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Wen C, Yuan Z, Zhang X, Chen H, Luo L, Li W, Li T, Ma N, Mao F, Lin D, Lin Z, Lin C, Xu T, Lü P, Lin J, Zhu F. Sea-ATI unravels novel vocabularies of plant active cistrome. Nucleic Acids Res 2023; 51:11568-11583. [PMID: 37850650 PMCID: PMC10681729 DOI: 10.1093/nar/gkad853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/11/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging. In this study, we report the assay sequential extraction assisted-active TF identification (sea-ATI), a low-input method that profiles the DNA sequences recognized by TFs in a target tissue. We applied sea-ATI to seven plant tissues to survey their active cistrome and generated 41 motif models, including 15 new models that represent previously unidentified cis-regulatory vocabularies. ATAC-seq and RNA-seq analyses confirmed the functionality of the cis-elements from the new models, in that they are actively bound in vivo, located near the transcription start site, and influence chromatin accessibility and transcription. Furthermore, comparing dimeric WRKY CREs between sea-ATI and DAP-seq libraries revealed that thermodynamics and genetic drifts cooperatively shaped their evolution. Notably, sea-ATI can identify not only positive but also negative regulatory cis-elements, thereby providing unique insights into the functional non-coding genome of plants.
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Affiliation(s)
- Chenjin Wen
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhen Yuan
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaotian Zhang
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hao Chen
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Lin Luo
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Wanying Li
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Tian Li
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Nana Ma
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Fei Mao
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Dongmei Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhanxi Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Chentao Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Tongda Xu
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Peitao Lü
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Juncheng Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Fangjie Zhu
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
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2
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Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
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3
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Lim CJ, Park KS, Ali A, Park J, Ryou SM, Shen M, Khan HA, Bader ZE, Zareen S, Bae MJ, Choi JH, Xu ZY, Pardo JM, Yun DJ. Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1105988. [PMID: 36684790 PMCID: PMC9853073 DOI: 10.3389/fpls.2022.1105988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis HOS15/PWR/HDA9 repressor complex, which is similar to the TBL1/NcoR1/HDAC complex in animals, plays a well-known role in epigenetic regulation. PWR and HDA9 have been reported to interact with each other and modulate the flowering time by repressing AGL19 expression, whereas HOS15 and HDA9, together with the photoperiodic evening complex, regulate flowering time through repression of GI transcription. However, the role of the HOS15/PWR/HDA9 core repressor complex as a functional unit in the regulation of flowering time is yet to be explored. In this study, we reported that the loss-of-function hos15-2/pwr/hda9 triple mutant accumulates higher transcript levels of AGL19 and exhibits an early flowering phenotype similar to those of hos15, pwr, and hda9 single mutants. Interestingly, the accumulation of HOS15 in the nucleus was drastically reduced in pwr and hda9 mutants. As a result, HOS15 could not perform its role in histone deacetylation or interaction with H3 in the nucleus. Furthermore, HOS15 is also associated with the same region of the AGL19 promoter known for PWR-HDA9 binding. The acetylation level of the AGL19 promoter was increased in the hos15-2 mutant, similar to the pwr and hda9 mutants. Therefore, our findings reveal that the HOS15/PWR/HDA9 repressor complex deacetylates the promoter region of AGL19, thereby negatively regulating AGL19 transcription, which leads to early flowering in Arabidopsis.
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Affiliation(s)
- Chae Jin Lim
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Seung Min Ryou
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Department of Agronomy, Agricultural College, Yanbian University, Yanji, China
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zein Eddin Bader
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shah Zareen
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Min Jae Bae
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jong Hyoo Choi
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jose M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones 17 Cientificas and Universidad de Sevilla, Seville, Spain
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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4
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Irigoyen S, Ramasamy M, Misra A, McKnight TD, Mandadi KK. A BTB-TAZ protein is required for gene activation by Cauliflower mosaic virus 35S multimerized enhancers. PLANT PHYSIOLOGY 2022; 188:397-410. [PMID: 34597402 PMCID: PMC8774732 DOI: 10.1093/plphys/kiab450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) BTB-TAZ DOMAIN PROTEIN 2 (BT2) contains an N-terminal BTB domain, a central TAZ zinc-finger protein-protein interaction domain, and a C-terminal calmodulin-binding domain. We previously demonstrated that BT2 regulates telomerase activity and mediates multiple responses to nutrients, hormones, and abiotic stresses in Arabidopsis. Here, we describe the essential role of BT2 in activation of genes by multimerized Cauliflower mosaic virus 35S (35S) enhancers. Loss of BT2 function in several well-characterized 35S enhancer activation-tagged lines resulted in suppression of the activation phenotypes. Suppression of the phenotypes was associated with decreased transcript abundance of the tagged genes. Nuclear run-on assays, mRNA decay studies, and bisulfite sequencing revealed that BT2 is required to maintain the transcriptionally active state of the multimerized 35S enhancers, and lack of BT2 leads to hypermethylation of the 35S enhancers. The TAZ domain and the Ca++/calmodulin-binding domain of BT2 are critical for its function and 35S enhancer activity. We further demonstrate that BT2 requires CULLIN3 and two bromodomain-containing Global Transcription factor group E proteins (GTE9 and GTE11), to regulate 35S enhancer activity. We propose that the BT2-CULLIN3 ubiquitin ligase, through interactions with GTE9 and GTE11, regulates 35S enhancer activity in Arabidopsis.
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Affiliation(s)
- Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
| | | | - Anjali Misra
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Thomas D McKnight
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
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5
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Salvato F, Figueiredo R, Mazzafera P. Nuclei Enrichment from Sugarcane Stems for Proteomics Analyses. Methods Mol Biol 2022; 2469:79-87. [PMID: 35508831 DOI: 10.1007/978-1-0716-2185-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nuclei enrichment procedures enable a large variety of investigations. These studies include structural characterization of nuclear proteins, identification of posttranslational modifications, and regulation of stress or development-related gene expression. Successful enrichment of nuclei samples from plant tissues is crucial for a comprehensive analysis of the plant nuclear proteome. Here, we describe a method for nuclei enrichment from sugarcane stems and its assessment by western blot.
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Affiliation(s)
- Fernanda Salvato
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA
| | - Raquel Figueiredo
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, Brazil
- Department of Biology, Faculty of Sciences and LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, Brazil.
- Department of Crop Science, College of Agriculture Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil.
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6
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Skalický V, Vojtková T, Pěnčík A, Vrána J, Juzoń K, Koláčková V, Sedlářová M, Kubeš MF, Novák O. Auxin Metabolite Profiling in Isolated and Intact Plant Nuclei. Int J Mol Sci 2021; 22:12369. [PMID: 34830250 PMCID: PMC8620152 DOI: 10.3390/ijms222212369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
The plant nucleus plays an irreplaceable role in cellular control and regulation by auxin (indole-3-acetic acid, IAA) mainly because canonical auxin signaling takes place here. Auxin can enter the nucleus from either the endoplasmic reticulum or cytosol. Therefore, new information about the auxin metabolome (auxinome) in the nucleus can illuminate our understanding of subcellular auxin homeostasis. Different methods of nuclear isolation from various plant tissues have been described previously, but information about auxin metabolite levels in nuclei is still fragmented and insufficient. Herein, we tested several published nucleus isolation protocols based on differential centrifugation or flow cytometry. The optimized sorting protocol leading to promising yield, intactness, and purity was then combined with an ultra-sensitive mass spectrometry analysis. Using this approach, we can present the first complex report on the auxinome of isolated nuclei from cell cultures of Arabidopsis and tobacco. Moreover, our results show dynamic changes in auxin homeostasis at the intranuclear level after treatment of protoplasts with free IAA, or indole as a precursor of auxin biosynthesis. Finally, we can conclude that the methodological procedure combining flow cytometry and mass spectrometry offers new horizons for the study of auxin homeostasis at the subcellular level.
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Affiliation(s)
- Vladimír Skalický
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
| | - Tereza Vojtková
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (J.V.); (V.K.)
| | - Katarzyna Juzoń
- Department of Biotechnology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Krakow, Poland;
| | - Veronika Koláčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (J.V.); (V.K.)
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic;
| | - Martin F. Kubeš
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
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7
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Sun X, Lapin D, Feehan JM, Stolze SC, Kramer K, Dongus JA, Rzemieniewski J, Blanvillain-Baufumé S, Harzen A, Bautor J, Derbyshire P, Menke FLH, Finkemeier I, Nakagami H, Jones JDG, Parker JE. Pathogen effector recognition-dependent association of NRG1 with EDS1 and SAG101 in TNL receptor immunity. Nat Commun 2021; 12:3335. [PMID: 34099661 PMCID: PMC8185089 DOI: 10.1038/s41467-021-23614-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/30/2021] [Indexed: 02/05/2023] Open
Abstract
Plants utilise intracellular nucleotide-binding, leucine-rich repeat (NLR) immune receptors to detect pathogen effectors and activate local and systemic defence. NRG1 and ADR1 "helper" NLRs (RNLs) cooperate with enhanced disease susceptibility 1 (EDS1), senescence-associated gene 101 (SAG101) and phytoalexin-deficient 4 (PAD4) lipase-like proteins to mediate signalling from TIR domain NLR receptors (TNLs). The mechanism of RNL/EDS1 family protein cooperation is not understood. Here, we present genetic and molecular evidence for exclusive EDS1/SAG101/NRG1 and EDS1/PAD4/ADR1 co-functions in TNL immunity. Using immunoprecipitation and mass spectrometry, we show effector recognition-dependent interaction of NRG1 with EDS1 and SAG101, but not PAD4. An EDS1-SAG101 complex interacts with NRG1, and EDS1-PAD4 with ADR1, in an immune-activated state. NRG1 requires an intact nucleotide-binding P-loop motif, and EDS1 a functional EP domain and its partner SAG101, for induced association and immunity. Thus, two distinct modules (NRG1/EDS1/SAG101 and ADR1/EDS1/PAD4) mediate TNL receptor defence signalling.
