1
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Tondepu SAG, Manova V, Vadivel D, Dondi D, Pagano A, Macovei A. MicroRNAs potentially targeting DDR-related genes are differentially expressed upon exposure to γ-rays during seed germination in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108771. [PMID: 38820913 DOI: 10.1016/j.plaphy.2024.108771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
DNA damage response (DDR), a complex network of cellular pathways that cooperate to sense and repair DNA lesions, is regulated by several mechanisms, including microRNAs. As small, single-stranded RNA molecules, miRNAs post-transcriptionally regulate their target genes by mRNA cleavage or translation inhibition. Knowledge regarding miRNAs influence on DDR-associated genes is still scanty in plants. In this work, an in silico analysis was performed to identify putative miRNAs that could target DDR sensors, signal transducers and effector genes in wheat. Selected putative miRNA-gene pairs were tested in an experimental system where seeds from two wheat mutant lines were irradiated with 50 Gy and 300 Gy gamma(γ)-rays. To evaluate the effect of the treatments on wheat germination, phenotypic and molecular (DNA damage, ROS accumulation, gene/miRNA expression profile) analyses have been carried out. The results showed that in dry seeds ROS accumulated immediately after irradiation and decayed soon after while the negative impact on seedling growth was supported by enhanced accumulation of DNA damage. When a qRT-PCR analysis was performed, the selected miRNAs and DDR-related genes were differentially modulated by the γ-rays treatments in a dose-, time- and genotype-dependent manner. A significant negative correlation was observed between the expression of tae-miR5086 and the RAD50 gene, involved in double-strand break sensing and homologous recombination repair, one of the main processes that repairs DNA breaks induced by γ-rays. The results hereby reported can be relevant for wheat breeding programs and screening of the radiation response and tolerance of novel wheat varieties.
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Affiliation(s)
- Sri Amarnadh Gupta Tondepu
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Vasilissa Manova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences "Acad. G. Bonchev", Street Bldg. 21, 1113, Sofia, Bulgaria.
| | - Dhanalakshmi Vadivel
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Daniele Dondi
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy.
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2
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Zhao L, Li Z, Huang B, Mi D, Xu D, Sun Y. Integrating evolutionarily conserved mechanism of response to radiation for exploring novel Caenorhabditis elegans radiation-responsive genes for estimation of radiation dose associated with spaceflight. CHEMOSPHERE 2024; 351:141148. [PMID: 38211791 DOI: 10.1016/j.chemosphere.2024.141148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/09/2023] [Accepted: 01/06/2024] [Indexed: 01/13/2024]
Abstract
During space exploration, space radiation is widely recognized as an inescapable perilous stressor, owing to its capacity to induce genomic DNA damage and escalate the likelihood of detrimental health outcomes. Rapid and reliable estimation of space radiation dose holds paramount significance in accurately assessing the health risks associated with spaceflight. However, the identification of space radiation-responsive genes, with their potential to serve as early indicators for diagnosing radiation dose associated with spaceflight, continues to pose a significant challenge. In this study, based on the evolutionarily conserved mechanism of radiation response, an in silico analysis method of homologous comparison was performed to identify the Caenorhabditis elegans orthologues of human radiation-responsive genes with possible roles in the major processes of response to radiation, and thereby to explore the potential C. elegans radiation-responsive genes for evaluating the levels of space radiation exposure. The results showed that there were 60 known C. elegans radiation-responsive genes and 211 C. elegans orthologues of human radiation-responsive genes implicated in the major processes of response to radiation. Through an investigation of all available transcriptomic datasets obtained from space-flown C. elegans, it was observed that the expression levels of the majority of these putative C. elegans radiation-responsive genes identified in this study were notably changed across various spaceflight conditions. Furthermore, this study indicated that within the identified genes, 19 known C. elegans radiation-responsive genes and 40 newly identified C. elegans orthologues of human radiation-responsive genes exhibited a remarkable positive correlation with the duration of spaceflight. Moreover, a noteworthy presence of substantial multi-collinearity among the majority of these identified genes was observed. This observation lends support to the possibility of treating each identified gene as an independent indicator of radiation dose in space. Ultimately, a subset of 15 potential radiation-responsive genes was identified, presenting the most promising indicators for estimation of radiation dose associated with spaceflight in C. elegans.
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Affiliation(s)
- Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, Liaoning, China.
| | - Zejun Li
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, Liaoning, China
| | - Baohang Huang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, Liaoning, China
| | - Dong Mi
- College of Science, Dalian Maritime University, Dalian, 116026, Liaoning, China
| | - Dan Xu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, Liaoning, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, Liaoning, China.
