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Amritha PP, Shah JM. Essential role of the BRCA2B gene in somatic homologous recombination in Arabidopsis thaliana. BIOTECHNOLOGIA 2023; 104:371-380. [PMID: 38213474 PMCID: PMC10777725 DOI: 10.5114/bta.2023.132773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/15/2023] [Accepted: 08/29/2023] [Indexed: 01/13/2024] Open
Abstract
Constant exposure to various environmental and endogenous stresses can cause structural DNA damage, resulting in genome instability. Higher eukaryotic cells deploy conserved DNA repair systems, which include various DNA repair pathways, to maintain genome stability. Homologous recombination (HR), one of these repair pathways, involves multiple proteins. BRCA2, one of the proteins in the HR pathway, is of substantial research interest in humans because it is an oncogene. However, the study of this gene is limited due to the lack of availability of homozygous BRCA2-knockout mutants in mammals, which results in embryonic lethality. Arabidopsis thaliana has two copies of the BRCA2 homologs: BRCA2A and BRCA2B . Therefore, the single mutants remain nonlethal and fertile in Arabidopsis. The BRCA2A homolog, which plays a significant role in the HR pathway of germline cells and during the defense response, is well-studied in Arabidopsis. Our study focuses on the functional characterization of the BRCA2B homolog in the somatic cells of Arabidopsis, using the homozygous ΔBRCA2B mutant line. The phenotypic differences of ΔBRCA2B mutants were characterized and compared with wild Arabidopsis plants. The role of BRCA2B in spontaneous somatic HR (SHR) was studied using the ΔBRCA2B-gus detector line. ΔBRCA2B plants have a 6.3-fold lower SHR frequency than the control detector plants. Expression of four other HR pathway genes, including BRE, BRCC36A, RAD50, and RAD54, was significantly reduced in ΔBRCA2B mutants. Thus, our findings convey that the BRCA2B homolog plays an important role in maintaining spontaneous SHR rates and has a direct or indirect regulatory effect on the expression of other HR-related genes.
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Affiliation(s)
| | - Jasmine M. Shah
- Department of Plant Science, Central University of Kerala, Kasaragod, Kerala, India
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Xu W, Wang T, Xu S, Li F, Deng C, Wu L, Wu Y, Bian P. UV-C-Induced alleviation of transcriptional gene silencing through plant-plant communication: Key roles of jasmonic acid and salicylic acid pathways. Mutat Res 2016; 790:56-67. [PMID: 27131397 DOI: 10.1016/j.mrfmmm.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 04/04/2016] [Accepted: 04/18/2016] [Indexed: 05/22/2023]
Abstract
Plant stress responses at the epigenetic level are expected to allow more permanent changes of gene expression and potentially long-term adaptation. While it has been reported that plants subjected to adverse environments initiate various stress responses in their neighboring plants, little is known regarding epigenetic responses to external stresses mediated by plant-plant communication. In this study, we show that DNA repetitive elements of Arabidopsis thaliana, whose expression is inhibited epigenetically by transcriptional gene silencing (TGS) mechanism, are activated by UV-C irradiation through airborne plant-plant and plant-plant-plant communications, accompanied by DNA demethylation at CHH sites. Moreover, the TGS is alleviated by direct treatments with exogenous methyl jasmonate (MeJA) and methyl salicylate (MeSA). Further, the plant-plant and plant-plant-plant communications are blocked by mutations in the biosynthesis or signaling of jasmonic acid (JA) or salicylic acid (SA), indicating that JA and SA pathways are involved in the interplant communication for epigenetic responses. For the plant-plant-plant communication, stress cues are relayed to the last set of receiver plants by promoting the production of JA and SA signals in relaying plants, which exhibit upregulated expression of genes for JA and SA biosynthesis and enhanced emanation of MeJA and MeSA.
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Affiliation(s)
- Wei Xu
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Ting Wang
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Shaoxin Xu
- School of physics and materials science, Anhui University, Hefei, Anhui, 230601, PR China
| | - Fanghua Li
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Chenguang Deng
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Lijun Wu
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Yuejin Wu
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Po Bian
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China.