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Affiliation(s)
- Xinhua Sun
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Joanna M Feehan
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Sara C Stolze
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Katharina Kramer
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Joram A Dongus
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jakub Rzemieniewski
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Servane Blanvillain-Baufumé
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anne Harzen
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Iris Finkemeier
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biology and Biotechnology of Plants, University of Muenster, Muenster, Germany
| | - Hirofumi Nakagami
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
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8
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Sun X, Lapin D, Feehan JM, Stolze SC, Kramer K, Dongus JA, Rzemieniewski J, Blanvillain-Baufumé S, Harzen A, Bautor J, Derbyshire P, Menke FLH, Finkemeier I, Nakagami H, Jones JDG, Parker JE. Pathogen effector recognition-dependent association of NRG1 with EDS1 and SAG101 in TNL receptor immunity. Nat Commun 2021; 12:3335. [PMID: 34099661 DOI: 10.1101/2020.12.21.423810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/30/2021] [Indexed: 05/21/2023] Open
Abstract
Plants utilise intracellular nucleotide-binding, leucine-rich repeat (NLR) immune receptors to detect pathogen effectors and activate local and systemic defence. NRG1 and ADR1 "helper" NLRs (RNLs) cooperate with enhanced disease susceptibility 1 (EDS1), senescence-associated gene 101 (SAG101) and phytoalexin-deficient 4 (PAD4) lipase-like proteins to mediate signalling from TIR domain NLR receptors (TNLs). The mechanism of RNL/EDS1 family protein cooperation is not understood. Here, we present genetic and molecular evidence for exclusive EDS1/SAG101/NRG1 and EDS1/PAD4/ADR1 co-functions in TNL immunity. Using immunoprecipitation and mass spectrometry, we show effector recognition-dependent interaction of NRG1 with EDS1 and SAG101, but not PAD4. An EDS1-SAG101 complex interacts with NRG1, and EDS1-PAD4 with ADR1, in an immune-activated state. NRG1 requires an intact nucleotide-binding P-loop motif, and EDS1 a functional EP domain and its partner SAG101, for induced association and immunity. Thus, two distinct modules (NRG1/EDS1/SAG101 and ADR1/EDS1/PAD4) mediate TNL receptor defence signalling.
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Affiliation(s)
- Xinhua Sun
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Joanna M Feehan
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Sara C Stolze
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Katharina Kramer
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Joram A Dongus
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jakub Rzemieniewski
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Servane Blanvillain-Baufumé
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anne Harzen
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Iris Finkemeier
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biology and Biotechnology of Plants, University of Muenster, Muenster, Germany
| | - Hirofumi Nakagami
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
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9
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Lopez FB, Fort A, Tadini L, Probst AV, McHale M, Friel J, Ryder P, Pontvianne F, Pesaresi P, Sulpice R, McKeown P, Brychkova G, Spillane C. Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number. THE PLANT CELL 2021; 33:1135-1150. [PMID: 33793816 PMCID: PMC8225240 DOI: 10.1093/plcell/koab020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/24/2020] [Indexed: 05/08/2023]
Abstract
The 45S rRNA genes (rDNA) are among the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as 'back-up' copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis thaliana female gametophyte, we reduced 45S rDNA copy number (CN) to a plateau of ∼10%. Two independent lines had rDNA CNs reduced by up to 90% at the T7 generation, named low copy number (LCN) lines. Despite drastic reduction of rDNA copies, rRNA transcriptional rates, and steady-state levels remained the same as wild-type plants. Gene dosage compensation of rRNA transcript levels was associated with reduction of silencing histone marks at rDNA loci and altered Nucleolar Organiser Region 2 organization. Although overall genome integrity of LCN lines appears unaffected, a chromosome segmental duplication occurred in one of the lines. Transcriptome analysis of LCN seedlings identified several shared dysregulated genes and pathways in both independent lines. Cas9 genome editing of rRNA repeats to generate LCN lines provides a powerful technique to elucidate rDNA dosage compensation mechanisms and impacts of low rDNA CN on genome stability, development, and cellular processes.
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Affiliation(s)
- Francesca B Lopez
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Luca Tadini
- Dipartimento di Bioscienze, Universit� degli Studi di Milano, 20133 Milano, Italy
| | - Aline V Probst
- CNRS, GReD, Universit� Clermont Auvergne, INSERM, 63001 Clermont–Ferrand, France
| | - Marcus McHale
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - James Friel
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Fr�d�ric Pontvianne
- CNRS, Laboratoire G�nome et D�veloppement des Plantes (LGDP), Universit� de Perpignan Via Domitia, Perpignan, France
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Universit� degli Studi di Milano, 20133 Milano, Italy
| | - Ronan Sulpice
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Peter McKeown
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Author for correspondence:
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10
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Fang J, Guo T, Xie Z, Chun Y, Zhao J, Peng L, Zafar SA, Yuan S, Xiao L, Li X. The URL1-ROC5-TPL2 transcriptional repressor complex represses the ACL1 gene to modulate leaf rolling in rice. PLANT PHYSIOLOGY 2021; 185:1722-1744. [PMID: 33793928 PMCID: PMC8133684 DOI: 10.1093/plphys/kiaa121] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/13/2020] [Indexed: 05/31/2023]
Abstract
Moderate leaf rolling is beneficial for leaf erectness and compact plant architecture. However, our understanding regarding the molecular mechanisms of leaf rolling is still limited. Here, we characterized a semi-dominant rice (Oryza sativa L.) mutant upward rolled leaf 1 (Url1) showing adaxially rolled leaves due to a decrease in the number and size of bulliform cells. Map-based cloning revealed that URL1 encodes the homeodomain-leucine zipper (HD-Zip) IV family member RICE OUTERMOST CELL-SPECIFIC 8 (ROC8). A single-base substitution in one of the two conserved complementary motifs unique to the 3'-untranslated region of this family enhanced URL1 mRNA stability and abundance in the Url1 mutant. URL1 (UPWARD ROLLED LEAF1) contains an ethylene-responsive element binding factor-associated amphiphilic repression motif and functions as a transcriptional repressor via interaction with the TOPLESS co-repressor OsTPL2. Rather than homodimerizing, URL1 heterodimerizes with another HD-ZIP IV member ROC5. URL1 could bind directly to the promoter and suppress the expression of abaxially curled leaf 1 (ACL1), a positive regulator of bulliform cell development. Knockout of OsTPL2 or ROC5 or overexpression of ACL1 in the Url1 mutant partially suppressed the leaf-rolling phenotype. Our results reveal a regulatory network whereby a transcriptional repression complex composed of URL1, ROC5, and the transcriptional corepressor TPL2 suppresses the expression of the ACL1 gene, thus modulating bulliform cell development and leaf rolling in rice.
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Affiliation(s)
- Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tingting Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Zhiwei Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Chun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lixiang Peng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Syed Adeel Zafar
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shoujiang Yuan
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Zhu YF, Guo J, Zhang Y, Huang CF. The THO/TREX Complex Component RAE2/TEX1 Is Involved in the Regulation of Aluminum Resistance and Low Phosphate Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:698443. [PMID: 34322147 PMCID: PMC8311497 DOI: 10.3389/fpls.2021.698443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/18/2021] [Indexed: 05/15/2023]
Abstract
The C2H2-type zinc finger transcription factor SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) plays a critical role in aluminum (Al) resistance and low phosphate (Pi) response mainly through promoting the expression of the malate transporter-encoding gene ARABIDOPSIS THALIANA ALUMINUM ACTIVATED MALATE TRANSPORTER 1 (AtALMT1). We previously showed that REGULATION OF ATALMT1 EXPRESSION 3 (RAE3/HPR1), a core component of the THO/TREX complex, is involved in the regulation of nucleocytoplasmic STOP1 mRNA export to modulate Al resistance and low Pi response. Here, we report that RAE2/TEX1, another core component of the THO complex, is also involved in the regulation of Al resistance and low Pi response. Mutation of RAE2 reduced the expression of STOP1-downstream genes, including AtALMT1. rae2 was less sensitive to Al than rae3, which was consistent with less amount of malate secreted from rae3 roots than from rae2 roots. Nevertheless, low Pi response was impaired more in rae2 than in rae3, suggesting that RAE2 also regulates AtALMT1-independent pathway to modulate low Pi response. Furthermore, unlike RAE3 that regulates STOP1 mRNA export, mutating RAE2 did not affect STOP1 mRNA accumulation in the nucleus, although STOP1 protein level was reduced in rae2. Introduction of rae1 mutation into rae2 mutant background could partially recover the deficient phenotypes of rae2. Together, our results demonstrate that RAE2 and RAE3 play overlapping but distinct roles in the modulation of Al resistance and low Pi response.
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Affiliation(s)
- Yi-Fang Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinliang Guo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yang Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chao-Feng Huang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Chao-Feng Huang,
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12
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Guo J, Zhang Y, Gao H, Li S, Wang ZY, Huang CF. Mutation of HPR1 encoding a component of the THO/TREX complex reduces STOP1 accumulation and aluminium resistance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2020; 228:179-193. [PMID: 32406528 DOI: 10.1111/nph.16658] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 04/30/2020] [Indexed: 05/28/2023]
Abstract
C2H2-type zinc finger transcription factor sensitive to proton rhizotoxicity 1 (STOP1) plays an essential role in aluminium (Al) resistance in Arabidopsis thaliana by controlling the expression of a set of Al-resistance genes, including the malate transporter-encoding gene A. thaliana aluminium activated malate transporter 1 (AtALMT1) that is critically required for Al resistance. STOP1 is suggested to be modulated by Al at post-transcriptional and/or post-translational levels. However, the underlying molecular mechanisms remain to be demonstrated. We carried out a forward genetic screen on an ethyl methanesulphonate mutagenized population, which contains the AtALMT1 promoter-driven luciferase reporter gene (pAtALMT1:LUC), and identified hyperrecombination protein 1 (HPR1), which encodes a subunit of the THO/TREX complex. We investigate the effect of hpr1 mutations on the expression of Al-resistance genes and Al resistance, and we also examined the regulatory role of HPR1 in nuclear messenger RNA (mRNA) and protein accumulation of STOP1 gene. Mutation of HPR1 reduces the expression of STOP1-regulated genes and the associated Al resistance. The hpr1 mutations increase STOP1 mRNA retention in the nucleus and consequently decrease STOP1 protein abundance. Mutation of regulation of AtALMT1 expression 1 (RAE1) that mediates STOP1 degradation in the hpr1 mutant background can partially rescue the deficient phenotypes of hpr1 mutants. Our results demonstrate that HPR1 modulates Al resistance partly through the regulation of nucleocytoplasmic STOP1 mRNA export.