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3
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Żabka A, Gocek N, Polit JT, Maszewski J. Epigenetic modifications evidenced by isolation of proteins on nascent DNA and immunofluorescence in hydroxyurea-treated root meristem cells of Vicia faba. PLANTA 2023; 258:95. [PMID: 37814174 PMCID: PMC10562345 DOI: 10.1007/s00425-023-04249-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
MAIN CONCLUSION By implementation of the iPOND technique for plant material, changes in posttranslational modifications of histones were identified in hydroxyurea-treated root meristem cells of Vicia. Replication stress (RS) disrupts or inhibits replication forks and by altering epigenetic information of the newly formed chromatin can affect gene regulation and/or spatial organisation of DNA. Experiments on Vicia faba root meristem cells exposed to short-term treatment with 3 mM hydroxyurea (HU, an inhibitor of DNA replication) were aimed to understand epigenetic changes related to RS. To achieve this, the following histone modifications were studied using isolation of proteins on nascent DNA (iPOND) technique (for the first time on plant material) combined with immunofluorescence labeling: (i) acetylation of histone H3 at lysine 56 (H3K56Ac), (ii) acetylation of histone H4 at Lys 5 (H4K5Ac), and (iii) phosphorylation of histone H3 at threonine 45 (H3T45Ph). Certainly, the implementation of the iPOND method for plants may prove to be a key step for a more in-depth understanding of the cell's response to RS at the chromatin level.
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Affiliation(s)
- Aneta Żabka
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland.
| | - Natalia Gocek
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland
| | - Justyna Teresa Polit
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland
| | - Janusz Maszewski
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland
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4
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Su J, Su Q, Hu S, Ruan X, Ouyang S. Research Progress on the Anti-Aging Potential of the Active Components of Ginseng. Nutrients 2023; 15:3286. [PMID: 37571224 PMCID: PMC10421173 DOI: 10.3390/nu15153286] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Aging is a cellular state characterized by a permanent cessation of cell division and evasion of apoptosis. DNA damage, metabolic dysfunction, telomere damage, and mitochondrial dysfunction are the main factors associated with senescence. Aging increases β-galactosidase activity, enhances cell spreading, and induces Lamin B1 loss, which further accelerate the aging process. It is associated with a variety of diseases, such as Alzheimer's disease, Parkinson's, type 2 diabetes, and chronic inflammation. Ginseng is a traditional Chinese medicine with anti-aging effects. The active components of ginseng, including saponins, polysaccharides, and active peptides, have antioxidant, anti-apoptotic, neuroprotective, and age-delaying effects. DNA damage is the main factor associated with aging, and the mechanism through which the active ingredients of ginseng reduce DNA damage and delay aging has not been comprehensively described. This review focuses on the anti-aging mechanisms of the active ingredients of ginseng. Furthermore, it broadens the scope of ideas for further research on natural products and aging.
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Affiliation(s)
- Jingqian Su
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Q.S.); (S.H.)
- Provincial University Key Laboratory of Microbial Pathogenesis and Interventions, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Qiaofen Su
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Q.S.); (S.H.)
- Provincial University Key Laboratory of Microbial Pathogenesis and Interventions, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Shan Hu
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Q.S.); (S.H.)
- Provincial University Key Laboratory of Microbial Pathogenesis and Interventions, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Xinglin Ruan
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 350001, China;
| | - Songying Ouyang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Q.S.); (S.H.)
- Provincial University Key Laboratory of Microbial Pathogenesis and Interventions, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
- Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China
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5
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Adel S, Carels N. Plant Tolerance to Drought Stress with Emphasis on Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112170. [PMID: 37299149 DOI: 10.3390/plants12112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 06/12/2023]
Abstract
Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.
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Affiliation(s)
- Sarah Adel
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development for Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, Brazil
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6
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Mercado SAS, Galvis DGV. Paracetamol ecotoxicological bioassay using the bioindicators Lens culinaris Med. and Pisum sativum L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:61965-61976. [PMID: 36934188 PMCID: PMC10024602 DOI: 10.1007/s11356-023-26475-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/11/2023] [Indexed: 05/10/2023]
Abstract
Paracetamol is one of the most widely used drugs worldwide, yet its environmental presence and hazardous impact on non-target organisms could rapidly increase. In this study, the possible cytotoxic effects of paracetamol were evaluated using two bioindicator plants Lens culinaris and Pisum sativum. Concentrations of 500, 400, 300, 200, 100, 50, 25, 5, 1 mg L-1, and a control (distilled water) were used for a total of 10 treatments, which were subsequently applied on seeds of Lens culinaris Med. and Pisum sativum L.; after 72 h of exposure, root growth, mitotic index, percentage of chromosomal abnormalities, and the presence of micronucleus were evaluated. The cytotoxic effect of paracetamol on L. culinaris and P. sativum was demonstrated, reporting the inhibition of root growth, the presence of abnormalities, and a significant micronucleus index at all concentrations used, which shows that this drug has a high degree of toxicity.
