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Takahashi N, Suita K, Koike T, Ogita N, Zhang Y, Umeda M. DNA double-strand breaks enhance brassinosteroid signaling to activate quiescent center cell division in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1364-1375. [PMID: 37882240 DOI: 10.1093/jxb/erad424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
In Arabidopsis roots, the quiescent center (QC), a group of slowly dividing cells located at the center of the stem cell niche, functions as an organizing center to maintain the stemness of neighboring cells. Recent studies have shown that they also act as a reservoir for backup cells, which replenish DNA-damaged stem cells by activating cell division. The latter function is essential for maintaining stem cells under stressful conditions, thereby guaranteeing post-embryonic root development in fluctuating environments. In this study, we show that one of the brassinosteroid receptors in Arabidopsis, BRASSINOSTEROID INSENSITIVE1-LIKE3 (BRL3), plays a major role in activating QC division in response to DNA double-strand breaks. SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor governing DNA damage response, directly induces BRL3. DNA damage-induced QC division was completely suppressed in brl3 mutants, whereas QC-specific overexpression of BRL3 activated QC division. Our data also showed that BRL3 is required to induce the AP2-type transcription factor ETHYLENE RESPONSE FACTOR 115, which triggers regenerative cell division. We propose that BRL3-dependent brassinosteroid signaling plays a unique role in activating QC division and replenishing dead stem cells, thereby enabling roots to restart growing after recovery from genotoxic stress.
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Affiliation(s)
| | - Kazuki Suita
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Toshiya Koike
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Nobuo Ogita
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Ye Zhang
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
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2
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Barcenilla BB, Meyers AD, Castillo-González C, Young P, Min JH, Song J, Phadke C, Land E, Canaday E, Perera IY, Bailey SM, Aquilano R, Wyatt SE, Shippen DE. Arabidopsis telomerase takes off by uncoupling enzyme activity from telomere length maintenance in space. Nat Commun 2023; 14:7854. [PMID: 38030615 PMCID: PMC10686995 DOI: 10.1038/s41467-023-41510-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/07/2023] [Indexed: 12/01/2023] Open
Abstract
Spaceflight-induced changes in astronaut telomeres have garnered significant attention in recent years. While plants represent an essential component of future long-duration space travel, the impacts of spaceflight on plant telomeres and telomerase have not been examined. Here we report on the telomere dynamics of Arabidopsis thaliana grown aboard the International Space Station. We observe no changes in telomere length in space-flown Arabidopsis seedlings, despite a dramatic increase in telomerase activity (up to 150-fold in roots), as well as elevated genome oxidation. Ground-based follow up studies provide further evidence that telomerase is induced by different environmental stressors, but its activity is uncoupled from telomere length. Supporting this conclusion, genetically engineered super-telomerase lines with enhanced telomerase activity maintain wildtype telomere length. Finally, genome oxidation is inversely correlated with telomerase activity levels. We propose a redox protective capacity for Arabidopsis telomerase that may promote survivability in harsh environments.
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Affiliation(s)
- Borja Barbero Barcenilla
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Alexander D Meyers
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
- NASA Postdoctoral Program, Oak Ridge Associated Universities, Kennedy Space Center FL, Merritt Island, FL, 32899, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Pierce Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Ji-Hee Min
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Chinmay Phadke
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Eric Land
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emma Canaday
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
| | - Imara Y Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Roberto Aquilano
- National Technological University, Rosario Regional Faculty, Zeballos 1341, S2000, Rosario, Argentina
| | - Sarah E Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA.
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA.
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA.
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3
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Zhang J, Peng Z, Liu Q, Yang G, Zhou L, Li W, Wang H, Chen Z, Guo T. Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice ( Oryza sativa L.). Genes (Basel) 2021; 12:genes12091391. [PMID: 34573373 PMCID: PMC8469171 DOI: 10.3390/genes12091391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Heavy-ion irradiation is a powerful mutagen and is widely used for mutation breeding. In this study, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques, we comprehensively characterized these dynamic changes caused by mutations at three time points (48, 96, and 144 h after irradiation) and the expression profiles of rice seeds irradiated with C ions at two doses. Subsequent WGS analysis revealed that more mutations were detected in response to 40 Gy carbon ion beam (CIB) irradiation than 80 Gy of CIB irradiation at the initial stage (48 h post-irradiation). In the mutants generated from both irradiation doses, single-base substitutions (SBSs) were the most frequent type of mutation induced by CIB irradiation. Among the mutations, the predominant ones were C:T and A:G transitions. CIB irradiation also induced many short InDel mutations. RNA-seq analysis at the three time points showed that the number of differentially expressed genes (DEGs) was highest at 48 h post-irradiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs showed that the "replication and repair" pathway was enriched specifically 48 h post-irradiation. These results indicate that the DNA damage response (DDR) and the mechanism of DNA repair tend to quickly start within the initial stage (48 h) after irradiation.