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Affiliation(s)
- Jinliang Guo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yang Zhang
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Huiling Gao
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shengben Li
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhen-Yu Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Chao-Feng Huang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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13
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An Z, Yin L, Liu Y, Peng M, Shen WH, Dong A. The histone methylation readers MRG1/MRG2 and the histone chaperones NRP1/NRP2 associate in fine-tuning Arabidopsis flowering time. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1010-1024. [PMID: 32324922 DOI: 10.1111/tpj.14780] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Histones are highly basic proteins involved in packaging DNA into chromatin, and histone modifications are fundamental in epigenetic regulation in eukaryotes. Among the numerous chromatin modifiers identified in Arabidopsis (Arabidopsis thaliana), MORF-RELATED GENE (MRG)1 and MRG2 have redundant functions in reading histone H3 lysine 36 trimethylation (H3K36me3). Here, we show that MRG2 binds histone chaperones belonging to the NUCLEOSOME ASSEMBLY PROTEIN 1 (NAP1) family, including NAP1-RELATED PROTEIN (NRP)1 and NRP2. Characterization of the loss-of-function mutants mrg1 mrg2, nrp1 nrp2 and mrg1 mrg2 nrp1 nrp2 revealed that MRG1/MRG2 and NRP1/NRP2 regulate flowering time through fine-tuning transcription of floral genes by distinct molecular mechanisms. In particular, the physical interaction between NRP1/NRP2 and MRG1/MRG2 inhibited the binding of MRG1/MRG2 to the transcription factor CONSTANS (CO), leading to a transcriptional repression of FLOWERING LOCUS T (FT) through impeded H4K5 acetylation (H4K5ac) within the FT chromatin. By contrast, NRP1/NRP2 and MRG1/MRG2 act together, likely in a multiprotein complex manner, in promoting the transcription of FLOWERING LOCUS C (FLC) via an increase of both H4K5ac and H3K9ac in the FLC chromatin. Because the expression pattern of FLC represents the major category of differentially expressed genes identified by genome-wide RNA-sequencing analysis in the mrg1 mrg2, nrp1 nrp2 and mrg1 mrg2 nrp1 nrp2 mutants, it is reasonable to speculate that the NRP1/NRP2-MRG1/MRG2 complex may be involved in transcriptional activation of genes beyond FLC and flowering time control.
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Affiliation(s)
- Zengxuan An
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Liufan Yin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuhao Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Maolin Peng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Universitè de Strasbourg, CNRS, IBMP UPR 2357, Strasbourg, F-67000, France
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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14
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Zhu J, Liu M, Liu X, Dong Z. RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis. NATURE PLANTS 2018; 4:1112-1123. [PMID: 30374093 DOI: 10.1038/s41477-018-0280-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 09/14/2018] [Indexed: 05/25/2023]
Abstract
RNA polymerase II (Pol II) plays an essential role in gene expression. We used plant native elongating transcript sequencing and global run-on sequencing to profile nascent RNAs genome wide in Arabidopsis. We found that Pol II tends to accumulate downstream of the transcription start site (TSS). Moreover, Pol II with an unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream of the TSS, while Pol II with a Ser 5P CTD associates with spliceosomes, and Pol II with a Ser 2P CTD presents a sharp peak within 250 base pairs downstream of the polyadenylation site (PAS). Pol II pausing both at promoter-proximal regions and after PAS affects the transcription rate. Interestingly, active genes can be classified into three clusters based on the different modes of transcription. We demonstrate that these two methods are suitable to study Pol II dynamics in planta. Although transcription is conserved overall within eukaryotes, there is plant-specific regulation.
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Affiliation(s)
- Jiafu Zhu
- Plant Gene Engineering Centre, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Liu
- Plant Gene Engineering Centre, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xiaobin Liu
- Plant Gene Engineering Centre, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhicheng Dong
- Plant Gene Engineering Centre, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
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15
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The Receptor-like Cytoplasmic Kinase BIK1 Localizes to the Nucleus and Regulates Defense Hormone Expression during Plant Innate Immunity. Cell Host Microbe 2018; 23:485-497.e5. [PMID: 29649442 DOI: 10.1016/j.chom.2018.03.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 02/13/2018] [Accepted: 03/16/2018] [Indexed: 01/20/2023]
Abstract
Plants employ cell-surface pattern recognition receptors (PRRs) to detect pathogens. Although phytohormones produced during PRR signaling play an essential role in innate immunity, a direct link between PRR activation and hormone regulation is unknown. EFR is a PRR that recognizes bacterial EF-Tu and activates immune signaling. Here we report that EFR regulates the phytohormone jasmonic acid (JA) through direct phosphorylation of a receptor-like cytoplasmic kinase, BIK1. The BIK1 structure revealed that the EFR-phosphorylated sites reside on a uniquely extended loop away from the BIK1 kinase core domain. Phosphomimetic mutations of these sites resulted in increased phytohormones and enhanced resistance to bacterial infections. In addition to its documented plasma membrane localization, BIK1 also localizes to the nucleus and interacts directly with WRKY transcription factors involved in the JA and salicylic acid (SA) regulation. These findings demonstrate the mechanistic basis of signal transduction from PRR to phytohormones, mediated through a PRR-BIK1-WRKY axis.
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16
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Park J, Lim CJ, Shen M, Park HJ, Cha JY, Iniesto E, Rubio V, Mengiste T, Zhu JK, Bressan RA, Lee SY, Lee BH, Jin JB, Pardo JM, Kim WY, Yun DJ. Epigenetic switch from repressive to permissive chromatin in response to cold stress. Proc Natl Acad Sci U S A 2018; 115:E5400-E5409. [PMID: 29784800 PMCID: PMC6003311 DOI: 10.1073/pnas.1721241115] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Switching from repressed to active status in chromatin regulation is part of the critical responses that plants deploy to survive in an ever-changing environment. We previously reported that HOS15, a WD40-repeat protein, is involved in histone deacetylation and cold tolerance in Arabidopsis However, it remained unknown how HOS15 regulates cold responsive genes to affect cold tolerance. Here, we show that HOS15 interacts with histone deacetylase 2C (HD2C) and both proteins together associate with the promoters of cold-responsive COR genes, COR15A and COR47 Cold induced HD2C degradation is mediated by the CULLIN4 (CUL4)-based E3 ubiquitin ligase complex in which HOS15 acts as a substrate receptor. Interference with the association of HD2C and the COR gene promoters by HOS15 correlates with increased acetylation levels of histone H3. HOS15 also interacts with CBF transcription factors to modulate cold-induced binding to the COR gene promoters. Our results here demonstrate that cold induces HOS15-mediated chromatin modifications by degrading HD2C. This switches the chromatin structure status and facilitates recruitment of CBFs to the COR gene promoters. This is an apparent requirement to acquire cold tolerance.
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Affiliation(s)
- Junghoon Park
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Chae Jin Lim
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Mingzhe Shen
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Hee Jin Park
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea
- Institute of Glocal Disease Control, Konkuk University, 05029 Seoul, Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Elisa Iniesto
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Vicente Rubio
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907
| | - Ray A Bressan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, 04107 Seoul, South Korea
| | - Jing Bo Jin
- Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Jose M Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas, 41092 Seville, Spain
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea;
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17
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Shekariesfahlan A, Lindermayr C. Detection of S-Nitrosated Nuclear Proteins in Pathogen-Treated Arabidopsis Cell Cultures Using Biotin Switch Technique. Methods Mol Biol 2018; 1747:205-221. [PMID: 29600461 DOI: 10.1007/978-1-4939-7695-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule involved in various plant physiological processes. The main effect of NO arises from its reaction with proteins. S-Nitrosation is the most studied NO-mediated protein posttranslational modification in plants. Via S-nitrosation, NO derivatives react with thiol groups (SHs) of protein cysteine residues and produce nitrosothiol groups (SNOs). From the time of discovering the biological function of NO in plants, an interesting case of study has been the detection of the endogenous S-nitrosated proteins in different plants, tissues, organelles, and various conditions. Maps of S-nitrosated proteins provide hints for deeper studies on the function of this modification in specific proteins, biochemical pathways, and physiological processes. Many functions of NO have been found to be related to plant defense; on the other hand the involvement of nuclear proteins in regulation of plant defense reactions is well studied. Here, an approach is described in which the Arabidopsis cell cultures first are treated with P. syringae, afterward their bioactive nuclear proteins are extracted, then the nuclear proteins are subjected to biotin switch assay in which S-nitrosated proteins are specifically converted to S-biotinylated proteins. The biotin switch technique (BST) which was introduced by Jaffrey et al. (Nat Cell Biol 3:193-197, 2001) solves the instability issue of SNOs. Additionally, it provides detection and purification of biotinylated proteins by anti-biotin antibody and affinity chromatography, respectively.
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Affiliation(s)
- Azam Shekariesfahlan
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Christian Lindermayr
- Helmholtz Zentrum München-German Research GmbH, Center for Environment Health, Institute of Biochemical Plant Pathology, Ingolstädter Landstraße 1, 85764, Munich-Neuherberg, Germany.
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18
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Albaqami M, Reddy ASN. Development of an in vitro pre-mRNA splicing assay using plant nuclear extract. PLANT METHODS 2018; 14:1. [PMID: 29321806 PMCID: PMC5757305 DOI: 10.1186/s13007-017-0271-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/21/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Pre-mRNA splicing is an essential post-transcriptional process in all eukaryotes. In vitro splicing systems using nuclear or cytoplasmic extracts from mammalian cells, yeast, and Drosophila have provided a wealth of mechanistic insights into assembly and composition of the spliceosome, splicing regulatory proteins and mechanisms of pre-mRNA splicing in non-plant systems. The lack of an in vitro splicing system prepared from plant cells has been a major limitation in splicing research in plants. RESULTS Here we report an in vitro splicing assay system using plant nuclear extract. Several lines of evidence indicate that nuclear extract derived from Arabidopsis seedlings can convert pre-mRNA substrate (LHCB3) into a spliced product. These include: (1) generation of an RNA product that corresponds to the size of expected mRNA, (2) a junction-mapping assay using S1 nuclease revealed that the two exons are spliced together, (3) the reaction conditions are similar to those found with non-plant extracts and (4) finally mutations in conserved donor and acceptor sites abolished the production of the spliced product. CONCLUSIONS This first report on the plant in vitro splicing assay opens new avenues to investigate plant spliceosome assembly and composition, and splicing regulatory mechanisms specific to plants.