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7
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Pagano A, Macovei A, Balestrazzi A. Molecular dynamics of seed priming at the crossroads between basic and applied research. PLANT CELL REPORTS 2023; 42:657-688. [PMID: 36780009 PMCID: PMC9924218 DOI: 10.1007/s00299-023-02988-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The potential of seed priming is still not fully exploited. Our limited knowledge of the molecular dynamics of seed pre-germinative metabolism is the main hindrance to more effective new-generation techniques. Climate change and other recent global crises are disrupting food security. To cope with the current demand for increased food, feed, and biofuel production, while preserving sustainability, continuous technological innovation should be provided to the agri-food sector. Seed priming, a pre-sowing technique used to increase seed vigor, has become a valuable tool due to its potential to enhance germination and stress resilience under changing environments. Successful priming protocols result from the ability to properly act on the seed pre-germinative metabolism and stimulate events that are crucial for seed quality. However, the technique still requires constant optimization, and researchers are committed to addressing some key open questions to overcome such drawbacks. In this review, an update of the current scientific and technical knowledge related to seed priming is provided. The rehydration-dehydration cycle associated with priming treatments can be described in terms of metabolic pathways that are triggered, modulated, or turned off, depending on the seed physiological stage. Understanding the ways seed priming affects, either positively or negatively, such metabolic pathways and impacts gene expression and protein/metabolite accumulation/depletion represents an essential step toward the identification of novel seed quality hallmarks. The need to expand the basic knowledge on the molecular mechanisms ruling the seed response to priming is underlined along with the strong potential of applied research on primed seeds as a source of seed quality hallmarks. This route will hasten the implementation of seed priming techniques needed to support sustainable agriculture systems.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy.
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy.
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8
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Hirao AS, Watanabe Y, Hasegawa Y, Takagi T, Ueno S, Kaneko S. Mutational effects of chronic gamma radiation throughout the life cycle of Arabidopsis thaliana: Insight into radiosensitivity in the reproductive stage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156224. [PMID: 35644386 DOI: 10.1016/j.scitotenv.2022.156224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Organisms living on Earth have always been exposed to natural sources of ionizing radiation, but following recent nuclear disasters, these background levels have often increased regionally due to the addition of man-made sources of radiation. To assess the mutational effects of ubiquitously present radiation on plants, we performed a whole-genome resequencing analysis of mutations induced by chronic irradiation throughout the life cycle of Arabidopsis thaliana grown under controlled conditions. We obtained resequencing data from 36 second generation post-mutagenesis (M2) progeny derived from 12 first generation (M1) lines grown under gamma-irradiation conditions, ranging from 0.0 to 2.0 Gray per day (Gy/day), to identify de novo mutations, including single base substitutions (SBSs) and small insertions/deletions (INDELs). The relationship between de novo mutation frequency and radiation dose rate from 0.0 to 2.0 Gy/day was assessed by statistical modeling. The increase in de novo mutations in response to irradiation dose fit the negative binomial model, which accounted for the high variability of mutation frequency observed. Among the different types of mutations, SBSs were more prevalent than INDELs, and deletions were more frequent than insertions. Furthermore, we observed that the mutational effects of chronic radiation were greater during the reproductive stage. These results will provide valuable insights into practical strategies for analyzing mutational effects in wild plants growing in environments with various mutagens.
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Affiliation(s)
- Akira S Hirao
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yoshito Watanabe
- Fukushima Project Headquarters, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Yoichi Hasegawa
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan.
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9
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Pagano A, Zannino L, Pagano P, Doria E, Dondi D, Macovei A, Biggiogera M, Araújo SDS, Balestrazzi A. Changes in genotoxic stress response, ribogenesis and PAP (3'-phosphoadenosine 5'-phosphate) levels are associated with loss of desiccation tolerance in overprimed Medicago truncatula seeds. PLANT, CELL & ENVIRONMENT 2022; 45:1457-1473. [PMID: 35188276 PMCID: PMC9311706 DOI: 10.1111/pce.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 05/06/2023]
Abstract
Re-establishment of desiccation tolerance is essential for the survival of germinated seeds facing water deficit in the soil. The molecular and ultrastructural features of desiccation tolerance maintenance and loss within the nuclear compartment are not fully resolved. In the present study, the impact of desiccation-induced genotoxic stress on nucleolar ultrastructure and ribogenesis was explored along the rehydration-dehydration cycle applied in standard seed vigorization protocols. Primed and overprimed Medicago truncatula seeds, obtained through hydropriming followed by desiccation (dry-back), were analysed. In contrast to desiccation-tolerant primed seeds, overprimed seeds enter irreversible germination and do not survive dry-back. Reactive oxygen species, DNA damage and expression profiles of antioxidant/DNA Damage Response genes were measured, as main hallmarks of the seed response to desiccation stress. Nuclear ultrastructural features were also investigated. Overprimed seeds subjected to dry-back revealed altered rRNA accumulation profiles and up-regulation of genes involved in ribogenesis control. The signal molecule PAP (3'-phosphoadenosine 5'-phosphate) accumulated during dry-back only in primed seeds, as a distinctive feature of desiccation tolerance. The presented results show the molecular and ultrastructural landscapes of the seed desiccation response, including substantial changes in nuclear organization.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Lorena Zannino
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Paola Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Enrico Doria
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Daniele Dondi
- Department of ChemistryUniversity of PaviaPaviaItaly
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Marco Biggiogera
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Susana de Sousa Araújo
- Association BLC3‐Technology and Innovation CampusCentre Bio R&D UnitMacedo de CavaleirosPortugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
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10
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Pagano A, Gualtieri C, Mutti G, Raveane A, Sincinelli F, Semino O, Balestrazzi A, Macovei A. Identification and Characterization of SOG1 (Suppressor of Gamma-Response 1) Homologues in Plants Using Data Mining Resources and Gene Expression Profiling. Genes (Basel) 2022; 13:genes13040667. [PMID: 35456473 PMCID: PMC9026448 DOI: 10.3390/genes13040667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022] Open
Abstract
SOG1 (Suppressor of the Gamma response 1) is the master-regulator of plant DNA damage response (DDR), a highly coordinated network of DNA damage sensors, transducers, mediators, and effectors, with highly coordinated activities. SOG1 transcription factor belongs to the NAC/NAM protein family, containing the well-conserved NAC domain and five serine-glutamine (SQ) motifs, preferential targets for phosphorylation by ATM and ATR. So far, the information gathered for the SOG1 function comes from studies on the model plant Arabidopsis thaliana. To expand the knowledge on plant-specific DDR, it is opportune to gather information on other SOG1 orthologues. The current study identified plants where multiple SOG1 homologues are present and evaluated their functions by leveraging the information contained in publicly available transcriptomics databases. This analysis revealed the presence of multiple SOG1 sequences in thirteen plant species, and four (Medicago truncatula, Glycine max, Kalankoe fedtschenkoi, Populus trichocarpa) were selected for gene expression data mining based on database availability. Additionally, M. truncatula seeds and seedlings exposed to treatments known to activate DDR pathways were used to evaluate the expression profiles of MtSOG1a and MtSOG1b. The experimental workflow confirmed the data retrieved from transcriptomics datasets, suggesting that the SOG1 homologues have redundant functions in different plant species.