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Affiliation(s)
- Jian Zhang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Ziai Peng
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Qiling Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Libin Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; (L.Z.); (W.L.)
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; (L.Z.); (W.L.)
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
- Correspondence: ; Tel./Fax: +86-20-3860-4903
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4
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Manian V, Orozco-Sandoval J, Diaz-Martinez V. Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight. Genes (Basel) 2021; 12:938. [PMID: 34205326 PMCID: PMC8234954 DOI: 10.3390/genes12060938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
Ionizing radiation present in extraterrestrial environment is an important factor that affects plants grown in spaceflight. Pearson correlation-based gene regulatory network inferencing from transcriptional responses of the plant Arabidopsis thaliana L. grown in real and simulated spaceflight conditions acquired by GeneLab, followed by topological and spectral analysis of the networks is performed. Gene regulatory subnetworks are extracted for DNA damage response processes. Analysis of radiation-induced ATR/ATM protein-protein interactions in Arabidopsis reveals interaction profile similarities under low radiation doses suggesting novel mechanisms of DNA damage response involving non-radiation-induced genes regulating other stress responses in spaceflight. The Jaccard similarity index shows that the genes AT2G31320, AT4G21070, AT2G46610, and AT3G27060 perform similar functions under low doses of radiation. The incremental association Markov blanket method reveals non-radiation-induced genes linking DNA damage response to root growth and plant development. Eighteen radiation-induced genes and sixteen non-radiation-induced gene players have been identified from the ATR/ATM protein interaction complexes involved in heat, salt, water, osmotic stress responses, and plant organogenesis. Network analysis and logistic regression ranking detected AT3G27060, AT1G07500, AT5G66140, and AT3G21280 as key gene players involved in DNA repair processes. High atomic weight, high energy, and gamma photon radiation result in higher intensity of DNA damage response in the plant resulting in elevated values for several network measures such as spectral gap and girth. Nineteen flavonoid and carotenoid pigment activations involved in pigment biosynthesis processes are identified in low radiation dose total light spaceflight environment but are not found to have significant regulations under very high radiation dose environment.
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Affiliation(s)
- Vidya Manian
- Department of Electrical & Computer Engineering, University of Puerto Rico, Mayaguez, PR 00681-9000, USA; (J.O.-S.); (V.D.-M.)
- Bioengineering, University of Puerto Rico, Mayaguez, PR 00681-9000, USA
| | - Jairo Orozco-Sandoval
- Department of Electrical & Computer Engineering, University of Puerto Rico, Mayaguez, PR 00681-9000, USA; (J.O.-S.); (V.D.-M.)
| | - Victor Diaz-Martinez
- Department of Electrical & Computer Engineering, University of Puerto Rico, Mayaguez, PR 00681-9000, USA; (J.O.-S.); (V.D.-M.)
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5
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Network Analysis of Local Gene Regulators in Arabidopsis thaliana under Spaceflight Stress. COMPUTERS 2021. [DOI: 10.3390/computers10020018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Spaceflight microgravity affects normal plant growth in several ways. The transcriptional dataset of the plant model organism Arabidopsis thaliana grown in the international space station is mined using graph-theoretic network analysis approaches to identify significant gene transcriptions in microgravity essential for the plant’s survival and growth in altered environments. The photosynthesis process is critical for the survival of the plants in spaceflight under different environmentally stressful conditions such as lower levels of gravity, lesser oxygen availability, low atmospheric pressure, and the presence of cosmic radiation. Lasso regression method is used for gene regulatory network inferencing from gene expressions of four different ecotypes of Arabidopsis in spaceflight microgravity related to the photosynthetic process. The individual behavior of hub-genes and stress response genes in the photosynthetic process and their impact on the whole network is analyzed. Logistic regression on centrality measures computed from the networks, including average shortest path, betweenness centrality, closeness centrality, and eccentricity, and the HITS algorithm is used to rank genes and identify interactor or target genes from the networks. Through the hub and authority gene interactions, several biological processes associated with photosynthesis and carbon fixation genes are identified. The altered conditions in spaceflight have made all the ecotypes of Arabidopsis sensitive to dehydration-and-salt stress. The oxidative and heat-shock stress-response genes regulate the photosynthesis genes that are involved in the oxidation-reduction process in spaceflight microgravity, enabling the plant to adapt successfully to the spaceflight environment.