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Affiliation(s)
- Mohammed Albaqami
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1878 USA
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1878 USA
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19
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Vazač J, Füssy Z, Hladová I, Killi S, Oborník M. Ploidy and Number of Chromosomes in the Alveolate Alga Chromera velia. Protist 2017; 169:53-63. [PMID: 29367153 DOI: 10.1016/j.protis.2017.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/06/2017] [Accepted: 12/09/2017] [Indexed: 11/16/2022]
Abstract
Chromera velia is an alveolate alga which represents the closest known phototrophic relative to apicomplexan parasites. Although the nuclear, mitochondrial, and plastid genomes of this alga have been sequenced, the number of chromosomes and ploidy of C. velia are unknown. We explored ploidy in the vegetative cell, the predominant stage in cultures of Chromera, using the tyramide signal amplification-fluorescence in situ hybridization (TSA-FISH) in isolated nuclei of C. velia. Probes were derived from three single copy genes coding for 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) kinase, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP) synthase and Topoisomerase II. Our results indicate that the vegetative cell of C. velia is haploid, as each probe produced a single fluorescent signal, although the possibility of diploidy with somatic pairing of homologous chromosomes cannot be completely excluded. Restriction analysis and hybridization with the telomere probe produced eight bands suggesting the presence of four chromosomes in haploid vegetative cells of C. velia. However, when the chromerid-specific telomere probe (TTTAGGG)4 was used for TSA-FISH, we consistently obtained a double signal. This may indicate that the four chromosomes are organized in clusters in interphase nuclei of C. velia, which is a chromosome organization similar to that of their apicomplexan relatives.
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Affiliation(s)
- Jan Vazač
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Zoltán Füssy
- Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Irena Hladová
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Sireesha Killi
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Miroslav Oborník
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic; Institute of Microbiology, Czech Academy of Sciences, Algatech, Novohradská 237, Opatovický mlýn, 37901 Třeboň, Czech Republic.
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20
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Cortijo S, Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA. Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. MOLECULAR PLANT 2017; 10:1258-1273. [PMID: 28893714 PMCID: PMC6175055 DOI: 10.1016/j.molp.2017.08.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/21/2017] [Accepted: 08/24/2017] [Indexed: 05/18/2023]
Abstract
Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade of Arabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.
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Affiliation(s)
- Sandra Cortijo
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Varodom Charoensawan
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi District, Bangkok 10400, Thailand; Integrative Computational BioScience (ICBS) Center, Mahidol University, 999 Phuttamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
| | - Anna Brestovitsky
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Ruth Buning
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Charles Ravarani
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniela Rhodes
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Structural Biology, Nanyang Technical University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Katja E Jaeger
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Philip A Wigge
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
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21
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In Situ Hi-C Library Preparation for Plants to Study Their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale. Methods Mol Biol 2017. [PMID: 28623585 DOI: 10.1007/978-1-4939-7125-1_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The spatial organization of the genome in the nucleus is critical for many cellular processes. It has been broadly accepted that the packing of chromatin inside the nucleus is not random, but structured at several hierarchical levels. The Hi-C method combines Chromatin Conformation Capture and high-throughput sequencing, which allows interrogating genome-wide chromatin interactions. Depending on the sequencing depth, chromatin packing patterns derived from Hi-C experiments can be viewed on a chromosomal scale or at a local genic level. Here, I describe a protocol of plant in situ Hi-C library preparation, which covers procedures starting from tissue fixation to library amplification.
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22
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Sánchez-Lamas M, Lorenzo CD, Cerdán PD. Bottom-up Assembly of the Phytochrome Network. PLoS Genet 2016; 12:e1006413. [PMID: 27820825 PMCID: PMC5098793 DOI: 10.1371/journal.pgen.1006413] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
Plants have developed sophisticated systems to monitor and rapidly acclimate to environmental fluctuations. Light is an essential source of environmental information throughout the plant's life cycle. The model plant Arabidopsis thaliana possesses five phytochromes (phyA-phyE) with important roles in germination, seedling establishment, shade avoidance, and flowering. However, our understanding of the phytochrome signaling network is incomplete, and little is known about the individual roles of phytochromes and how they function cooperatively to mediate light responses. Here, we used a bottom-up approach to study the phytochrome network. We added each of the five phytochromes to a phytochrome-less background to study their individual roles and then added the phytochromes by pairs to study their interactions. By analyzing the 16 resulting genotypes, we revealed unique roles for each phytochrome and identified novel phytochrome interactions that regulate germination and the onset of flowering. Furthermore, we found that ambient temperature has both phytochrome-dependent and -independent effects, suggesting that multiple pathways integrate temperature and light signaling. Surprisingly, none of the phytochromes alone conferred a photoperiodic response. Although phyE and phyB were the strongest repressors of flowering, both phyB and phyC were needed to confer a flowering response to photoperiod. Thus, a specific combination of phytochromes is required to detect changes in photoperiod, whereas single phytochromes are sufficient to respond to light quality, indicating how phytochromes signal different light cues.
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Affiliation(s)
| | | | - Pablo D. Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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23
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Yin X, Komatsu S. Plant nuclear proteomics for unraveling physiological function. N Biotechnol 2016; 33:644-654. [PMID: 27004615 DOI: 10.1016/j.nbt.2016.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
The nucleus is the subcellular organelle that functions as the regulatory hub of the cell and is responsible for regulating several critical cellular functions, including cell proliferation, gene expression, and cell survival. Nuclear proteomics is a useful approach for investigating the mechanisms underlying plant responses to abiotic stresses, including protein-protein interactions, enzyme activities, and post-translational modifications. Among abiotic stresses, flooding is a major limiting factor for plant growth and yields, particularly for soybean. In this review, plant nuclei purification methods, modifications of plant nuclear proteins, and recent contributions to the field of plant nuclear proteomics are summarized. In addition, to reveal the upstream regulating mechanisms controlling soybean responses to flooding stress, the functions of flooding-responsive nuclear proteins are reviewed based on the results of nuclear proteomic analysis of soybean in the early stages of flooding stress.
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Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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24
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Sun X, Qi W, Yue Y, Ling H, Wang G, Song R. Maize ZmVPP5 is a truncated Vacuole H(+) -PPase that confers hypersensitivity to salt stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:518-528. [PMID: 26728417 PMCID: PMC5071666 DOI: 10.1111/jipb.12462] [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: 11/12/2015] [Accepted: 12/31/2015] [Indexed: 05/30/2023]
Abstract
In plants, Vacuole H(+) -PPases (VPPs) are important proton pumps and encoded by multiple genes. In addition to full-length VPPs, several truncated forms are expressed, but their biological functions are unknown. In this study, we functionally characterized maize vacuole H(+) -PPase 5 (ZmVPP5), a truncated VPP in the maize genome. Although ZmVPP5 shares high sequence similarity with ZmVPP1, ZmVPP5 lacks the complete structure of the conserved proton transport and the inorganic pyrophosphatase-related domain. Phylogenetic analysis suggests that ZmVPP5 might be derived from an incomplete gene duplication event. ZmVPP5 is expressed in multiple tissues, and ZmVPP5 was detected in the plasma membrane, vacuole membrane and nuclei of maize cells. The overexpression of ZmVPP5 in yeast cells caused a hypersensitivity to salt stress. Transgenic maize lines with overexpressed ZmVPP5 also exhibited the salt hypersensitivity phenotype. A yeast two-hybrid analysis identified the ZmBag6-like protein as a putative ZmVPP5-interacting protein. The results of bimolecular luminescence complementation (BiLC) assay suggest an interaction between ZmBag6-like protein and ZmVPP5 in vivo. Overall, this study suggests that ZmVPP5 might act as a VPP antagonist and participate in the cellular response to salt stress. Our study of ZmVPP5 has expanded the understanding of the origin and functions of truncated forms of plant VPPs.
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Affiliation(s)
- Xiaoliang Sun
- Shanghai key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Weiwei Qi
- Shanghai key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
- Coordinated Crop Biology Research Center(CBRC), Beijing 100193, China
| | - Yihong Yue
- Shanghai key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Huiling Ling
- Shanghai key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Gang Wang
- Shanghai key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
- Coordinated Crop Biology Research Center(CBRC), Beijing 100193, China
| | - Rentao Song
- Shanghai key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
- Coordinated Crop Biology Research Center(CBRC), Beijing 100193, China
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25
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Stuttmann J, Peine N, Garcia AV, Wagner C, Choudhury SR, Wang Y, James GV, Griebel T, Alcázar R, Tsuda K, Schneeberger K, Parker JE. Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity. PLoS Genet 2016; 12:e1005990. [PMID: 27082651 PMCID: PMC4833295 DOI: 10.1371/journal.pgen.1005990] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 03/24/2016] [Indexed: 11/18/2022] Open
Abstract
Plants have a large panel of nucleotide-binding/leucine rich repeat (NLR) immune receptors which monitor host interference by diverse pathogen molecules (effectors) and trigger disease resistance pathways. NLR receptor systems are necessarily under tight control to mitigate the trade-off between induced defenses and growth. Hence, mis-regulated NLRs often cause autoimmunity associated with stunting and, in severe cases, necrosis. Nucleocytoplasmic ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) is indispensable for effector-triggered and autoimmune responses governed by a family of Toll-Interleukin1-Receptor-related NLR receptors (TNLs). EDS1 operates coincidently or immediately downstream of TNL activation to transcriptionally reprogram cells for defense. We show here that low levels of nuclear-enforced EDS1 are sufficient for pathogen resistance in Arabidopsis thaliana, without causing negative effects. Plants expressing higher nuclear EDS1 amounts have the genetic, phenotypic and transcriptional hallmarks of TNL autoimmunity. In a screen for genetic suppressors of nuclear EDS1 autoimmunity, we map multiple, independent mutations to one gene, DM2h, lying within the polymorphic DANGEROUS MIX2 cluster of TNL RPP1-like genes from A. thaliana accession Landsberg erecta (Ler). The DM2 locus is a known hotspot for deleterious epistatic interactions leading to immune-related incompatibilities between A. thaliana natural accessions. We find that DM2hLer underlies two further genetic incompatibilities involving the RPP1-likeLer locus and EDS1. We conclude that the DM2hLer TNL protein and nuclear EDS1 cooperate, directly or indirectly, to drive cells into an immune response at the expense of growth. A further conclusion is that regulating the available EDS1 nuclear pool is fundamental for maintaining homeostatic control of TNL immune pathways. Plants tune their cellular and developmental programs to different environmental stimuli. Central players in the plant biotic stress response network are intracellular NLR receptors which intercept specific disease-inducing molecules (effectors) produced by pathogenic microbes. Variation in NLR gene repertoires between plant genetic lines is driven by pathogen selection pressure. One evolutionary question is how new, functional NLRs are assembled within a plant genome without mis-activating defense pathways, which can have strong negative effects on growth and fitness. This study focuses on a large, polymorphic sub-class of NLR receptors called TNLs present in dicotyledenous plant lineages. TNL receptors confer immunity to a broad range of pathogens. They also frequently underlie autoimmunity caused by their mis-regulation or deleterious allelic interactions with other genes in crosses between different genetic lines (hybrid incompatibility, HI). TNL pathogen-triggered and autoimmune responses require the conserved nucleocytoplasmic protein EDS1 to transcriptionally reprogram cells for defense. We discover in Arabidopsis thaliana that high levels of nuclear-enriched EDS1 induce transcriptional activation of defenses and growth inhibition without a pathogen effector stimulus. In a mutational screen, we identify one rapidly evolving TNL gene, DM2hLer, as a driver of nuclear EDS1 autoimmunity. DM2hLer also contributes to two separate cases of EDS1-dependent autoimmunity. Genetic cooperation between DM2hLer and EDS1 suggests a functional relationship in the transcriptional feed-forward regulation of defense pathways.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
- * E-mail: (JS); (JEP)
| | - Nora Peine
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ana V. Garcia
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Christine Wagner
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Sayan R. Choudhury
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yiming Wang
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Griebel
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Alcázar
- Department of Natural Products, Plant Biology and Soil Science, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail: (JS); (JEP)
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26
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Wear EE, Concia L, Brooks AM, Markham EA, Lee TJ, Allen GC, Thompson WF, Hanley-Bowdoin L. Isolation of Plant Nuclei at Defined Cell Cycle Stages Using EdU Labeling and Flow Cytometry. Methods Mol Biol 2016; 1370:69-86. [PMID: 26659955 DOI: 10.1007/978-1-4939-3142-2_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
5-Ethynyl-2'-deoxyuridine (EdU) is a nucleoside analog of thymidine that can be rapidly incorporated into replicating DNA in vivo and, subsequently, detected by using "click" chemistry to couple its terminal alkyne group to fluorescent azides such as Alexa Fluor 488. Recently, EdU incorporation followed by coupling with a fluorophore has been used to visualize newly synthesized DNA in a wide range of plant species. One particularly useful application is in flow cytometry, where two-parameter sorting can be employed to analyze different phases of the cell cycle, as defined both by total DNA content and the amount of EdU pulse-labeled DNA. This approach allows analysis of the cell cycle without the need for synchronous cell populations, which can be difficult to obtain in many plant systems. The approach presented here, which was developed for fixed, EdU-labeled nuclei, can be used to prepare analytical profiles as well as to make highly purified preparations of G1, S, or G2/M phase nuclei for molecular or biochemical analysis. We present protocols for EdU pulse labeling, tissue fixation and harvesting, nuclei preparation, and flow sorting. Although developed for Arabidopsis suspension cells and maize root tips, these protocols should be modifiable to many other plant systems.
