealed various subnuclear localizations, indicating their possible association with chromatin and the nuclear matrix with a foci or speckle-like distribution. Some also showed dual distribution in the nucleus and cytoplasm. In the novel protein fraction, a protein was further identified for its chromatin-associated localization in a specific organ of rice by immunostaining. Thus, a variety of novel nuclear architectural proteins with chromatin or matrix associating abilities, which are important in nuclear organization by influencing certain organ developments or cell responsiveness, can be isolated using the NTT method. Because nuclear proteins other than transcription regulators have rarely been characterized in plants, such as matrix proteins and development-specific chromatin proteins, their identification and subsequent characterization could provide important information for genome-wide regulatory mechanisms controlled by nuclear organization.
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Affiliation(s)
- Kazuki Moriguchi
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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30
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Abstract
In a eukaryotic cell, the nuclear envelope (NE) separates genetic information from the environment of biosynthesis and metabolism. Transfer of macromolecules across the NE involves the nuclear pores--large multisubunit protein complexes--and machinery that facilitates rapid, directional, and selective transport. While core elements of the transport process are conserved between kingdoms, different solutions to similar problems have also evolved. Although the structure and composition of the yeast and mammalian nuclear pore have been unraveled recently, the plant nuclear pore remains largely enigmatic. Like any other process, nucleocytoplasmic transport can be regulated. Several examples from plants are discussed that promise insights into the regulation of signaling pathways. While controlling the partitioning of cellular components, the nuclear envelope also presents an obstacle to viruses and transforming agents that need access to the genome, and different mechanisms have evolved to overcome this obstacle. Finally, the recent recognition of the importance of small RNAs for gene regulation emphasizes the need to understand small RNA nuclear export and the levels of its regulation. This review attempts to wed our molecular-mechanistic understanding of nucleocytoplasmic trafficking drawn from all model systems with the intriguing examples of regulated nucleocytoplasmic partitioning in plants.
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Affiliation(s)
- Iris Meier
- Plant Biotechnology Center and Department of Plant Cellular and Molecular Biology, The Ohio State University, Columbus, Ohio 43210, USA
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31
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Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier I. Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division. THE PLANT CELL 2004; 16:3260-73. [PMID: 15548735 PMCID: PMC535872 DOI: 10.1105/tpc.104.026740] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Accepted: 10/04/2004] [Indexed: 05/20/2023]
Abstract
The nuclear envelope (NE) acts as a selective barrier to macromolecule trafficking between the nucleus and the cytoplasm and undergoes a complex reorganization during mitosis. Different eukaryotic kingdoms show specializations in NE function and composition. In contrast with vertebrates, the protein composition of the NE and the function of NE proteins are barely understood in plants. MFP1 attachment factor 1 (MAF1) is a plant-specific NE-associated protein first identified in tomato (Lycopersicon esculentum). Here, we demonstrate that two Arabidopsis thaliana MAF1 homologs, WPP1 and WPP2, are associated with the NE specifically in undifferentiated cells of the root tip. Reentry into cell cycle after callus induction from differentiated root segments reprograms their NE association. Based on green fluorescent protein fusions and immunogold labeling data, the proteins are associated with the outer NE and the nuclear pores in interphase cells and with the immature cell plate during cytokinesis. RNA interference-based suppression of the Arabidopsis WPP family causes shorter primary roots, a reduced number of lateral roots, and reduced mitotic activity of the root meristem. Together, these data demonstrate the existence of regulated NE targeting in plants and identify a class of plant-specific NE proteins involved in mitotic activity.