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11
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Pedroza-Garcia JA, Xiang Y, De Veylder L. Cell cycle checkpoint control in response to DNA damage by environmental stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:490-507. [PMID: 34741364 DOI: 10.1111/tpj.15567] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant-specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant-specific SOG1 transcription factor, which drives the activity of cyclin-dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species-specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change.
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Affiliation(s)
- José Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Yanli Xiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
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12
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Gentric N, Genschik P, Noir S. Connections between the Cell Cycle and the DNA Damage Response in Plants. Int J Mol Sci 2021; 22:ijms22179558. [PMID: 34502465 PMCID: PMC8431409 DOI: 10.3390/ijms22179558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
Due to their sessile lifestyle, plants are especially exposed to various stresses, including genotoxic stress, which results in altered genome integrity. Upon the detection of DNA damage, distinct cellular responses lead to cell cycle arrest and the induction of DNA repair mechanisms. Interestingly, it has been shown that some cell cycle regulators are not only required for meristem activity and plant development but are also key to cope with the occurrence of DNA lesions. In this review, we first summarize some important regulatory steps of the plant cell cycle and present a brief overview of the DNA damage response (DDR) mechanisms. Then, the role played by some cell cycle regulators at the interface between the cell cycle and DNA damage responses is discussed more specifically.
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Pedroza-Garcia JA, Eekhout T, Achon I, Nisa MU, Coussens G, Vercauteren I, Van den Daele H, Pauwels L, Van Lijsebettens M, Raynaud C, De Veylder L. Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death. THE PLANT CELL 2021; 33:2662-2684. [PMID: 34086963 PMCID: PMC8408457 DOI: 10.1093/plcell/koab158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/31/2021] [Indexed: 05/06/2023]
Abstract
The ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR) kinases coordinate the DNA damage response. The roles described for Arabidopsis thaliana ATR and ATM are assumed to be conserved over other plant species, but molecular evidence is scarce. Here, we demonstrate that the functions of ATR and ATM are only partially conserved between Arabidopsis and maize (Zea mays). In both species, ATR and ATM play a key role in DNA repair and cell cycle checkpoint activation, but whereas Arabidopsis plants do not suffer from the absence of ATR under control growth conditions, maize mutant plants accumulate replication defects, likely due to their large genome size. Moreover, contrarily to Arabidopsis, maize ATM deficiency does not trigger meiotic defects, whereas the ATR kinase appears to be crucial for the maternal fertility. Strikingly, ATR is required to repress premature endocycle onset and cell death in the maize endosperm. Its absence results in a reduction of kernel size, protein and starch content, and a stochastic death of kernels, a process being counteracted by ATM. Additionally, while Arabidopsis atr atm double mutants are viable, no such mutants could be obtained for maize. Therefore, our data highlight that the mechanisms maintaining genome integrity may be more important for vegetative and reproductive development than previously anticipated.