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Shah JM, Ramakrishnan AM, Singh AK, Ramachandran S, Unniyampurath U, Jayshankar A, Balasundaram N, Dhanapal S, Hyde G, Baskar R. Suppression of different classes of somatic mutations in Arabidopsis by vir gene-expressing Agrobacterium strains. BMC PLANT BIOLOGY 2015; 15:210. [PMID: 26307100 PMCID: PMC4549908 DOI: 10.1186/s12870-015-0595-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 08/14/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Agrobacterium infection, which is widely used to generate transgenic plants, is often accompanied by T-DNA-linked mutations and transpositions in flowering plants. It is not known if Agrobacterium infection also affects the rates of point mutations, somatic homologous recombinations (SHR) and frame-shift mutations (FSM). We examined the effects of Agrobacterium infection on five types of somatic mutations using a set of mutation detector lines of Arabidopsis thaliana. To verify the effect of secreted factors, we exposed the plants to different Agrobacterium strains, including wild type (Ach5), its derivatives lacking vir genes, oncogenes or T-DNA, and the heat-killed form for 48 h post-infection; also, for a smaller set of strains, we examined the rates of three types of mutations at multiple time-points. The mutation detector lines carried a non-functional β-glucuronidase gene (GUS) and a reversion of mutated GUS to its functional form resulted in blue spots. Based on the number of blue spots visible in plants grown for a further two weeks, we estimated the mutation frequencies. RESULTS For plants co-cultivated for 48 h with Agrobacterium, if the strain contained vir genes, then the rates of transversions, SHRs and FSMs (measured 2 weeks later) were lower than those of uninfected controls. In contrast, co-cultivation for 48 h with any of the Agrobacterium strains raised the transposition rates above control levels. The multiple time-point study showed that in seedlings co-cultivated with wild type Ach5, the reduced rates of transversions and SHRs after 48 h co-cultivation represent an apparent suppression of an earlier short-lived increase in mutation rates (peaking for plants co-cultivated for 3 h). An increase after 3 h co-cultivation was also seen for rates of transversions (but not SHR) in seedlings exposed to the strain lacking vir genes, oncogenes and T-DNA. However, the mutation rates in plants co-cultivated for longer times with this strain subsequently dropped below levels seen in uninfected controls, consistent with the results of the single time-point study. CONCLUSIONS The rates of various classes of mutations that result from Agrobacterium infection depend upon the duration of infection and the type of pathogen derived factors (such as Vir proteins, oncoproteins or T-DNA) possessed by the strain. Strains with vir genes, including the type used for plant transformation, suppressed selected classes of somatic mutations. Our study also provides evidence of a pathogen that can at least partly counter the induction of mutations in an infected plant.
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Affiliation(s)
- Jasmine M Shah
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
- Department of Plant Science, Central University of Kerala, Kasaragod, 671328, India.
| | - Anantha Maharasi Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Amit Kumar Singh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Subalakshmi Ramachandran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | | | - Ajitha Jayshankar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Nithya Balasundaram
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Shanmuhapreya Dhanapal
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Geoff Hyde
- , 14 Randwick St, Sydney, 2031, Australia.
| | - Ramamurthy Baskar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
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Eichten SR, Schmitz RJ, Springer NM. Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation. PLANT PHYSIOLOGY 2014; 165:933-947. [PMID: 24872382 PMCID: PMC4081347 DOI: 10.1104/pp.113.234211] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Chromatin modifications and epigenetics may play important roles in many plant processes, including developmental regulation, responses to environmental stimuli, and local adaptation. Chromatin modifications describe biochemical changes to chromatin state, such as alterations in the specific type or placement of histones, modifications of DNA or histones, or changes in the specific proteins or RNAs that associate with a genomic region. The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation or inheritance. Here, we specifically define epigenetics to include the key aspects of heritability (stable transmission of gene expression states through mitotic or meiotic cell divisions) and independence from DNA sequence changes. We argue against generically equating chromatin and epigenetics; although many examples of epigenetics involve chromatin changes, those chromatin changes are not always heritable or may be influenced by genetic changes. Careful use of the terms chromatin modifications and epigenetics can help separate the biochemical mechanisms of regulation from the inheritance patterns of altered chromatin states. Here, we also highlight examples in which chromatin modifications and epigenetics affect important plant processes.
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Affiliation(s)
- Steven R Eichten
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
| | - Robert J Schmitz
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
| | - Nathan M Springer
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
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Richter KS, Kleinow T, Jeske H. Somatic homologous recombination in plants is promoted by a geminivirus in a tissue-selective manner. Virology 2014; 452-453:287-96. [PMID: 24606706 DOI: 10.1016/j.virol.2014.01.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/15/2013] [Accepted: 01/25/2014] [Indexed: 01/11/2023]
Abstract
Four transgenic Arabidopsis thaliana lines carrying different reporter gene constructs based on split glucuronidase genes were used to monitor the frequency of somatic homologous recombination after geminivirus infections. Euphorbia mosaic virus and Cleome leaf crumple virus were chosen as examples, because they induce only mild symptoms and are expected to induce less general stress responses than other geminiviruses. After comparing the different plant lines and viruses as well as optimizing the infection procedure, Euphorbia mosaic virus enhanced recombination rates significantly in the transgenic reporter line 1445. The effect was tissue-specific in cells of the leaf veins as expected for this phloem-limited virus. The advantage for geminiviruses to activate a general recombination pathway is discussed with reference to an increased fitness by generating virus recombinants which have been observed frequently as an epidemiologic driving force.
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Affiliation(s)
- K S Richter
- Biologisches Institut, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - T Kleinow
- Biologisches Institut, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - H Jeske
- Biologisches Institut, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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Puchta H, Hohn B. In planta somatic homologous recombination assay revisited: a successful and versatile, but delicate tool. THE PLANT CELL 2012; 24:4324-31. [PMID: 23144182 PMCID: PMC3531836 DOI: 10.1105/tpc.112.101824] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Marker-transgene-dependent lines of Arabidopsis thaliana measuring somatic homologous recombination (SHR) have been available for almost two decades. Here we discuss mechanisms of marker-gene restoration, comment on results obtained using the reporter lines, and stress how caution must be applied to avoid experimental problems or false interpretation in the use of SHR reporter lines. Although theoretically possible, we conclude that explanations other than SHR are unlikely to account for restoration of marker gene expression in the SHR lines when used with appropriate controls. We provide an overview of some of the most important achievements obtained with the SHR lines, give our view of the limitations of the system, and supply the reader with suggestions on the proper handling of the SHR lines. We are convinced that SHR lines are and will remain in the near future a valuable tool to explore the mechanism and influence of external and internal factors on genome stability and DNA repair in plants.
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Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.
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