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Affiliation(s)
- Shalaka Patel
- Plant Biotechnology Center and Department of Plant Molecular and Cellular Biology, The Ohio State University, Columbus, Ohio 43210, USA
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32
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Fujimoto S, Matsunaga S, Yonemura M, Uchiyama S, Azuma T, Fukui K. Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. PLANT MOLECULAR BIOLOGY 2004; 56:225-39. [PMID: 15604740 DOI: 10.1007/s11103-004-3249-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We identified a novel nucleoplasm localized protein in Arabidopsis called AT-hook motif nuclear localized protein 1 (AHL1), which was isolated by visual screening of transformants using random GFP::cDNA fusions. AHL1 contains an AT-hook motif and unknown conserved PPC (plants and prokaryotes conserved) domain that includes a hydrophobic region. Approximately 30 paralogues were identified in the Arabidopsis genome. Proteins with PPC-like domains are found in Bacteria, Archaea and the plant kingdom, but in Bacteria and Archaea the PPC containing proteins of do not have an AT-hook motif. Thus, the PPC domain is evolutionary conserved and has a new function such as AT-rich DNA binding. AHL1 was mainly localized in the nucleoplasm, but little in the nucleolus and heterochromatic region, and was concentrated in the boundary region between euchromatin and heterochromatin. Biochemically, AHL1 was also found in the nuclear matrix fraction. In the M phase, AHL1 was localized on the chromosomal surface. The AT-hook motif was essential for matrix attachment region (MAR) binding, and the hydrophobic region of the PPC was indispensable for nuclear localization. Our results suggest that AHL1 is a novel plant MAR binding protein, which is related to the positioning of chromatin fibers in the nucleus by the presence of an AT-hook motif and PPC domain. In addition, AHL1 is located on the surface of chromosomes during mitosis.
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Affiliation(s)
- Satoru Fujimoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka, 565-0871, Japan
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33
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Brandizzi F, Irons SL, Evans DE. The plant nuclear envelope: new prospects for a poorly understood structure. THE NEW PHYTOLOGIST 2004; 163:227-246. [PMID: 33873618 DOI: 10.1111/j.1469-8137.2004.01118.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The nuclear envelope (NE) is one of the least characterized cellular structures in plant cells. In particular, knowledge of its dynamic behaviour during the cell cycle and of its protein composition is limited. This review summarizes current views on the plant NE and highlights fundamental differences with other organisms. We also introduce the power of new technology available to investigate the NE and how this has already begun to revolutionize our knowledge of the biology of the plant NE. Contents Summary 227 I. Introduction 227 II. The membranes of the nuclear envelope 228 III. Functions of the nuclear envelope 231 IV. Proteins associated with the nuclear envelope 236 V. New tools for studying the nuclear envelope 239 VI. Conclusions and future prospects 241 Acknowledgements 242 References 242.
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Affiliation(s)
- Federica Brandizzi
- Biology Department, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E2
| | - Sarah L Irons
- Research School of Biological and Molecular Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - David E Evans
- Research School of Biological and Molecular Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
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34
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Tian GW, Mohanty A, Chary SN, Li S, Paap B, Drakakaki G, Kopec CD, Li J, Ehrhardt D, Jackson D, Rhee SY, Raikhel NV, Citovsky V. High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta. PLANT PHYSIOLOGY 2004; 135:25-38. [PMID: 15141064 PMCID: PMC429330 DOI: 10.1104/pp.104.040139] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Revised: 03/09/2004] [Accepted: 03/12/2004] [Indexed: 05/17/2023]
Abstract
We developed a high-throughput methodology, termed fluorescent tagging of full-length proteins (FTFLP), to analyze expression patterns and subcellular localization of Arabidopsis gene products in planta. Determination of these parameters is a logical first step in functional characterization of the approximately one-third of all known Arabidopsis genes that encode novel proteins of unknown function. Our FTFLP-based approach offers two significant advantages: first, it produces internally-tagged full-length proteins that are likely to exhibit native intracellular localization, and second, it yields information about the tissue specificity of gene expression by the use of native promoters. To demonstrate how FTFLP may be used for characterization of the Arabidopsis proteome, we tagged a series of known proteins with diverse subcellular targeting patterns as well as several proteins with unknown function and unassigned subcellular localization.
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Affiliation(s)
- Guo-Wei Tian
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York 11794-5215, USA
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35
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Rose A, Patel S, Meier I. The plant nuclear envelope. PLANTA 2004; 218:327-36. [PMID: 14610677 DOI: 10.1007/s00425-003-1132-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2003] [Accepted: 10/01/2003] [Indexed: 05/08/2023]
Abstract
This review summarizes our present knowledge about the composition and function of the plant nuclear envelope. Compared with animals or yeast, our molecular understanding of the nuclear envelope in higher plants is in its infancy. However, fundamental differences in the structure and function of the plant and animal nuclear envelope have already been found. Here, we compare and contrast these differences with respect to nuclear pore complexes, targeting of Ran signaling to the nuclear envelope, inner nuclear envelope proteins, and the role and fate of the nuclear envelope during mitosis. Further investigation of the emerging fundamental differences as well as the similarities between kingdoms might illuminate why there appears to be more than one blueprint for building a nucleus.