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6
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Barker R, Lombardino J, Rasmussen K, Gilroy S. Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. FRONTIERS IN PLANT SCIENCE 2020; 11:147. [PMID: 32265943 PMCID: PMC7076552 DOI: 10.3389/fpls.2020.00147] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/30/2020] [Indexed: 05/04/2023]
Abstract
Recent advances in the routine access to space along with increasing opportunities to perform plant growth experiments on board the International Space Station have led to an ever-increasing body of transcriptomic, proteomic, and epigenomic data from plants experiencing spaceflight. These datasets hold great promise to help understand how plant biology reacts to this unique environment. However, analyses that mine across such expanses of data are often complex to implement, being impeded by the sheer number of potential comparisons that are possible. Complexities in how the output of these multiple parallel analyses can be presented to the researcher in an accessible and intuitive form provides further barriers to such research. Recent developments in computational systems biology have led to rapid advances in interactive data visualization environments designed to perform just such tasks. However, to date none of these tools have been tailored to the analysis of the broad-ranging plant biology spaceflight data. We have therefore developed the Test Of Arabidopsis Space Transcriptome (TOAST) database (https://astrobiology.botany.wisc.edu/astrobotany-toast) to address this gap in our capabilities. TOAST is a relational database that uses the Qlik database management software to link plant biology, spaceflight-related omics datasets, and their associated metadata. This environment helps visualize relationships across multiple levels of experiments in an easy to use gene-centric platform. TOAST draws on data from The US National Aeronautics and Space Administration's (NASA's) GeneLab and other data repositories and also connects results to a suite of web-based analytical tools to facilitate further investigation of responses to spaceflight and related stresses. The TOAST graphical user interface allows for quick comparisons between plant spaceflight experiments using real-time, gene-specific queries, or by using functional gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, or other filtering systems to explore genetic networks of interest. Testing of the database shows that TOAST confirms patterns of gene expression already highlighted in the literature, such as revealing the modulation of oxidative stress-related responses across multiple plant spaceflight experiments. However, this data exploration environment can also drive new insights into patterns of spaceflight responsive gene expression. For example, TOAST analyses highlight changes to mitochondrial function as likely shared responses in many plant spaceflight experiments.
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Affiliation(s)
- Richard Barker
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Jonathan Lombardino
- Department of Botany, University of Wisconsin, Madison, WI, United States
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, United States
| | - Kai Rasmussen
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI, United States
- *Correspondence: Simon Gilroy,
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7
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SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:E12453-E12462. [PMID: 30541889 PMCID: PMC6310815 DOI: 10.1073/pnas.1810582115] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To combat DNA damage, organisms mount a DNA damage response (DDR) that results in cell cycle regulation, DNA repair and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all of the aforementioned processes rely on SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a NAC family transcription factor (TF) that has been functionally equated to the mammalian tumor suppressor, p53. However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data correspond to single time-point snapshots. Here, we generated transcriptional models of the DDR from GAMMA (γ)-irradiated wild-type and sog1 seedlings during a 24-hour time course using DREM, the Dynamic Regulatory Events Miner, revealing 11 coexpressed gene groups with distinct biological functions and cis-regulatory features. Within these networks, additional chromatin immunoprecipitation and transcriptomic experiments revealed that SOG1 is the major activator, directly targeting the most strongly up-regulated genes, including TFs, repair factors, and early cell cycle regulators, while three MYB3R TFs are the major repressors, specifically targeting the most strongly down-regulated genes, which mainly correspond to G2/M cell cycle-regulated genes. Together these models reveal the temporal dynamics of the transcriptional events triggered by γ-irradiation and connects these events to TFs and biological processes over a time scale commensurate with key processes coordinated in response to DNA damage, greatly expanding our understanding of the DDR.