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Affiliation(s)
- Jose Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Maher-Un Nisa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
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14
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Gualtieri C, Gianella M, Pagano A, Cadeddu T, Araújo S, Balestrazzi A, Macovei A. Exploring microRNA Signatures of DNA Damage Response Using an Innovative System of Genotoxic Stress in Medicago truncatula Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:645323. [PMID: 33767724 PMCID: PMC7985446 DOI: 10.3389/fpls.2021.645323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/15/2021] [Indexed: 05/08/2023]
Abstract
One of the challenges that living organisms face is to promptly respond to genotoxic stress to avoid DNA damage. To this purpose, all organisms, including plants, developed complex DNA damage response (DDR) mechanisms. These mechanisms are highly conserved among organisms and need to be finely regulated. In this scenario, microRNAs (miRNAs) are emerging as active players, thus attracting the attention of the research community. The involvement of miRNAs in DDR has been investigated prominently in human cells whereas studies in plants are still scarce. To experimentally investigate the involvement of plant miRNAs in the regulation of DDR-associated pathways, an ad hoc system was developed, using the model legume Medicago truncatula. Specific treatments with camptothecin (CPT) and/or NSC120686 (NSC), targeting distinct components of DDR, namely topoisomerase I (TopI) and tyrosyl-DNA phosphodiesterase 1 (TDP1), were used. Phenotypic (germination percentage and speed, seedling growth) and molecular (cell death, DNA damage, and gene expression profiles) analyses demonstrated that the imposed treatments impact DDR. Our results show that these treatments do not influence the germination process but rather inhibit seedling development, causing an increase in cell death and accumulation of DNA damage. Moreover, treatment-specific changes in the expression of suppressor of gamma response 1 (SOG1), master-regulator of plant DDR, were observed. Additionally, the expression of multiple genes playing important roles in different DNA repair pathways and cell cycle regulation were differentially expressed in a treatment-specific manner. Subsequently, specific miRNAs identified from our previous bioinformatics approaches as putatively targeting genes involved in DDR processes were investigated alongside their targets. The obtained results indicate that under most conditions when a miRNA is upregulated the corresponding candidate target gene is downregulated, providing an indirect evidence of miRNAs action over these targets. Hence, the present study extends the present knowledge on the information available regarding the roles played by miRNAs in the post-transcriptional regulation of DDR in plants.
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Affiliation(s)
- Carla Gualtieri
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Maraeva Gianella
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Andrea Pagano
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Tiziano Cadeddu
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Susana Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3, Technology and Innovation Campus, Centre BIO- R&D Unit, Lagares da Beira, Portugal
| | - Alma Balestrazzi
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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15
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Macovei A, Rubio-Somoza I, Paiva JAP, Araújo S, Donà M. Editorial: MicroRNA Signatures in Plant Genome Stability and Genotoxic Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:683302. [PMID: 33968124 PMCID: PMC8100575 DOI: 10.3389/fpls.2021.683302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 03/25/2021] [Indexed: 05/21/2023]
Affiliation(s)
- Anca Macovei
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
- *Correspondence: Anca Macovei
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution Laboratory (MoRE), Centre for Research in Agricultural Genomics (CRAG), Barcelona, Spain
| | - Jorge Almiro Pinto Paiva
- Institute of Plant Genetics of the Polish Academy of Sciences, Poznan, Poland
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Susana Araújo
- Association BLC3, Technology and Innovation Campus, Centre BIO–R&D Unit, Lagares da Beira, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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16
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Nikitaki Z, Pariset E, Sudar D, Costes SV, Georgakilas AG. In Situ Detection of Complex DNA Damage Using Microscopy: A Rough Road Ahead. Cancers (Basel) 2020; 12:E3288. [PMID: 33172046 PMCID: PMC7694657 DOI: 10.3390/cancers12113288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Complexity of DNA damage is considered currently one if not the primary instigator of biological responses and determinant of short and long-term effects in organisms and their offspring. In this review, we focus on the detection of complex (clustered) DNA damage (CDD) induced for example by ionizing radiation (IR) and in some cases by high oxidative stress. We perform a short historical perspective in the field, emphasizing the microscopy-based techniques and methodologies for the detection of CDD at the cellular level. We extend this analysis on the pertaining methodology of surrogate protein markers of CDD (foci) colocalization and provide a unique synthesis of imaging parameters, software, and different types of microscopy used. Last but not least, we critically discuss the main advances and necessary future direction for the better detection of CDD, with important outcomes in biological and clinical setups.