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Affiliation(s)
- Annkatrin Rose
- Department of Plant Biology, The Ohio State University, 244 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210, USA
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36
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Improvements of the Molecular Toolbox for Cell Cycle Studies in Tobacco BY-2 Cells. TOBACCO BY-2 CELLS 2004. [DOI: 10.1007/978-3-662-10572-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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37
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Abstract
Development requires a precise program of gene expression to be carried out. Much work has focussed on the regulatory networks that control gene expression, for example in response to external cues. However, it is important to recognize that these regulatory events take place within the physical context of the nucleus, and that the physical position of a gene within the nuclear volume can have strong influences on its regulation and interactions. The first part of this review will summarize what is currently known about nuclear architecture, that is, the large-scale three-dimensional arrangement of chromosome loci within the nucleus. The remainder of the review will examine developmental processes from the point of view of the nucleus.
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Affiliation(s)
- Wallace F Marshall
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
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38
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Merkle T. Nucleo-cytoplasmic partitioning of proteins in plants: implications for the regulation of environmental and developmental signalling. Curr Genet 2003; 44:231-60. [PMID: 14523572 DOI: 10.1007/s00294-003-0444-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2003] [Revised: 08/21/2003] [Accepted: 09/01/2003] [Indexed: 12/21/2022]
Abstract
Considerable progress has been made in the past few years in characterising Arabidopsis nuclear transport receptors and in elucidating plant signal transduction pathways that employ nucleo-cytoplasmic partitioning of a member of the signal transduction chain. This review briefly introduces the major principles of nuclear transport of macromolecules across the nuclear envelope and the proteins involved, as they have been described in vertebrates and yeast. Proteins of the plant nuclear transport machinery that have been identified to date are discussed, the focus being on Importin beta-like nuclear transport receptors. Finally, the importance of nucleo-cytoplasmic partitioning as a regulatory tool for signalling is highlighted, and different plant signal transduction pathways that make use of this regulatory potential are presented.
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Affiliation(s)
- Thomas Merkle
- Institute of Biology II, Cell Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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39
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Capron A, Serralbo O, Fülöp K, Frugier F, Parmentier Y, Dong A, Lecureuil A, Guerche P, Kondorosi E, Scheres B, Genschik P. The Arabidopsis anaphase-promoting complex or cyclosome: molecular and genetic characterization of the APC2 subunit. THE PLANT CELL 2003; 15:2370-82. [PMID: 14508008 PMCID: PMC197302 DOI: 10.1105/tpc.013847] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2003] [Accepted: 07/26/2003] [Indexed: 05/18/2023]
Abstract
In yeast and animals, the anaphase-promoting complex or cyclosome (APC/C) is an essential ubiquitin protein ligase that regulates mitotic progression and exit by controlling the stability of cell cycle regulatory proteins, such as securin and the mitotic cyclins. In plants, the function, regulation, and substrates of the APC/C are poorly understood. To gain more insight into the roles of the plant APC/C, we characterized at the molecular level one of its subunits, APC2, which is encoded by a single-copy gene in Arabidopsis. We show that the Arabidopsis gene is able to partially complement a budding yeast apc2 ts mutant. By yeast two-hybrid assays, we demonstrate an interaction of APC2 with two other APC/C subunits: APC11 and APC8/CDC23. A reverse-genetic approach identified Arabidopsis plants carrying T-DNA insertions in the APC2 gene. apc2 null mutants are impaired in female megagametogenesis and accumulate a cyclin-beta-glucuronidase reporter protein but do not display metaphase arrest, as observed in other systems. The APC2 gene is expressed in various plant organs and does not seem to be cell cycle regulated. Finally, we report intriguing differences in APC2 protein subcellular localization compared with that in other systems. Our observations support a conserved function of the APC/C in plants but a different mode of regulation.