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8
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Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators. PLoS Genet 2018; 14:e1007797. [PMID: 30500810 PMCID: PMC6268010 DOI: 10.1371/journal.pgen.1007797] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/30/2018] [Indexed: 01/06/2023] Open
Abstract
Retinoblastoma (pRb) is a multifunctional regulator, which was likely present in the last common ancestor of all eukaryotes. The Arabidopsis pRb homolog RETINOBLASTOMA RELATED 1 (RBR1), similar to its animal counterparts, controls not only cell proliferation but is also implicated in developmental decisions, stress responses and maintenance of genome integrity. Although most functions of pRb-type proteins involve chromatin association, a genome-wide understanding of RBR1 binding sites in Arabidopsis is still missing. Here, we present a plant chromatin immunoprecipitation protocol optimized for genome-wide studies of indirectly DNA-bound proteins like RBR1. Our analysis revealed binding of Arabidopsis RBR1 to approximately 1000 genes and roughly 500 transposable elements, preferentially MITES. The RBR1-decorated genes broadly overlap with previously identified targets of two major transcription factors controlling the cell cycle, i.e. E2F and MYB3R3 and represent a robust inventory of RBR1-targets in dividing cells. Consistently, enriched motifs in the RBR1-marked domains include sequences related to the E2F consensus site and the MSA-core element bound by MYB3R transcription factors. Following up a key role of RBR1 in DNA damage response, we performed a meta-analysis combining the information about the RBR1-binding sites with genome-wide expression studies under DNA stress. As a result, we present the identification and mutant characterization of three novel genes required for growth upon genotoxic stress. The Retinoblastoma (pRb) tumor suppressor is a master regulator of the cell cycle and its inactivation is associated with many types of cancer. Since pRb’s first description as a transcriptional repressor of genes important for cell cycle progression, many more functions have been elucidated, e.g. in developmental decisions and genome integrity. Homologs of human pRb have been identified in most eukaryotes, including plants, indicating an ancient evolutionary origin of pRb-type proteins. We describe here the first genome-wide DNA-binding study for a plant pRb protein, i.e. RBR1, the only pRb homolog in Arabidopsis thaliana. We see prominent binding of RBR1 to the 5’ region of genes involved in cell cycle regulation, chromatin organization and DNA repair. Moreover, we also reveal extensive binding of RBR1 to specific classes of DNA transposons. Since RBR1 is involved in a plethora of processes, our dataset provides a valuable resource for researches from different fields. As an example, we used our dataset to successfully identify new genes necessary for growth upon DNA damage exerted by drugs such as cisplatin or the environmentally prevalent metal aluminum.
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9
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Ray S, Gebre S, Fogle H, Berrios DC, Tran PB, Galazka JM, Costes SV. GeneLab: Omics database for spaceflight experiments. Bioinformatics 2018; 35:1753-1759. [DOI: 10.1093/bioinformatics/bty884] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Shayoni Ray
- Space Biosciences Division, USRA/NASA Ames Research Center, Moffett Field, CA, USA
| | - Samrawit Gebre
- Space Biosciences Division, KBRwyle/NASA Ames Research Center, Moffett Field, CA, USA
| | - Homer Fogle
- Space Biosciences Division, KBRwyle/NASA Ames Research Center, Moffett Field, CA, USA
| | - Daniel C Berrios
- Space Biosciences Division, USRA/NASA Ames Research Center, Moffett Field, CA, USA
| | - Peter B Tran
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
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10
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Beheshti A, Miller J, Kidane Y, Berrios D, Gebre SG, Costes SV. NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies. Radiat Res 2018; 189:553-559. [DOI: 10.1667/rr15062.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Afshin Beheshti
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Jack Miller
- Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Yared Kidane
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Daniel Berrios
- USRA, NASA Ames Research Center, Moffett Field, Calfornia 94035
| | - Samrawit G. Gebre
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Sylvain V. Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, California 94035
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11
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Ogita N, Okushima Y, Tokizawa M, Yamamoto YY, Tanaka M, Seki M, Makita Y, Matsui M, Okamoto-Yoshiyama K, Sakamoto T, Kurata T, Hiruma K, Saijo Y, Takahashi N, Umeda M. Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:439-453. [PMID: 29430765 DOI: 10.1111/tpj.13866] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 05/17/2023]
Abstract
In mammalian cells, the transcription factor p53 plays a crucial role in transmitting DNA damage signals to maintain genome integrity. However, in plants, orthologous genes for p53 and checkpoint proteins are absent. Instead, the plant-specific transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) controls most of the genes induced by gamma irradiation and promotes DNA repair, cell cycle arrest, and stem cell death. To date, the genes directly controlled by SOG1 remain largely unknown, limiting the understanding of DNA damage signaling in plants. Here, we conducted a microarray analysis and chromatin immunoprecipitation (ChIP)-sequencing, and identified 146 Arabidopsis genes as direct targets of SOG1. By using ChIP-sequencing data, we extracted the palindromic motif [CTT(N)7 AAG] as a consensus SOG1-binding sequence, which mediates target gene induction in response to DNA damage. Furthermore, DNA damage-triggered phosphorylation of SOG1 is required for efficient binding to the SOG1-binding sequence. Comparison between SOG1 and p53 target genes showed that both transcription factors control genes responsible for cell cycle regulation, such as CDK inhibitors, and DNA repair, whereas SOG1 preferentially targets genes involved in homologous recombination. We also found that defense-related genes were enriched in the SOG1 target genes. Consistent with this finding, SOG1 is required for resistance against the hemi-biotrophic fungus Colletotrichum higginsianum, suggesting that SOG1 has a unique function in controlling the immune response.