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Affiliation(s)
- Zacharenia Nikitaki
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
| | - Eloise Pariset
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
- Universities Space Research Association (USRA), Mountain View, CA 94043, USA
| | - Damir Sudar
- Life Sciences Department, Quantitative Imaging Systems LLC, Portland, OR 97209, USA;
| | - Sylvain V. Costes
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
| | - Alexandros G. Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
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17
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Antonova EV, Fuchs J, Röder MS. Influence of Chronic Man-made Pollution on Bromus inermis Genome Size. RUSS J ECOL+ 2020. [DOI: 10.1134/s1067413620040025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Pagano A, L'Andolina C, Sabatini ME, de Sousa Araújo S, Balestrazzi A, Macovei A. Sodium butyrate induces genotoxic stress in function of photoperiod variations and differentially modulates the expression of genes involved in chromatin modification and DNA repair in Petunia hybrida seedlings. PLANTA 2020; 251:102. [PMID: 32350684 DOI: 10.1007/s00425-020-03392-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Sodium butyrate applied to Petunia hybrida seeds under a long-day photoperiod has a negative impact (reduced seedling length, decreased production of photosynthetic pigments, and accumulation of DNA damage) on early seedling development, whereas its administration under dark/light conditions (complete dark conditions for 5 days followed by exposure to long-day photoperiod for 5 days) bypasses some of the adverse effects. Genotoxic stress impairs plant development. To circumvent DNA damage, plants activate DNA repair pathways in concert with chromatin dynamics. These are essential during seed germination and seedling establishment, and may be influenced by photoperiod variations. To assess this interplay, an experimental design was developed in Petunia hybrida, a relevant horticultural crop and model species. Seeds were treated with different doses of sodium butyrate (NaB, 1 mM and 5 mM) as a stress agent applied under different light/dark conditions throughout a time period of 10 days. Phenotypic (germination percentage and speed, seedling length, and photosynthetic pigments) and molecular (DNA damage and gene expression profiles) analyses were performed to monitor the response to the imposed conditions. Seed germination was not affected by the treatments. Seedling development was hampered by increasing NaB concentrations applied under a long-day photoperiod (L) as reflected by the decreased seedling length accompanied by increased DNA damage. When seedlings were grown under dark conditions for 5 days and then exposed to long-day photoperiod for the remaining 5 days (D/L), the damaging effects of NaB were circumvented. NaB exposure under L conditions resulted in enhanced expression of HAT/HDAC (HISTONE ACETYLTRANSFERASES/HISTONE DEACTEYLASES) genes along with repression of genes involved in DNA repair. Differently, under D/L conditions, the expression of DNA repair genes was increased by NaB treatment and this was associated with lower levels of DNA damage. The observed DNA damage and gene expression profiles suggest the involvement of chromatin modification- and DNA repair-associated pathways in response to NaB and dark/light exposure during seedling development.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Corrado L'Andolina
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Maria Elisa Sabatini
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
- Viral Control of Cellular Pathways and Biology of Tumorigenesis Unit, European Institute of Oncology (IFOM-IEO), via Adamello 16, 20139, Milano, Italy
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química E Biológica António Xavier (ITQB-NOVA), Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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19
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Zhao L, He X, Shang Y, Bao C, Peng A, Lei X, Han P, Mi D, Sun Y. Identification of potential radiation-responsive biomarkers based on human orthologous genes with possible roles in DNA repair pathways by comparison between Arabidopsis thaliana and homo sapiens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 702:135076. [PMID: 31734608 DOI: 10.1016/j.scitotenv.2019.135076] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Rapid and reliable ionization radiation (IR) exposure estimation has become increasingly important in environment due to the urgent requirement of medical evaluation and treatment in the event of nuclear accident emergency. Human DNA repair genes can be identified as important candidate biomarkers to assess IR exposure, while how to find the enough sensitive and specific biomarkers in the DNA repair networks is still challenged and not fully determined. The conserved features of DNA repair pathways may facilitate interdisciplinary studies that cross the traditional boundaries between animal and plant biology, with the aim of identifying undiscovered human DNA repair genes for potential radiation-responsive biomarkers. In this work, an in silico method of homologous comparison was performed to identify the human orthologues of A. thaliana DNA repair genes, and thereby to explore the sensitive and specific human radiation-responsive genes to evaluate the IR exposure levels. The results showed that a total of 16 putative candidate genes were involved in the human DNA repair pathways of homologous recombination (HR) and non-homologous end joining (NHEJ), and most of them were confirmed by previous experiments. Additionally, we analyzed the gene expression patterns of these 16 candidate genes in several human transcript microarray datasets with different IR treatments. The results indicated that most of the gene expression levels for these candidate genes were significantly changed under different radiation treatments. Based on these results, we integrated these putative human DNA repair genes into the DNA repair pathways to propose new insights of the HR and NHEJ pathways, which can also provide the potential targets for the development of radiation biomarkers. Notably, two putative DNA repair genes, named ERCC1 and ESCO2, were identified and were considered to be the sensitive and specific biomarkers in response to γ-ray exposures.
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Affiliation(s)
- Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Xinye He
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Yuxuan Shang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Chengyu Bao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Ailin Peng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Xiaohua Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Pei Han
- Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, China
| | - Dong Mi
- College of Science, Dalian Maritime University, Dalian, Liaoning, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China.
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20
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Goffová I, Vágnerová R, Peška V, Franek M, Havlová K, Holá M, Zachová D, Fojtová M, Cuming A, Kamisugi Y, Angelis KJ, Fajkus J. Roles of RAD51 and RTEL1 in telomere and rDNA stability in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:1090-1105. [PMID: 30834585 DOI: 10.1111/tpj.14304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 05/11/2023]
Abstract
Telomeres and ribosomal RNA genes (rDNA) are essential for cell survival and particularly sensitive to factors affecting genome stability. Here, we examine the role of RAD51 and its antagonist, RTEL1, in the moss Physcomitrella patens. In corresponding mutants, we analyse their sensitivity to DNA damage, the maintenance of telomeres and rDNA, and repair of double-stranded breaks (DSBs) induced by genotoxins with various modes of action. While the loss of RTEL1 results in rapid telomere shortening, concurrent loss of both RAD51 genes has no effect on telomere lengths. We further demonstrate here the linked arrangement of 5S and 45S rRNA genes in P. patens. The spacer between 5S and 18S rRNA genes, especially the region downstream from the transcription start site, shows conspicuous clustering of sites with a high propensity to form quadruplex (G4) structures. Copy numbers of 5S and 18S rDNA are reduced moderately in the pprtel1 mutant, and significantly in the double pprad51-1-2 mutant, with no progression during subsequent cultivation. While reductions in 45S rDNA copy numbers observed in pprtel1 and pprad51-1-2 plants apply also to 5S rDNA, changes in transcript levels are different for 45S and 5S rRNA, indicating their independent transcription by RNA polymerase I and III, respectively. The loss of SOL (Sog One-Like), a transcription factor regulating numerous genes involved in DSB repair, increases the rate of DSB repair in dividing as well as differentiated tissue, and through deactivation of G2/M cell-cycle checkpoint allows the cell-cycle progression manifested as a phenotype resistant to bleomycin.