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Affiliation(s)
- Arnaud Capron
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg Cédex, France
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40
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Abstract
We provide a genetic analysis of the meiotic drive system on maize abnormal chromosome 10 (Ab10) that causes preferential segregation of specific chromosomal regions to the reproductive megaspore. The data indicate that at least four chromosomal regions contribute to meiotic drive, each providing distinct functions that can be differentiated from each other genetically and/or phenotypically. Previous reports established that meiotic drive requires neocentromere activity at specific tandem repeat arrays (knobs) and that two regions on Ab10 are involved in trans-activating neocentromeres. Here we confirm and extend data suggesting that only one of the neocentromere-activating regions is sufficient to move many knobs. We also confirm the localization of a locus/loci on Ab10, thought to be a prerequisite for meiotic drive, which promotes recombination in structural heterozygotes. In addition, we identified two new and independent functions required for meiotic drive. One was identified through the characterization of a deletion derivative of Ab10 [Df(L)] and another as a newly identified meiotic drive mutation (suppressor of meiotic drive 3). In the absence of either function, meiotic drive is abolished but neocentromere activity and the recombination effect typical of Ab10 are unaffected. These results demonstrate that neocentromere activity and increased recombination are not the only events required for meiotic drive.
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Affiliation(s)
- Evelyn N Hiatt
- Department of Genetics, University of Georgia, Athens 30602, USA
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41
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Rose A, Gindullis F, Meier I. A novel alpha-helical protein, specific to and highly conserved in plants, is associated with the nuclear matrix fraction. JOURNAL OF EXPERIMENTAL BOTANY 2003; 54:1133-1141. [PMID: 12654864 DOI: 10.1093/jxb/erg114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A cDNA for a novel plant protein was isolated from tomato. Nuclear Matrix Protein 1 (NMP1) is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants, including gymnosperms, moss, and the liverwort Marchantia polymorpha. NMP1 is predominantly alpha-helical with multiple stretches of short amphipathic regions. Cell fractionation, immunofluorescence, and GFP localization experiments showed that NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm.
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Affiliation(s)
- Annkatrin Rose
- Plant Biotechnology Center and Department of Plant Biology, Ohio State University, Columbus, OH 43210, USA
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42
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Girod PA, Mermod N. Use of scaffold/matrix-attachment regions for protein production. GENE TRANSFER AND EXPRESSION IN MAMMALIAN CELLS 2003. [DOI: 10.1016/s0167-7306(03)38022-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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43
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Abstract
The nuclear lamina is composed of both A- and B-type lamins and lamin-binding proteins. Many lamin-binding proteins are integral proteins of the inner nuclear membrane. Lamins and inner nuclear membrane proteins are important for a variety of cell functions, including nuclear assembly, replication, transcription, and nuclear integrity. Recent advances in the field in the past year include the identification of a family of spectrin-repeat-containing inner nuclear membrane proteins and other novel inner-membrane proteins, and the discovery of a nuclear membrane fusion complex. There is also growing evidence that A- and B-type lamins and their binding partners have distinct roles during nuclear assembly and interphase.
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Affiliation(s)
- James M Holaska
- Department of Cell Biology, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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44
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Pay A, Resch K, Frohnmeyer H, Fejes E, Nagy F, Nick P. Plant RanGAPs are localized at the nuclear envelope in interphase and associated with microtubules in mitotic cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 30:699-709. [PMID: 12061901 DOI: 10.1046/j.1365-313x.2002.01324.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In animals and yeast, the small GTP-binding protein Ran has multiple functions - it is involved in mediating (i) the directional passage of proteins and RNA through the nuclear pores in interphase cells; and (ii) the formation of spindle asters, the polymerization of microtubules, and the re-assembly of the nuclear envelope in mitotic cells. Nucleotide binding of Ran is modulated by a series of accessory proteins. For instance, the hydrolysis of RanGTP requires stimulation by the RanGTPase protein RanGAP. Here we report the complementation of the yeast RanGAP mutant rna1 with Medicago sativa and Arabidopsis thaliana cDNAs encoding RanGAP-like proteins. Confocal laser microscopy of Arabidopsis plants overexpressing chimeric constructs of GFP with AtRanGAP1 and 2 demonstrated that the fusion protein is localized to patchy areas at the nuclear envelope of interphase cells. In contrast, the cellular distribution of RanGAPs in synchronized tobacco cells undergoing mitosis is characteristically different. Double-immunofluorescence shows that RanGAPs are co-localized with spindle microtubules during anaphase, with the microtubular phragmoplast and the surface of the daughter nuclei during telophase. Co-assembly of RanGAPs with tubulin correlates with these in vivo observations. The detected localization pattern is consistent with the postulated function of plant RanGAPs in the regulation of nuclear transport during interphase, and suggests a role for these proteins in the organization of the microtubular mitotic structures.