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Affiliation(s)
- Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Lorenzo Concia
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ashley M Brooks
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emily A Markham
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - George C Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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27
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Pham PA, Wahl V, Tohge T, de Souza LR, Zhang Y, Do PT, Olas JJ, Stitt M, Araújo WL, Fernie AR. Analysis of knockout mutants reveals non-redundant functions of poly(ADP-ribose)polymerase isoforms in Arabidopsis. PLANT MOLECULAR BIOLOGY 2015; 89:319-38. [PMID: 26428915 PMCID: PMC4631723 DOI: 10.1007/s11103-015-0363-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 08/18/2015] [Indexed: 05/19/2023]
Abstract
The enzyme poly(ADP-ribose)polymerase (PARP) has a dual function being involved both in the poly(ADP-ribosyl)ation and being a constituent of the NAD(+) salvage pathway. To date most studies, both in plant and non-plant systems, have focused on the signaling role of PARP in poly(ADP-ribosyl)ation rather than any role that can be ascribed to its metabolic function. In order to address this question we here used a combination of expression, transcript and protein localization studies of all three PARP isoforms of Arabidopsis alongside physiological analysis of the corresponding mutants. Our analyses indicated that whilst all isoforms of PARP were localized to the nucleus they are also present in non-nuclear locations with parp1 and parp3 also localised in the cytosol, and parp2 also present in the mitochondria. We next isolated and characterized insertional knockout mutants of all three isoforms confirming a complete knockout in the full length transcript levels of the target genes as well as a reduced total leaf NAD hydrolase activity in the two isoforms (PARP1, PARP2) that are highly expressed in leaves. Physiological evaluation of the mutant lines revealed that they displayed distinctive metabolic and root growth characteristics albeit unaltered leaf morphology under optimal growth conditions. We therefore conclude that the PARP isoforms play non-redundant non-nuclear metabolic roles and that their function is highly important in rapidly growing tissues such as the shoot apical meristem, roots and seeds.
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Affiliation(s)
- Phuong Anh Pham
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Vanessa Wahl
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Laise Rosado de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Phuc Thi Do
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Hanoi, Vietnam
| | - Justyna J Olas
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Mark Stitt
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Wagner L Araújo
- Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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28
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Loziuk PL, Parker J, Li W, Lin CY, Wang JP, Li Q, Sederoff RR, Chiang VL, Muddiman DC. Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa. J Proteome Res 2015; 14:4158-68. [PMID: 26325666 DOI: 10.1021/acs.jproteome.5b00233] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa.
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Affiliation(s)
- Philip L Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jennifer Parker
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Wei Li
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Vincent L Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - David C Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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Chaki M, Shekariesfahlan A, Ageeva A, Mengel A, von Toerne C, Durner J, Lindermayr C. Identification of nuclear target proteins for S-nitrosylation in pathogen-treated Arabidopsis thaliana cell cultures. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:115-26. [PMID: 26259180 DOI: 10.1016/j.plantsci.2015.06.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 05/18/2023]
Abstract
Nitric oxide (NO) is a significant signalling molecule involved in the regulation of many different physiological processes in plants. One of the most imperative regulatory modes of action of NO is protein S-nitrosylation--the covalent attachment of an NO group to the sulfur atom of cysteine residues. In this study, we focus on S-nitrosylation of Arabidopsis nuclear proteins after pathogen infection. After treatment of Arabidopsis suspension cell cultures with pathogens, nuclear proteins were extracted and treated with the S-nitrosylating agent S-nitrosoglutathione (GSNO). A biotin switch assay was performed and biotin-labelled proteins were purified by neutravidin affinity chromatography and identified by mass spectrometry. A total of 135 proteins were identified, whereas nuclear localization has been described for 122 proteins of them. 117 of these proteins contain at least one cysteine residue. Most of the S-nitrosylated candidates were involved in protein and RNA metabolism, stress response, and cell organization and division. Interestingly, two plant-specific histone deacetylases were identified suggesting that nitric oxide regulated epigenetic processes in plants. In sum, this work provides a new collection of targets for protein S-nitrosylation in Arabidopsis and gives insight into the regulatory function of NO in the nucleus during plant defense response. Moreover, our data extend the knowledge on the regulatory function of NO in events located in the nucleus.
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Affiliation(s)
- Mounira Chaki
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Azam Shekariesfahlan
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Alexandra Ageeva
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Alexander Mengel
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Christine von Toerne
- Research Unit Protein Science, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Chair of Biochemical Plant Pathology, Technische Universität München, 85354 Freising, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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Roberts TC, Hart JR, Kaikkonen MU, Weinberg MS, Vogt PK, Morris KV. Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR. Nat Protoc 2015; 10:1198-211. [PMID: 26182239 PMCID: PMC4790731 DOI: 10.1038/nprot.2015.076] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear run-on (NRO) is a method that measures transcriptional activity via the quantification of biochemically labeled nascent RNA molecules derived from nuclear isolates. Widespread use of this technique has been limited because of its technical difficulty relative to steady-state total mRNA analyses. Here we describe a detailed protocol for the quantification of transcriptional activity in human cell cultures. Nuclei are first isolated and NRO transcription is performed in the presence of bromouridine. Labeled nascent transcripts are purified by immunoprecipitation, and transcript levels are determined by reverse-transcription quantitative PCR (RT-qPCR). Data are then analyzed using standard techniques described elsewhere. This method is rapid (the protocol can be completed in 2 d) and cost-effective, exhibits negligible detection of background noise from unlabeled transcripts, requires no radioactive materials and can be performed from as few as 500,000 nuclei. It also takes advantage of the high sensitivity, specificity and dynamic range of RT-qPCR.
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Affiliation(s)
- Thomas C. Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, United Kingdom
- Sanford-Burnham Medical Research Institute, Development, Aging and Regeneration Program, 10901 N. Torrey pines Road, La Jolla, CA, 92037, USA
| | - Jonathan R. Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Minna U. Kaikkonen
- University of Eastern Finland, A.I. Virtanen institute, Department of Biotechnology and Molecular Medicine, P.O.B. 1627, 70211 Kuopio, Finland
| | - Marc S. Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, WITS 2050, South Africa
| | - Peter K. Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kevin V. Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW 2052, Australia
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Chen J, Gao J, Peng M, Wang Y, Yu Y, Yang P, Jin H. In-gel NHS-propionate derivatization for histone post-translational modifications analysis in Arabidopsis thaliana. Anal Chim Acta 2015; 886:107-13. [PMID: 26320642 DOI: 10.1016/j.aca.2015.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/26/2015] [Accepted: 06/04/2015] [Indexed: 11/16/2022]
Abstract
Post-translational modifications (PTMs) on histone are highly correlated with genetic and epigenetic regulation of gene expression from chromatin. Mass spectrometry (MS) has developed to be an optimal tool for the identification and quantification of histone PTMs. Derivatization of histones with chemicals such as propionic anhydride, N-hydroxysuccinimide ester (NHS-propionate) has been widely used in histone PTMs analysis in bottom-up MS strategy, which requires high purity for histone samples. However, biological samples are not always prepared with high purity, containing detergents or other interferences in most cases. As an alternative approach, an adaptation of in gel derivatization method, termed In-gel NHS, is utilized for a broader application in histone PTMs analysis and it is shown to be a more time-saving preparation method. The proposed method was optimized for a better derivatization efficiency and displayed high reproducibility, indicating quantification of histone PTMs based on In-gel NHS was achievable. Without any traditional fussy histone purification procedures, we succeeded to quantitatively profile the histone PTMs from Arabidopsis with selective knock down of CLF (clf-29) and the original parental (col) with In-gel NHS method in a rapid way, which indicated the high specificity of CLF on H3K27me3 in Arabidopsis. In-gel NHS quantification results also suggest distinctive histone modification patterns in plants, which is invaluable foundation for future studies on histone modifications in plants.