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Affiliation(s)
- Ivana Goffová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Radka Vágnerová
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Vratislav Peška
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Michal Franek
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Kateřina Havlová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Marcela Holá
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Dagmar Zachová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Andrew Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Karel J Angelis
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
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21
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Ryu TH, Go YS, Choi SH, Kim JI, Chung BY, Kim JH. SOG1-dependent NAC103 modulates the DNA damage response as a transcriptional regulator in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:83-96. [PMID: 30554433 DOI: 10.1111/tpj.14201] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 05/26/2023]
Abstract
The plant-specific transcription factor (TF) NAC103 was previously reported to modulate the unfolded protein response in Arabidopsis under endoplasmic reticulum (ER) stress. Alternatively, we report here that NAC103 is involved in downstream signaling of SOG1, a master regulator for expression of DNA damage response (DDR) genes induced by genotoxic stress. Arabidopsis NAC103 expression was strongly induced by genotoxic stress and nac103 mutants displayed substantial inhibition of DDR gene expression after gamma radiation or radiomimetic zeocin treatment. DDR phenotypes, such as true leaf inhibition, root cell death and root growth inhibition, were also suppressed significantly in the nac103 mutants, but to a lesser extent than in the sog1-1 mutant. By contrast, overexpression of NAC103 increased DDR gene expression without genotoxic stress and substantially rescued the phenotypic changes in the sog1-1 mutant after zeocin treatment. The putative promoters of some representative DDR genes, RAD51, PARP1, RPA1E, BRCA1 and At4g22960, were found to partly interact with NAC103. Together with the expected interaction of SOG1 with the promoter of NAC103, our study suggests that NAC103 is a putative SOG1-dependent transcriptional regulator of plant DDR genes, which are responsible for DDR phenotypes under genotoxic stress.
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Affiliation(s)
- Tae Ho Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Korea
- Department of Biotechnology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Young Sam Go
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Korea
| | - Seung Hee Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Korea
| | - Jeong-Il Kim
- Department of Biotechnology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Korea
| | - Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Korea
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22
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Mothersill C, Abend M, Bréchignac F, Copplestone D, Geras'kin S, Goodman J, Horemans N, Jeggo P, McBride W, Mousseau TA, O'Hare A, Papineni RVL, Powathil G, Schofield PN, Seymour C, Sutcliffe J, Austin B. The tubercular badger and the uncertain curve:- The need for a multiple stressor approach in environmental radiation protection. ENVIRONMENTAL RESEARCH 2019; 168:130-140. [PMID: 30296640 DOI: 10.1016/j.envres.2018.09.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/23/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
This article presents the results of a workshop held in Stirling, Scotland in June 2018, called to examine critically the effects of low-dose ionising radiation on the ecosphere. The meeting brought together participants from the fields of low- and high-dose radiobiology and those working in radioecology to discuss the effects that low doses of radiation have on non-human biota. In particular, the shape of the low-dose response relationship and the extent to which the effects of low-dose and chronic exposure may be predicted from high dose rate exposures were discussed. It was concluded that high dose effects were not predictive of low dose effects. It followed that the tools presently available were deemed insufficient to reliably predict risk of low dose exposures in ecosystems. The workshop participants agreed on three major recommendations for a path forward. First, as treating radiation as a single or unique stressor was considered insufficient, the development of a multidisciplinary approach is suggested to address key concerns about multiple stressors in the ecosphere. Second, agreed definitions are needed to deal with the multiplicity of factors determining outcome to low dose exposures as a term can have different meanings in different disciplines. Third, appropriate tools need to be developed to deal with the different time, space and organisation level scales. These recommendations permit a more accurate picture of prospective risks.
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Affiliation(s)
- Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Michael Abend
- Bundeswehr Institute of Radiobiology, Neuherbergstrasse 11, 80937 Munich, Germany.
| | - Francois Bréchignac
- Institute for Radioprotection and Nuclear Safety (IRSN) & International Union of Radioecology, Centre du Cadarache, Bldg 229, St Paul-lez-Durance, France.
| | - David Copplestone
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| | - Stanislav Geras'kin
- Russian Institute of Radiology & Agroecology, Kievskoe shosse, 109km, Obninsk 249020, Russia.
| | - Jessica Goodman
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| | - Nele Horemans
- Belgian Nuclear Research Centre SCK CEN, Biosphere Impact Studies, Boeretang 200, B-2400 Mol, Belgium.
| | - Penny Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
| | - William McBride
- University of California Los Angeles, David Geffen School of Medicine, Department of Radiation Oncology, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA.