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Affiliation(s)
- Aniko Pay
- Plant Biology Institute, Biological Research Center, H-6701 Szeged, PO Box 521, Hungary
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45
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Gindullis F, Rose A, Patel S, Meier I. Four signature motifs define the first class of structurally related large coiled-coil proteins in plants. BMC Genomics 2002; 3:9. [PMID: 11972898 PMCID: PMC102765 DOI: 10.1186/1471-2164-3-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2002] [Accepted: 04/09/2002] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Animal and yeast proteins containing long coiled-coil domains are involved in attaching other proteins to the large, solid-state components of the cell. One subgroup of long coiled-coil proteins are the nuclear lamins, which are involved in attaching chromatin to the nuclear envelope and have recently been implicated in inherited human diseases. In contrast to other eukaryotes, long coiled-coil proteins have been barely investigated in plants. RESULTS We have searched the completed Arabidopsis genome and have identified a family of structurally related long coiled-coil proteins. Filament-like plant proteins (FPP) were identified by sequence similarity to a tomato cDNA that encodes a coiled-coil protein which interacts with the nuclear envelope-associated protein, MAF1. The FPP family is defined by four novel unique sequence motifs and by two clusters of long coiled-coil domains separated by a non-coiled-coil linker. All family members are expressed in a variety of Arabidopsis tissues. A homolog sharing the structural features was identified in the monocot rice, indicating conservation among angiosperms. CONCLUSION Except for myosins, this is the first characterization of a family of long coiled-coil proteins in plants. The tomato homolog of the FPP family binds in a yeast two-hybrid assay to a nuclear envelope-associated protein. This might suggest that FPP family members function in nuclear envelope biology. Because the full Arabidopsis genome does not appear to contain genes for lamins, it is of interest to investigate other long coiled-coil proteins, which might functionally replace lamins in the plant kingdom.
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Affiliation(s)
- Frank Gindullis
- CellTec Biotechnologie GmbH, Frohmestrasse 110, D-22459 Hamburg, Germany
| | - Annkatrin Rose
- Plant Biotechnology Center and Department of Plant Biology, Ohio State University, 210 Rightmire Hall, 1060 Carmack Road, Columbus, Ohio 43210, USA
| | - Shalaka Patel
- Plant Biotechnology Center and Department of Plant Biology, Ohio State University, 210 Rightmire Hall, 1060 Carmack Road, Columbus, Ohio 43210, USA
| | - Iris Meier
- Plant Biotechnology Center and Department of Plant Biology, Ohio State University, 210 Rightmire Hall, 1060 Carmack Road, Columbus, Ohio 43210, USA
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46
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Abstract
Fluorescence in situ hybridization combined with three-dimensional microscopy has shown that chromosomes are not randomly strewn throughout the nucleus but are in fact fairly well organized, with different loci reproducibly found in different regions of the nucleus. At the same time, increasingly sophisticated methods to track and analyze the movements of specific chromosomal loci in vivo using four-dimensional microscopy have revealed that chromatin undergoes extensive Brownian motion. However, the diffusion of interphase chromatin is constrained, implying that chromosomes are physically anchored within the nucleus. This constraint on diffusion is the result of interactions between chromatin and structural elements within the nucleus, such as nuclear pores or the nuclear lamina. The combination of defined positioning with constrained diffusion has a strong impact on interactions between chromosomal loci, and appears to explain the tendency of certain chromosome rearrangements to occur during the development of cancer.
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Affiliation(s)
- Wallace F Marshall
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
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47
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Song W, Solimeo H, Rupert RA, Yadav NS, Zhu Q. Functional dissection of a Rice Dr1/DrAp1 transcriptional repression complex. THE PLANT CELL 2002; 14:181-95. [PMID: 11826307 PMCID: PMC150559 DOI: 10.1105/tpc.010320] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2001] [Accepted: 10/16/2001] [Indexed: 05/20/2023]
Abstract
We characterized rice cDNA sequences for OsDr1 and OsDrAp1, which encode structural homologs of the eukaryotic general repressors Dr1 and DrAp1, respectively. OsDr1 and OsDrAp1 are nuclear proteins that interact with each other and with the TATA binding protein/DNA complex. In vitro and in vivo functional analyses showed that OsDrAp1 functions as a repressor, unlike its role in other eukaryotic systems, in which DrAp1 is a corepressor. OsDr1 and OsDrAp1 functioned together as a much stronger repressor than either one alone. Functional dissections revealed that the N-terminal histone-fold domains of OsDr1 and OsDrAp1 were necessary and sufficient for their repression and protein-protein interaction with each other. The unique glutamine- and proline-rich domain of OsDr1 had no repression activity. The basic amino acid-rich region and an arginine and glycine repeat domain of OsDrAp1 enhanced its repression activity. Thus, although OsDr1 and OsDrAp1 function as repressors, the functions of the two components are reversed compared with those of their nonplant counterparts.