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Affiliation(s)
- Jiajia Chen
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Jun Gao
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China; China Novartis Institutes for BioMedical Research Co. Ltd., Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Maolin Peng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yi Wang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yanyan Yu
- China Novartis Institutes for BioMedical Research Co. Ltd., Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Pengyuan Yang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
| | - Hong Jin
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
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Kumar S, Bhatia S. Isolation of Catharanthus roseus (L.) G. Don Nuclei and Measurement of Rate of Tryptophan decarboxylase Gene Transcription Using Nuclear Run-On Transcription Assay. PLoS One 2015; 10:e0127892. [PMID: 26024519 PMCID: PMC4449189 DOI: 10.1371/journal.pone.0127892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 04/21/2015] [Indexed: 11/27/2022] Open
Abstract
Background An accurate assessment of transcription ‘rate’ is often desired to describe the promoter activity. In plants, isolation of transcriptionally active nuclei and their subsequent use in nuclear run-on assays has been challenging and therefore limit an accurate measurement of gene transcription ‘rate’. Catharanthus roseus has emerged as a model medicinal plant as it exhibits an unsurpassed spectrum of chemodiversity, producing over 130 alkaloids through the terpenoid indole alkaloid (TIA) pathway and therefore serves as a ‘molecular hub’ to understand gene expression profiles. Results The protocols presented here streamline, adapt and optimize the existing methods of nuclear run-on assay for use in C. roseus. Here, we fully describe all the steps to isolate transcriptionally active nuclei from C. roseus leaves and utilize them to perform nuclear run-on transcription assay. Nuclei isolated by this method transcribed at a level consistent with their response to external stimuli, as transcription rate of TDC gene was found to be higher in response to external stimuli i.e. when seedlings were subjected to UV-B light or to methyl jasmonate (MeJA). However, the relative transcript abundance measured parallel through qRT-PCR was found to be inconsistent with the synthesis rate indicating that some post transcriptional events might have a role in transcript stability in response to stimuli. Conclusions Our study provides an optimized, efficient and inexpensive method of isolation of intact nuclei and nuclear ‘run-on’ transcription assay to carry out in-situ measurement of gene transcription rate in Catharanthus roseus. This would be valuable in investigating the transcriptional and post transcriptional response of other TIA pathway genes in C. roseus. Isolated nuclei may also provide a resource that could be used for performing the chip assay as well as serve as the source of nuclear proteins for in-vitro EMSA studies. Moreover, nascent nuclear run-on transcript could be further subjected to RNA-Seq for global nuclear run-on assay (GNRO-Seq) for genome wide in-situ measurement of transcription rate of plant genes.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
- * E-mail:
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Henry E, Fung N, Liu J, Drakakaki G, Coaker G. Beyond glycolysis: GAPDHs are multi-functional enzymes involved in regulation of ROS, autophagy, and plant immune responses. PLoS Genet 2015; 11:e1005199. [PMID: 25918875 PMCID: PMC4412566 DOI: 10.1371/journal.pgen.1005199] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 04/08/2015] [Indexed: 11/17/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme in energy metabolism with diverse cellular regulatory roles in vertebrates, but few reports have investigated the importance of plant GAPDH isoforms outside of their role in glycolysis. While animals possess one GAPDH isoform, plants possess multiple isoforms. In this study, cell biological and genetic approaches were used to investigate the role of GAPDHs during plant immune responses. Individual Arabidopsis GAPDH knockouts (KO lines) exhibited enhanced disease resistance phenotypes upon inoculation with the bacterial plant pathogen Pseudomonas syringae pv. tomato. KO lines exhibited accelerated programmed cell death and increased electrolyte leakage in response to effector triggered immunity. Furthermore, KO lines displayed increased basal ROS accumulation as visualized using the fluorescent probe H2DCFDA. The gapa1-2 and gapc1 KOs exhibited constitutive autophagy phenotypes in the absence of nutrient starvation. Due to the high sequence conservation between vertebrate and plant cytosolic GAPDH, our experiments focused on cytosolic GAPC1 cellular dynamics using a complemented GAPC1-GFP line. Confocal imaging coupled with an endocytic membrane marker (FM4-64) and endosomal trafficking inhibitors (BFA, Wortmannin) demonstrated cytosolic GAPC1 is localized to the plasma membrane and the endomembrane system, in addition to the cytosol and nucleus. After perception of bacterial flagellin, GAPC1 dynamically responded with a significant increase in size of fluorescent puncta and enhanced nuclear accumulation. Taken together, these results indicate that plant GAPDHs can affect multiple aspects of plant immunity in diverse sub-cellular compartments.
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Affiliation(s)
- Elizabeth Henry
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Nicholas Fung
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Jun Liu
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America; Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Gitta Coaker
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
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Mergner J, Heinzlmeir S, Kuster B, Schwechheimer C. DENEDDYLASE1 deconjugates NEDD8 from non-cullin protein substrates in Arabidopsis thaliana. THE PLANT CELL 2015; 27:741-53. [PMID: 25783028 PMCID: PMC4558671 DOI: 10.1105/tpc.114.135996] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/05/2015] [Accepted: 02/26/2015] [Indexed: 05/25/2023]
Abstract
The evolutionarily conserved 8-kD protein NEDD8 (NEURAL PRECURSOR CELL EXPRESSED, DEVELOPMENTALLY DOWN-REGULATED8) belongs to the family of ubiquitin-like modifiers. Like ubiquitin, NEDD8 is conjugated to and deconjugated from target proteins. Many targets and functions of ubiquitylation have been described; by contrast, few targets of NEDD8 have been identified. In plants as well as in non-plant organisms, the cullin subunits of cullin-RING E3 ligases are NEDD8 conjugates with a demonstrated functional role for the NEDD8 modification. The existence of other non-cullin NEDD8 targets has generally been questioned. NEDD8 is translated as a precursor protein and proteolytic processing exposes a C-terminal glycine required for NEDD8 conjugation. In animals and yeast, DENEDDYLASE1 (DEN1) processes NEDD8. Here, we show that mutants of a DEN1 homolog from Arabidopsis thaliana have no detectable defects in NEDD8 processing but do accumulate a broad range of NEDD8 conjugates; this provides direct evidence for the existence of non-cullin NEDD8 conjugates. We further identify AUXIN RESISTANT1 (AXR1), a subunit of the heterodimeric NEDD8 E1 activating enzyme, as a NEDD8-modified protein in den1 mutants and wild type and provide evidence that AXR1 function may be compromised in the absence of DEN1 activity. Thus, in plants, neddylation may serve as a regulatory mechanism for cullin and non-cullin proteins.
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Affiliation(s)
- Julia Mergner
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Stephanie Heinzlmeir
- Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
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HYPER RECOMBINATION1 of the THO/TREX complex plays a role in controlling transcription of the REVERSION-TO-ETHYLENE SENSITIVITY1 gene in Arabidopsis. PLoS Genet 2015; 11:e1004956. [PMID: 25680185 PMCID: PMC4334170 DOI: 10.1371/journal.pgen.1004956] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 12/15/2014] [Indexed: 11/19/2022] Open
Abstract
Arabidopsis REVERSION-TO-ETHYLENE SENSITIVITY1 (RTE1) represses ethylene hormone responses by promoting ethylene receptor ETHYLENE RESPONSE1 (ETR1) signaling, which negatively regulates ethylene responses. To investigate the regulation of RTE1, we performed a genetic screening for mutations that suppress ethylene insensitivity conferred by RTE1 overexpression in Arabidopsis. We isolated HYPER RECOMBINATION1 (HPR1), which is required for RTE1 overexpressor (RTE1ox) ethylene insensitivity at the seedling but not adult stage. HPR1 is a component of the THO complex, which, with other proteins, forms the TRanscription EXport (TREX) complex. In yeast, Drosophila, and humans, the THO/TREX complex is involved in transcription elongation and nucleocytoplasmic RNA export, but its role in plants is to be fully determined. We investigated how HPR1 is involved in RTE1ox ethylene insensitivity in Arabidopsis. The hpr1-5 mutation may affect nucleocytoplasmic mRNA export, as revealed by in vivo hybridization of fluorescein-labeled oligo(dT)45 with unidentified mRNA in the nucleus. The hpr1-5 mutation reduced the total and nuclear RTE1 transcript levels to a similar extent, and RTE1 transcript reduction rate was not affected by hpr1-5 with cordycepin treatment, which prematurely terminates transcription. The defect in the THO-interacting TEX1 protein of TREX but not the mRNA export factor SAC3B also reduced the total and nuclear RTE1 levels. SERINE-ARGININE-RICH (SR) proteins are involved mRNA splicing, and we found that SR protein SR33 co-localized with HPR1 in nuclear speckles, which agreed with the association of human TREX with the splicing machinery. We reveal a role for HPR1 in RTE1 expression during transcription elongation and less likely during export. Gene expression involved in ethylene signaling suppression was not reduced by the hpr1-5 mutation, which indicates selectivity of HPR1 for RTE1 expression affecting the consequent ethylene response. Thus, components of the THO/TREX complex appear to have specific roles in the transcription or export of selected genes.
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Filichkin SA, Cumbie JS, Dharmawardhana P, Jaiswal P, Chang JH, Palusa SG, Reddy ASN, Megraw M, Mockler TC. Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis. MOLECULAR PLANT 2015; 8:207-27. [PMID: 25680774 DOI: 10.1016/j.molp.2014.10.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 10/10/2014] [Accepted: 10/20/2014] [Indexed: 05/21/2023]
Abstract
Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Thermal stress induced a time delay in accumulation of CCA1 I4Rb transcripts, whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out-of-phase oscillations of CCA1 IR transcripts. Taken together, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this splicing factor could be involved in regulation of intron retention. Transcriptomes of nonsense-mediated mRNA decay (NMD)-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.
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Affiliation(s)
- Sergei A Filichkin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
| | - Jason S Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Palitha Dharmawardhana
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Saiprasad G Palusa
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - A S N Reddy
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Molly Megraw
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Todd C Mockler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA.