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Affiliation(s)
- Nobuo Ogita
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yoko Okushima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Mutsutomo Tokizawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Gifu, 501-1193, Japan
| | - Yoshiharu Y Yamamoto
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, 501-1193, Japan
| | - Maho Tanaka
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- JST, CREST, Kawaguchi, Saitama, 332-0012, Japan
| | - Yuko Makita
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Minami Matsui
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kaoru Okamoto-Yoshiyama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Tomoaki Sakamoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Tetsuya Kurata
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Kei Hiruma
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yusuke Saijo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Naoki Takahashi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- JST, CREST, Ikoma, Nara, 630-0192, Japan
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Johnson RA, Conklin PA, Tjahjadi M, Missirian V, Toal T, Brady SM, Britt AB. SUPPRESSOR OF GAMMA RESPONSE1 Links DNA Damage Response to Organ Regeneration. PLANT PHYSIOLOGY 2018; 176:1665-1675. [PMID: 29222192 PMCID: PMC5813563 DOI: 10.1104/pp.17.01274] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/02/2017] [Indexed: 05/17/2023]
Abstract
In Arabidopsis, DNA damage-induced programmed cell death is limited to the meristematic stem cell niche and its early descendants. The significance of this cell-type-specific programmed cell death is unclear. Here, we demonstrate in roots that it is the programmed destruction of the mitotically compromised stem cell niche that triggers its regeneration, enabling growth recovery. In contrast to wild-type plants, sog1 plants, which are defective in damage-induced programmed cell death, maintain the cell identities and stereotypical structure of the stem cell niche after irradiation, but these cells fail to undergo cell division, terminating root growth. We propose DNA damage-induced programmed cell death is employed by plants as a developmental response, contrasting with its role as an anticarcinogenic response in animals. This role in plants may have evolved to restore the growth of embryos after the accumulation of DNA damage in seeds.
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Affiliation(s)
- Ross A Johnson
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Phillip A Conklin
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Michelle Tjahjadi
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Victor Missirian
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Ted Toal
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Anne B Britt
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
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Nikitaki Z, Holá M, Donà M, Pavlopoulou A, Michalopoulos I, Angelis KJ, Georgakilas AG, Macovei A, Balestrazzi A. Integrating plant and animal biology for the search of novel DNA damage biomarkers. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:21-38. [DOI: 10.1016/j.mrrev.2018.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
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Ma H, Song T, Wang T, Wang S. Influence of Human p53 on Plant Development. PLoS One 2016; 11:e0162840. [PMID: 27648563 PMCID: PMC5029891 DOI: 10.1371/journal.pone.0162840] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022] Open
Abstract
Mammalian p53 is a super tumor suppressor and plays a key role in guarding genome from DNA damage. However, p53 has not been found in plants which do not bear cancer although they constantly expose to ionizing radiation of ultraviolet light. Here we introduced p53 into the model plant Arabidopsis and examined p53-conferred phenotype in plant. Most strikingly, p53 caused early senescence and fasciation. In plants, fasciation has been shown as a result of the elevated homologous DNA recombination. Consistently, a reporter with overlapping segments of the GUS gene (1445) showed that the frequency of homologous recombination was highly induced in p53-transgenic plants. In contrast to p53, SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), as a negative regulator of homologous recombination in plants, is not present in mammals. Comet assay and clonogenic survival assay demonstrated that SNI1 inhibited DNA damage repair caused by either ionizing radiation or hydroxyurea in human osteosarcoma U2OS cancer cells. RAD51D is a recombinase in homologous recombination and functions downstream of SNI1 in plants. Interestingly, p53 rendered the sni1 mutants madly branching of inflorescence, a phenotype of fasciation, whereas rad51d mutant fully suppressed the p53-induced phenotype, indicating that human p53 action in plant is mediated by the SNI1-RAD51D signaling pathway. The reciprocal species-swap tests of p53 and SNI1 in human and Arabidopsis manifest that these species-specific proteins play a common role in homologous recombination across kingdoms of animals and plants.