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Affiliation(s)
- Wen Song
- Central Research and Development, DuPont Company, P.O. Box 80402, Wilmington, DE 19880-0402, USA
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48
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Rose A, Meier I. A domain unique to plant RanGAP is responsible for its targeting to the plant nuclear rim. Proc Natl Acad Sci U S A 2001; 98:15377-82. [PMID: 11752475 PMCID: PMC65037 DOI: 10.1073/pnas.261459698] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ran is a small signaling GTPase that is involved in nucleocytoplasmic transport. Two additional functions of animal Ran in the formation of spindle asters and the reassembly of the nuclear envelope in mitotic cells have been recently reported. In contrast to Ras or Rho, Ran is not associated with membranes. Instead, the spatial sequestering of its accessory proteins, the Ran GTPase-activating protein RanGAP and the nucleotide exchange factor RCC1, appears to define the local concentration of RanGTP vs. RanGDP involved in signaling. Mammalian RanGAP is bound to the nuclear pore by a mechanism involving the attachment of small ubiquitin-related modifier protein (SUMO) to its C terminus and the subsequent binding of the SUMOylated domain to the nucleoporin Nup358. Here we show that plant RanGAP utilizes a different mechanism for nuclear envelope association, involving a novel targeting domain that appears to be unique to plants. The N-terminal WPP domain is highly conserved among plant RanGAPs and the small, plant-specific nuclear envelope-associated protein MAF1, but not present in yeast or animal RanGAP. Confocal laser scanning microscopy of green fluorescent protein (GFP) fusion proteins showed that it is necessary for RanGAP targeting and sufficient to target the heterologous protein GFP to the plant nuclear rim. The highly conserved tryptophan and proline residues of the WPP motif are necessary for its function. The 110-aa WPP domain is the first nuclear-envelope targeting domain identified in plants. Its fundamental difference to its mammalian counterpart implies that different mechanisms have evolved in plants and animals to anchor RanGAP at the nuclear surface.
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Affiliation(s)
- A Rose
- Plant Biotechnology Center and Department of Plant Biology, Ohio State University, Columbus, OH 43210, USA
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Meier I. A novel link between ran signal transduction and nuclear envelope proteins in plants. PLANT PHYSIOLOGY 2000; 124:1507-10. [PMID: 11115866 PMCID: PMC1539304 DOI: 10.1104/pp.124.4.1507] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- I Meier
- Plant Biotechnology Center and Department of Plant Biology, Ohio State University, Columbus, Ohio 43210, USA
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Morisawa G, Han-Yama A, Moda I, Tamai A, Iwabuchi M, Meshi T. AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. THE PLANT CELL 2000; 12:1903-16. [PMID: 11041885 PMCID: PMC149128 DOI: 10.1105/tpc.12.10.1903] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2000] [Accepted: 07/20/2000] [Indexed: 05/18/2023]
Abstract
Interactions between the nuclear matrix and special regions of chromosomal DNA called matrix attachment regions (MARs) have been implicated in various nuclear functions. We have identified a novel protein from wheat, AT hook-containing MAR binding protein1 (AHM1), that binds preferentially to MARs. A multidomain protein, AHM1 has the special combination of a J domain-homologous region and a Zn finger-like motif (a J-Z array) and an AT hook. For MAR binding, the AT hook at the C terminus was essential, and an internal portion containing the Zn finger-like motif was additionally required in vivo. AHM1 was found in the nuclear matrix fraction and was localized in the nucleoplasm. AHM1 fused to green fluorescent protein had a speckled distribution pattern inside the nucleus. AHM1 is most likely a nuclear matrix component that functions between intranuclear framework and MARs. J-Z arrays can be found in a group of (hypothetical) proteins in plants, which may share some functions, presumably to recruit specific Hsp70 partners as co-chaperones.
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Affiliation(s)
- G Morisawa
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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