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Sarkar S, Jain S, Rai V, Sahoo DK, Raha S, Suklabaidya S, Senapati S, Rangnekar VM, Maiti IB, Dey N. Plant-derived SAC domain of PAR-4 (Prostate Apoptosis Response 4) exhibits growth inhibitory effects in prostate cancer cells. FRONTIERS IN PLANT SCIENCE 2015; 6:822. [PMID: 26500666 PMCID: PMC4595782 DOI: 10.3389/fpls.2015.00822] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/22/2015] [Indexed: 05/10/2023]
Abstract
The gene Par-4 (Prostate Apoptosis Response 4) was originally identified in prostate cancer cells undergoing apoptosis and its product Par-4 showed cancer specific pro-apoptotic activity. Particularly, the SAC domain of Par-4 (SAC-Par-4) selectively kills cancer cells leaving normal cells unaffected. The therapeutic significance of bioactive SAC-Par-4 is enormous in cancer biology; however, its large scale production is still a matter of concern. Here we report the production of SAC-Par-4-GFP fusion protein coupled to translational enhancer sequence (5' AMV) and apoplast signal peptide (aTP) in transgenic Nicotiana tabacum cv. Samsun NN plants under the control of a unique recombinant promoter M24. Transgene integration was confirmed by genomic DNA PCR, Southern and Northern blotting, Real-time PCR, and Nuclear run-on assays. Results of Western blot analysis and ELISA confirmed expression of recombinant SAC-Par-4-GFP protein and it was as high as 0.15% of total soluble protein. In addition, we found that targeting of plant recombinant SAC-Par-4-GFP to the apoplast and endoplasmic reticulum (ER) was essential for the stability of plant recombinant protein in comparison to the bacterial derived SAC-Par-4. Deglycosylation analysis demonstrated that ER-targeted SAC-Par-4-GFP-SEKDEL undergoes O-linked glycosylation unlike apoplast-targeted SAC-Par-4-GFP. Furthermore, various in vitro studies like mammalian cells proliferation assay (MTT), apoptosis induction assays, and NF-κB suppression suggested the cytotoxic and apoptotic properties of plant-derived SAC-Par-4-GFP against multiple prostate cancer cell lines. Additionally, pre-treatment of MAT-LyLu prostate cancer cells with purified SAC-Par-4-GFP significantly delayed the onset of tumor in a syngeneic rat prostate cancer model. Taken altogether, we proclaim that plant made SAC-Par-4 may become a useful alternate therapy for effectively alleviating cancer in the new era.
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Affiliation(s)
- Shayan Sarkar
- Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Sumeet Jain
- Department of Translational Research and Technology Development, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
- Manipal UniversityManipal, India
| | - Vineeta Rai
- Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Dipak K. Sahoo
- Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, LexingtonKY, USA
- Department of Agronomy, Iowa State University, AmesIA, USA
| | - Sumita Raha
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, ChicagoIL, USA
| | - Sujit Suklabaidya
- Department of Translational Research and Technology Development, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Shantibhusan Senapati
- Department of Translational Research and Technology Development, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Vivek M. Rangnekar
- Department of Radiation Medicine, Markey Cancer Center, University of Kentucky, LexingtonKY, USA
| | - Indu B. Maiti
- Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, LexingtonKY, USA
- *Correspondence: Nrisingha Dey, Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of India, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha-751 023, India, ; Indu B. Maiti, Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA,
| | - Nrisingha Dey
- Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
- *Correspondence: Nrisingha Dey, Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of India, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha-751 023, India, ; Indu B. Maiti, Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA,
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Estavillo GM, Verhertbruggen Y, Scheller HV, Pogson BJ, Heazlewood JL, Ito J. Isolation of the plant cytosolic fraction for proteomic analysis. Methods Mol Biol 2014; 1072:453-67. [PMID: 24136540 DOI: 10.1007/978-1-62703-631-3_31] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The cytosol is the fluid portion of the cell that is not partitioned by membranes. It contains a highly diverse collection of substances and is central to many essential cellular processes ranging from signal transduction, metabolite production and transport, protein biosynthesis and degradation to stress response and defense. Despite its importance, only a few proteomic studies have been performed on the plant cytosol. This is largely due to difficulties in isolating relatively pure samples from plant material free of disrupted organelle material. In this chapter we outline methods for isolating the cytosolic fraction from Arabidopsis cell cultures and seedlings and provide guidance on assessing purity for analysis by mass spectrometry.
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Affiliation(s)
- Gonzalo M Estavillo
- ARC Centre of Excellence in Plant Energy Biology and Research School of Biology, The Australian National University, Canberra, Australia
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Arabidopsis CRY2 and ZTL mediate blue-light regulation of the transcription factor CIB1 by distinct mechanisms. Proc Natl Acad Sci U S A 2013; 110:17582-7. [PMID: 24101505 DOI: 10.1073/pnas.1308987110] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plants possess multiple photoreceptors to mediate light regulation of growth and development, but it is not well understood how different photoreceptors coordinate their actions to jointly regulate developmental responses, such as flowering time. In Arabidopsis, the photoexcited cryptochrome 2 interacts with the transcription factor CRYPTOCHROME-INTERACTING basic helix-loop-helix 1 (CIB1) to activate transcription and floral initiation. We show that the CIB1 protein expression is regulated by blue light; CIB1 is highly expressed in plants exposed to blue light, but levels of the CIB1 protein decreases in the absence of blue light. We demonstrate that CIB1 is degraded by the 26S proteasome and that blue light suppresses CIB1 degradation. Surprisingly, although cryptochrome 2 physically interacts with CIB1 in response to blue light, it is not the photoreceptor mediating blue-light suppression of CIB1 degradation. Instead, two of the three light-oxygen-voltage (LOV)-domain photoreceptors, ZEITLUPE and LOV KELCH PROTEIN 2, but not FLAVIN-BINDING KELCH REPEAT 1, are required for the function and blue-light suppression of degradation of CIB1. These results support the hypothesis that the evolutionarily unrelated blue-light receptors, cryptochrome and LOV-domain F-box proteins, mediate blue-light regulation of the same transcription factor by distinct mechanisms.
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Sikorskaite S, Rajamäki ML, Baniulis D, Stanys V, Valkonen JPT. Protocol: Optimised methodology for isolation of nuclei from leaves of species in the Solanaceae and Rosaceae families. PLANT METHODS 2013; 9:31. [PMID: 23886449 PMCID: PMC3728069 DOI: 10.1186/1746-4811-9-31] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/24/2013] [Indexed: 05/22/2023]
Abstract
In this study, a protocol is described for rapid preparation of an enriched, reasonably pure fraction of nuclear proteins from the leaves of tobacco (Nicotiana tabacum), potato (Solanum tuberosum) and apple (Malus domestica). The protocol gives reproducible results and can be carried out quickly in 2 hours. Tissue extracts clarified with filtration were treated with non-ionic detergent (Triton X-100) to lyse membranes of contaminating organelles. Nuclei were collected from a 60% Percoll layer of density gradient following low-speed centrifugation. Western blot analysis using antibodies to marker proteins of organelles indicated that the nuclear protein fractions were highly enriched and free or nearly free of proteins from the endoplasmic reticulum and chloroplasts.
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Affiliation(s)
- Sidona Sikorskaite
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas st 30, Babtai, LT-54333, Kaunas, Lithuania
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Minna-Liisa Rajamäki
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Danas Baniulis
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas st 30, Babtai, LT-54333, Kaunas, Lithuania
| | - Vidmantas Stanys
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas st 30, Babtai, LT-54333, Kaunas, Lithuania
| | - Jari PT Valkonen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
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41
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Chen L, Dempsey BR, Gyenis L, Menassa R, Brandle JE, Dhaubhadel S. Identification of the factors that control synthesis and accumulation of a therapeutic protein, human immune-regulatory interleukin-10, in Arabidopsis thaliana. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:546-554. [PMID: 23301867 DOI: 10.1111/pbi.12042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/01/2012] [Accepted: 11/27/2012] [Indexed: 06/01/2023]
Abstract
Plants are one of the most economical platforms for large-scale production of recombinant proteins for biopharmaceutical and industrial uses. A large number of human recombinant proteins of therapeutic value have been successfully produced in plant systems. One of the main technical challenges of producing recombinant proteins in plants is to obtain sufficient level of protein. This research aims to identify the factors that control synthesis and accumulation of recombinant proteins in stable transgenic plants. A stepwise dissection of human immune-regulatory interleukin-10 (IL-10) protein production was carried out using Arabidopsis thaliana as a model system. EMS-mutagenized transgenic Arabidopsis IL-10 lines, at2762 and at3262, produced significantly higher amount of IL-10 protein than the non-mutagenized IL-10 line (WT-IL-10). The fates of trans-gene in these sets of plants were compared in detail by measuring synthesis and accumulation of IL-10 transcript, transcript stability, protein synthesis and IL-10 protein accumulation. The IL-10 transcripts were more stable in at2762 and at3262 lines than WT-IL-10, which may contribute to higher protein synthesis in these lines. To evaluate whether translational regulation of IL-10 controls its synthesis in non-mutagenized WT-IL-10 and higher IL-10 accumulating mutant lines, we measured the efficiency of the translational machinery. Our results indicate that mutant lines with higher trans-gene expression contain more robust and efficient translational machinery compared with the control line.
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Affiliation(s)
- Ling Chen
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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42
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Sun Q, Csorba T, Skourti-Stathaki K, Proudfoot NJ, Dean C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 2013; 340:619-21. [PMID: 23641115 PMCID: PMC5144995 DOI: 10.1126/science.1234848] [Citation(s) in RCA: 271] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Roles for long noncoding RNAs (lncRNAs) in gene expression are emerging, but regulation of the lncRNA itself is poorly understood. We have identified a homeodomain protein, AtNDX, that regulates COOLAIR, a set of antisense transcripts originating from the 3' end of Arabidopsis FLOWERING LOCUS C (FLC). AtNDX associates with single-stranded DNA rather than double-stranded DNA non-sequence-specifically in vitro, and localizes to a heterochromatic region in the COOLAIR promoter in vivo. Single-stranded DNA was detected in vivo as part of an RNA-DNA hybrid, or R-loop, that covers the COOLAIR promoter. R-loop stabilization mediated by AtNDX inhibits COOLAIR transcription, which in turn modifies FLC expression. Differential stabilization of R-loops could be a general mechanism influencing gene expression in many organisms.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Chromatin/metabolism
- DNA, Plant/chemistry
- DNA, Plant/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/metabolism
- Gene Expression Regulation, Plant
- Homeodomain Proteins/chemistry
- Homeodomain Proteins/metabolism
- MADS Domain Proteins/genetics
- MADS Domain Proteins/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Promoter Regions, Genetic
- Protein Binding
- RNA, Antisense/chemistry
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Transcription Termination, Genetic
- Transcription, Genetic
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Affiliation(s)
- Qianwen Sun
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Tibor Csorba
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | | | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Lee KH, Minami A, Marshall RS, Book AJ, Farmer LM, Walker JM, Vierstra RD. The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis. THE PLANT CELL 2011; 23:4298-317. [PMID: 22158466 PMCID: PMC3269867 DOI: 10.1105/tpc.111.089482] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The regulatory particle (RP) of the 26S proteasome contains a heterohexameric ring of AAA-ATPases (RPT1-6) that unfolds and inserts substrates into the core protease (CP) for degradation. Through genetic analysis of the Arabidopsis thaliana gene pair encoding RPT2, we show that this subunit plays a critical role in 26S proteasome assembly, histone dynamics, and plant development. rpt2a rpt2b double null mutants are blocked in both male and female gamete transmission, demonstrating that the subunit is essential. Whereas rpt2b mutants are phenotypically normal, rpt2a mutants display a range of defects, including impaired leaf, root, trichome, and pollen development, delayed flowering, stem fasciation, hypersensitivity to mitomycin C and amino acid analogs, hyposensitivity to the proteasome inhibitor MG132, and decreased 26S complex stability. The rpt2a phenotype can be rescued by both RPT2a and RPT2b, indicative of functional redundancy, but not by RPT2a mutants altered in ATP binding/hydrolysis or missing the C-terminal hydrophobic sequence that docks the RPT ring onto the CP. Many rpt2a phenotypes are shared with mutants lacking the chromatin assembly factor complex CAF1. Like caf1 mutants, plants missing RPT2a or reduced in other RP subunits contain less histones, thus implicating RPT2 specifically, and the 26S proteasome generally, in plant nucleosome assembly.