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
| | - Anthony O'Hare
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| | - Rao V L Papineni
- Department of Surgery, University of Kansas Medical Center - KUMC (Adjunct), and PACT & Health, Branford, CT, USA.
| | - Gibin Powathil
- Department of Mathematics, College of Science, Swansea University, Singleton Park, Swansea, Wales SA2 8PP, UK.
| | - Paul N Schofield
- Dept of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Jill Sutcliffe
- Low Level Radiation and Health Conference, Ingrams Farm Fittleworth Road, Wisborough Green RH14 0JA, West Sussex, UK.
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, Scotland, UK.
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23
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Cimini S, Gualtieri C, Macovei A, Balestrazzi A, De Gara L, Locato V. Redox Balance-DDR-miRNA Triangle: Relevance in Genome Stability and Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:989. [PMID: 31428113 PMCID: PMC6688120 DOI: 10.3389/fpls.2019.00989] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/15/2019] [Indexed: 05/05/2023]
Abstract
Plants are continuously faced with complex environmental conditions which can affect the oxidative metabolism and photosynthetic efficiency, thus leading to the over-production of reactive oxygen species (ROS). Over a certain threshold, ROS can damage DNA. DNA damage, unless repaired, can affect genome stability, thus interfering with cell survival and severely reducing crop productivity. A complex network of pathways involved in DNA damage response (DDR) needs to be activated in order to maintain genome integrity. The expression of specific genes belonging to these pathways can be used as indicators of oxidative DNA damage and effective DNA repair in plants subjected to stress conditions. Managing ROS levels by modulating their production and scavenging systems shifts the role of these compounds from toxic molecules to key messengers involved in plant tolerance acquisition. Oxidative and anti-oxidative signals normally move among the different cell compartments, including the nucleus, cytosol, and organelles. Nuclei are dynamically equipped with different redox systems, such as glutathione (GSH), thiol reductases, and redox regulated transcription factors (TFs). The nuclear redox network participates in the regulation of the DNA metabolism, in terms of transcriptional events, replication, and repair mechanisms. This mainly occurs through redox-dependent regulatory mechanisms comprising redox buffering and post-translational modifications, such as the thiol-disulphide switch, glutathionylation, and S-nitrosylation. The regulatory role of microRNAs (miRNAs) is also emerging for the maintenance of genome stability and the modulation of antioxidative machinery under adverse environmental conditions. In fact, redox systems and DDR pathways can be controlled at a post-transcriptional level by miRNAs. This review reports on the interconnections between the DDR pathways and redox balancing systems. It presents a new dynamic picture by taking into account the shared regulatory mechanism mediated by miRNAs in plant defense responses to stress.
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Affiliation(s)
- Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Carla Gualtieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
- *Correspondence: Vittoria Locato,
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24
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Bellato M, De Marchi D, Gualtieri C, Sauta E, Magni P, Macovei A, Pasotti L. A Bioinformatics Approach to Explore MicroRNAs as Tools to Bridge Pathways Between Plants and Animals. Is DNA Damage Response (DDR) a Potential Target Process? FRONTIERS IN PLANT SCIENCE 2019; 10:1535. [PMID: 31850028 PMCID: PMC6901925 DOI: 10.3389/fpls.2019.01535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/04/2019] [Indexed: 05/10/2023]
Abstract
MicroRNAs, highly-conserved small RNAs, act as key regulators of many biological functions in both plants and animals by post-transcriptionally regulating gene expression through interactions with their target mRNAs. The microRNA research is a dynamic field, in which new and unconventional aspects are emerging alongside well-established roles in development and stress adaptation. A recent hypothesis states that miRNAs can be transferred from one species to another and potentially target genes across distant species. Here, we propose to look into the trans-kingdom potential of miRNAs as a tool to bridge conserved pathways between plant and human cells. To this aim, a novel multi-faceted bioinformatic analysis pipeline was developed, enabling the investigation of common biological processes and genes targeted in plant and human transcriptome by a set of publicly available Medicago truncatula miRNAs. Multiple datasets, including miRNA, gene, transcript and protein sequences, expression profiles and genetic interactions, were used. Three different strategies were employed, namely a network-based pipeline, an alignment-based pipeline, and a M. truncatula network reconstruction approach, to study functional modules and to evaluate gene/protein similarities among miRNA targets. The results were compared in order to find common features, e.g., microRNAs targeting similar processes. Biological processes like exocytosis and response to viruses were common denominators in the investigated species. Since the involvement of miRNAs in the regulation of DNA damage response (DDR)-associated pathways is barely explored, especially in the plant kingdom, a special attention is given to this aspect. Hereby, miRNAs predicted to target genes involved in DNA repair, recombination and replication, chromatin remodeling, cell cycle and cell death were identified in both plants and humans, paving the way for future interdisciplinary advancements.
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Affiliation(s)
- Massimo Bellato
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering—Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Davide De Marchi
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering—Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Carla Gualtieri
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Elisabetta Sauta
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering—Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Paolo Magni
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering—Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- *Correspondence: Anca Macovei, ; Lorenzo Pasotti,
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering—Centre for Health Technology, University of Pavia, Pavia, Italy
- *Correspondence: Anca Macovei, ; Lorenzo Pasotti,
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