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Affiliation(s)
- Huimin Ma
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Teng Song
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Tianhua Wang
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shui Wang
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
- * E-mail:
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Donà M, Mittelsten Scheid O. DNA Damage Repair in the Context of Plant Chromatin. PLANT PHYSIOLOGY 2015; 168:1206-18. [PMID: 26089404 PMCID: PMC4528755 DOI: 10.1104/pp.15.00538] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/17/2015] [Indexed: 05/03/2023]
Abstract
The integrity of DNA molecules is constantly challenged. All organisms have developed mechanisms to detect and repair multiple types of DNA lesions. The basic principles of DNA damage repair (DDR) in prokaryotes and unicellular and multicellular eukaryotes are similar, but the association of DNA with nucleosomes in eukaryotic chromatin requires mechanisms that allow access of repair enzymes to the lesions. This is achieved by chromatin-remodeling factors, and their necessity for efficient DDR has recently been demonstrated for several organisms and repair pathways. Plants share many features of chromatin organization and DNA repair with fungi and animals, but they differ in other, important details, which are both interesting and relevant for our understanding of genome stability and genetic diversity. In this Update, we compare the knowledge of the role of chromatin and chromatin-modifying factors during DDR in plants with equivalent systems in yeast and humans. We emphasize plant-specific elements and discuss possible implications.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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Furukawa T, Angelis KJ, Britt AB. Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double strand breaks but defective in integration of a transgene. FRONTIERS IN PLANT SCIENCE 2015; 6:357. [PMID: 26074930 PMCID: PMC4444747 DOI: 10.3389/fpls.2015.00357] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 05/05/2015] [Indexed: 05/20/2023]
Abstract
The DNA double-strand break (DSB) is a critical type of damage, and can be induced by both endogenous sources (e.g., errors of oxidative metabolism, transposable elements, programmed meiotic breaks, or perturbation of the DNA replication fork) and exogenous sources (e.g., ionizing radiation or radiomimetic chemicals). Although higher plants, like mammals, are thought to preferentially repair DSBs via nonhomologous end joining (NHEJ), much remains unclear about plant DSB repair pathways. Our reverse genetic approach suggests that DNA polymerase λ is involved in DSB repair in Arabidopsis. The Arabidopsis T-DNA insertion mutant (atpolλ-1) displayed sensitivity to both gamma-irradiation and treatment with radiomimetic reagents, but not to other DNA damaging treatments. The atpolλ-1 mutant showed a moderate sensitivity to DSBs, while Arabidopsis Ku70 and DNA ligase 4 mutants (atku70-3 and atlig4-2), both of which play critical roles in NHEJ, exhibited a hypersensitivity to these treatments. The atpolλ-1/atlig4-2 double mutant exhibited a higher sensitivity to DSBs than each single mutant, but the atku70/atpolλ-1 showed similar sensitivity to the atku70-3 mutant. We showed that transcription of the DNA ligase 1, DNA ligase 6, and Wee1 genes was quickly induced by BLM in several NHEJ deficient mutants in contrast to wild-type. Finally, the T-DNA transformation efficiency dropped in NHEJ deficient mutants and the lowest transformation efficiency was scored in the atpolλ-1/atlig4-2 double mutant. These results imply that AtPolλ is involved in both DSB repair and DNA damage response pathway.
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Affiliation(s)
- Tomoyuki Furukawa
- Department of Plant Biology, University of California at DavisDavis, CA, USA
| | - Karel J. Angelis
- DNA Repair Lab, Institute of Experimental Botany of the Academy of Sciences of the Czech RepublicPraha, Czech Republic
| | - Anne B. Britt
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- *Correspondence: Anne B. Britt, Department of Plant Biology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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