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Mukhopadhyay P, Reddy MK, Singla-Pareek SL, Sopory SK. Transcriptional downregulation of rice rpL32 gene under abiotic stress is associated with removal of transcription factors within the promoter region. PLoS One 2011; 6:e28058. [PMID: 22132208 PMCID: PMC3223225 DOI: 10.1371/journal.pone.0028058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Accepted: 10/31/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The regulation of ribosomal proteins in plants under stress conditions has not been well studied. Although a few reports have shown stress-specific post-transcriptional and translational mechanisms involved in downregulation of ribosomal proteins yet stress-responsive transcriptional regulation of ribosomal proteins is largely unknown in plants. METHODOLOGY/PRINCIPAL FINDINGS In the present work, transcriptional regulation of genes encoding rice 60S ribosomal protein L32 (rpL32) in response to salt stress has been studied. Northern and RT-PCR analyses showed a significant downregulation of rpL32 transcripts under abiotic stress conditions in rice. Of the four rpL32 genes in rice genome, the gene on chromosome 8 (rpL32_8.1) showed a higher degree of stress-responsive downregulation in salt sensitive rice variety than in tolerant one and its expression reverted to its original level upon withdrawal of stress. The nuclear run-on and promoter:reporter assays revealed that the downregulation of this gene is transcriptional and originates within the promoter region. Using in vivo footprinting and electrophoretic mobility shift assay (EMSA), cis-elements in the promoter of rpL32_8.1 showing reduced binding to proteins in shoots of salt stressed rice seedlings were identified. CONCLUSIONS The present work is one of the few reports on study of stress downregulated genes. The data revealed that rpL32 gene is transcriptionally downregulated under abiotic stress in rice and that this transcriptional downregulation is associated with the removal of transcription factors from specific promoter elements.
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Affiliation(s)
- Pradipto Mukhopadhyay
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
| | - Malireddy K. Reddy
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
| | - Sudhir K. Sopory
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
- * E-mail:
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Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TM, Lin D, Joshi NA, Martinez-Garcia PJ, Crisosto CH. Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics 2011; 12:569. [PMID: 22108025 PMCID: PMC3253712 DOI: 10.1186/1471-2164-12-569] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 11/22/2011] [Indexed: 11/24/2022] Open
Abstract
Background The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft 'Lovell' peach sequence as well as sufficient depth of coverage for 'in silico' SNP discovery. Description The sequences were aligned to the 'Lovell' peach genome released April 01, 2010 by the International Peach Genome Initiative (IPGI). 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle' were sequenced to add SNPs segregating in two breeding populations, Pop DF ('Dr. Davis' × 'F8, 1-42') and Pop DG ('Dr. Davis' × 'Georgia Belle'). Roche 454 sequencing produced 980,000 total reads with 236 Mb sequence for 'Dr. Davis' and 735,000 total reads with 172 Mb sequence for 'F8, 1-42'. 84 bp × 84 bp paired end Illumina/Solexa sequences yielded 25.5, 21.4, 25.5 million sequences for 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle', respectively. BWA/SAMtools were used for alignment of raw reads and SNP detection, with custom PERL scripts for SNP filtering. Velvet's Columbus module was used for sequence assembly. Comparison of aligned and overlapping sequences from both Roche 454 and Illumina/Solexa resulted in the selection of 6654 high quality SNPs for 'Dr. Davis' vs. 'F8, 1-42' and 'Georgia Belle', distributed on eight major peach genome scaffolds as defined from the 'Lovell' assembly. Conclusion The eight scaffolds contained about 215-225 Mb of peach genomic sequences with one SNP/~ 40,000 bases. All sequences from Roche 454 and Illumina/Solexa have been submitted to NCBI for public use in the Short Read Archive database. SNPs have been deposited in the NCBI SNP database.
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Affiliation(s)
- Riaz Ahmad
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
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Abstract
RNA interference (RNAi) is a mechanism regulating gene transcript levels either by transcriptional gene silencing or by posttranscriptional gene silencing, which act in the genome maintenance and the regulation of gene expression which is typically inferred from measuring transcript abundance. Nuclear "run-on" (or "run-off") transcription assays have been used to obtain quantitative information about the relative rates of transcription of different genes in nuclei isolated from a particular tissue or organ. Basically, these assays exploit the activity of RNA polymerases to synthesize radiolabeled transcripts that then can be hybridized to filter-bound, cold, excess single-stranded DNA probes representing genes of interest. The protocol presented here streamlines, adapts, and optimizes nuclear run-on transcription assays for use in RNAi studies.
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Affiliation(s)
- Basel Khraiwesh
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent University, Ghent, Belgium.
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Zhou Y, Zhang J, Lin H, Guo G, Guo Y. MORPHEUS' MOLECULE1 is required to prevent aberrant RNA transcriptional read-through in Arabidopsis. PLANT PHYSIOLOGY 2010; 154:1272-80. [PMID: 20826701 PMCID: PMC2971605 DOI: 10.1104/pp.110.162131] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 08/31/2010] [Indexed: 05/24/2023]
Abstract
Several pathways function to remove aberrant mRNA in eukaryotic cells; however, the exact mechanisms underlying the restriction of aberrant mRNA transcription are poorly understood. In this study, we found that MORPHEUS' MOLECULE1 (MOM1) is a key component of this regulatory machinery. The Arabidopsis (Arabidopsis thaliana) mom1-44 mutation was identified by luciferase imaging in transgenic plants harboring a cauliflower mosaic virus 35S promoter-LUCIFERASE transgene lacking the 3'-untranslated region. In the mom1-44 mutant, transcriptional read-though occurred in genes with an aberrant RNA structure. Analysis of an RNA-dependent RNA polymerase2 mom1 double mutant revealed that the RNA-directed DNA methylation pathway is not involved in this regulatory process. Moreover, the prevention of aberrant mRNA transcriptional read-through by MOM1 is gene locus and transgene copy number independent.
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Affiliation(s)
| | | | | | | | - Yan Guo
- Corresponding author; e-mail
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48
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Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, Frank W. Transcriptional control of gene expression by microRNAs. Cell 2010; 140:111-22. [PMID: 20085706 DOI: 10.1016/j.cell.2009.12.023] [Citation(s) in RCA: 311] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 07/30/2009] [Accepted: 11/28/2009] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) control gene expression in animals and plants. Like another class of small RNAs, siRNAs, they affect gene expression posttranscriptionally. While siRNAs in addition act in transcriptional gene silencing, a role of miRNAs in transcriptional regulation has been less clear. We show here that in moss Physcomitrella patens mutants without a DICER-LIKE1b gene, maturation of miRNAs is normal but cleavage of target RNAs is abolished and levels of these transcripts are drastically reduced. These mutants accumulate miRNA:target-RNA duplexes and show hypermethylation of the genes encoding target RNAs, leading to gene silencing. This pathway occurs also in the wild-type upon hormone treatment. We propose that initiation of epigenetic silencing by DNA methylation depends on the ratio of the miRNA and its target RNA.
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Affiliation(s)
- Basel Khraiwesh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
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Guo L, Zhou J, Elling AA, Charron JBF, Deng XW. Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions. PLANT PHYSIOLOGY 2008; 147:2070-83. [PMID: 18550682 PMCID: PMC2492627 DOI: 10.1104/pp.108.122929] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 06/03/2008] [Indexed: 05/19/2023]
Abstract
Here, we analyzed the effects of light regulation on four selected histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) and the relationship of these histone modifications with the expression of representative light-regulated genes. We observed that the histone modifications examined and gene transcription were cooperatively regulated in response to changing light environments. Using H3K9ac as an example, our analysis indicated that histone modification patterns are set up very early and are relatively stable during Arabidopsis (Arabidopsis thaliana) seedling development. Distinct photoreceptor systems are responsible for mediating the effects of different light qualities on histone modifications. Moreover, we found that light regulation of gene-specific histone modifications involved the known photomorphogenesis-related proteolytic system defined by the pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETOLIATED proteins and histone modification enzymes (such as HD1). Furthermore, our data suggest that light-regulated changes in histone modifications might be an intricate part of light-controlled gene transcription. Thus, it is possible that variations in histone modifications are an important physiological component of plant responses to changing light environments.
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Affiliation(s)
- Lan Guo
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
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Chawla R, Nicholson SJ, Folta KM, Srivastava V. Transgene-induced silencing of Arabidopsis phytochrome A gene via exonic methylation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:1105-1118. [PMID: 17931351 DOI: 10.1111/j.1365-313x.2007.03301.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Transgene-induced promoter or enhancer methylation clearly retards gene activity. While exonic methylation of genes is frequently observed in the RNAi process, only sporadic evidence has demonstrated its definitive role in gene suppression. Here, we report the isolation of a transcriptionally suppressed epi-allele of the Arabidopsis thaliana phytochrome A gene (PHYA) termed phyA' that shows methylation only in symmetric CG sites resident in exonic regions. These exonic modifications confer a strong phyA mutant phenotype, characterized by elongated hypocotyls in seedlings grown under continuous far-red light. De-methylation of phyA' in the DNA methyl transferase I (met1) mutant background increased PHYA expression and restored the wild-type phenotype, confirming the pivotal role of exonic CG methylation in maintaining the altered epigenetic state. PHYA epimutation was apparently induced by a transgene locus; however, it is stably maintained following segregation. Chromatin immunoprecipitation assays revealed association with dimethyl histone H3 lysine 9 (H3K9me2), a heterochromatic marker, within the phyA' coding region. Therefore, transgene-induced exonic methylation can lead to chromatin alteration that affects gene expression, most likely through reduction in the transcription rate.
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Affiliation(s)
- Rekha Chawla
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
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