Special Issue "DNA Damage Responses in Plants"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 31 October 2017

Special Issue Editors

Guest Editor
Dr. Alma Balestrazzi

Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, via Ferrata 9-27100, Pavia, Italy
Website | E-Mail
Interests: molecular and cellular biology; plant biotechnology; cell suspension cultures; seed germination; seed priming; genotoxic stress; DNA repair; tyrosyl-DNA phosphodiesterase
Guest Editor
Dr. Susana Araújo

Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Oeiras, Portugal
Website | E-Mail
Interests: abiotic stress responses in plants; seed development; seed invigoration; systems biology; genome integrity; regulation of gene expression
Guest Editor
Dr. Mattia Donà

Gregor Mendel Institute (GMI) Austrian Academy of Science, Vienna Biocenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
Website | E-Mail
Interests: chromatin remodeling; epigenetic modifications; meiotic and somatic recombination; diRNAs; endoreduplication; transposable elements; cell cycle

Special Issue Information

Dear Colleagues,

Maintenance of genome integrity represents a priority for all living organisms that are exposed to genotoxic stress triggered by metabolic by-products and DNA replication stress, as well as environmental chemical pollutants (pesticides, herbicides, heavy metals, ozone) and physical agents (UV and ionizing radiation). Genomic instability results from the accumulation of lesions that cause structural damage to DNA, impairing fundamental cellular processes, such as DNA replication and transcription. DNA damage includes base and sugar modifications, single- and double-strand breaks, DNA-protein cross-links, and abasic sites. Similar to the other eukaryotes, plants have evolved highly conserved, specialized DNA repair pathways (base excision repair, mismatch repair, nucleotide excision repair, and double-strand break repair which comprises both homologous recombination and non-homologous end-joining), targeting the different types of lesions to ensure the integrity of genetic information. However, being sessile organisms, plants are continuously exposed to genotoxic stress and their peculiar photosynthetic activity, localized within chloroplasts, is a constant source of reactive oxygen species and is extremely harmful to lipids, proteins and nucleic acids.

DNA damage response (DDR) is the sum of multiple cellular pathways, triggered on DNA damage detection in order to activate downstream mechanisms allowing the temporary cell cycle arrest and DNA repair. When damage is accumulated above a critical threshold and DNA repair is not able to reverse lesions, cells undergo programmed cell death, avoiding genetic defects that might impair plant development or limit crop performance in terms of seed quality and yields. In this context, DDR systems act as crucial regulators of cell cycle checkpoints, revealing that DNA damage sensing and signaling are strictly linked to growth. DNA lesions contribute to cell aging and there is renewed interest in plant telomere biology in the context of DNA repair and recombination. Plants can also better withstand genotoxic injury by activating endoreduplication mechanisms. Plant genomes host highly conserved DDR components, both regulators and effectors, but there are several plant-specific features of DDR that make this process unique compared to animals.

This Special Issue aims at providing an update of the last findings in basic and applied plant DDR research on model and crop plants investigated in vitro and/or in the field, under abiotic and biotic stress conditions or exposed to specific genotoxins. Original research articles, research notes, and review articles are welcomed.

Manuscripts should address, but are not restricted to the following topics:

  • Relevance of microRNAs in DNA damage response
  • Molecular mechanisms underlying DNA damage sensing and repair in plants
  • The DNA damage response in seeds
  • DNA repair in the context of genome editing
  • Genotoxic effects of abiotic stress
  • High-throughput approaches for the study of the DNA damage response in plants
  • The epigenetic components of the DNA damage response
  • Plant telomeres
  • The plant nucleolus
  • The DNA damage response in the context of mutation breeding
  • Bioinformatics tools for the study of DNA repair
  • Models for investigating DNA repair and mutagenesis mechanisms in plants
  • Transcription hubs controlling the DNA damage response

Dr. Alma Balestrazzi
Dr. Susana Araújo
Dr. Mattia Donà
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers

This special issue is now open for submission, see below for planned papers.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Working Title: Genotoxicity response in Medicago truncatula cells challenged with the human tyrosyl-DNA phosphodiesterase 1 (hTdp1) inhibitor NSC120686 

Putative Authors: Maria Elisa Sabatini1,#,⸹, Andrea Pagano1,⸹, Sofia Grandi1, Lorenzo Furiosi1, Alma Balestrazzi,1 Anca Macovei,1,* 

Affiliations: 1 Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100-Pavia, Italy

# Present Address: Viral Control of Cellular Pathways and Biology of Tumorigenesis Unit, European Institute of Oncology (IEO), via Adamello 16, 20139 Milano, Italy

Equal contribution

*Correspondence to: Anca Macovei

Abstract : The hTdp1 (human tyrosyl-DNA phosphodiesterase 1) inhibitor NSC120686 had been used as a pharmacophoric model to identify new compounds able to inhibit the hTdp1 activity, as this protein is associated with severe disorders in humans. In plants, the characterization of the Tdp1 functions is still at incipient phases. The present work provides evidence of the genotoxic effects of NSC120686, used for the first time in plant cells. The originality of our study consists in using the hTdp1 inhibitor in Medicago truncatula cells which contain two Tdp1 isoforms, unlike the human cells where only one gene is present. M. truncatula calli were exposed to increasing (75, 150 and 300 mM) concentrations of NSC120686. A Diffusion Assay test show that the highest concentration is responsible inducing cell death in more than 50% of cells. Moreover, upon exposure of to 300 mM NSC120686, a significant increase in the occurrence of DNA damage was evidenced, as revealed by Singe Cell Gel Electrophoresis. The expression profiles of MtTdp1a and MtTdp1b genes were equally affected by NSC120686. To gain a deeper insight into the DNA repair response induced by this inhibitor, we assessed the expression profiles of genes involved in Tdp1-alternative repair pathways. The exposure to NSC120686 resulted in modulation of multiple DNA repair genes, as previously highlighted in MtTdp1a-depleted cells. Particularly, the NSC120686-treated calli and untreated MtTdp1a-depleted calli share similar PCD and necrosis levels. These results are indicative for the use of hTdp1 inhibitor as a tool for future studies aiming to decipher the peculiar roles of the plant Tdp1 genes.

 

Working Title: Genome and epigenome surveillance processes underlying UV exposure in plants

Putative Authors: Jean Molinier

Affiliations: Institut de biologie moléculaire des plantes, Strasbourg, France

Abstract: Land plants and other photosynthetic organisms (algae, bacteria) use the beneficial effect of sun light as source of energy for the photosynthesis and as a major source of information from the environment. However, the ultraviolet (UVs) component of sunlight also produce several types of damage, which can affect cell and (epi)genome integrities, interfering with growth and development. In order to reduce the deleterious effects of UVs, photosynthetic organisms combine physiological adaptation and several types of DNA repair pathways to avoid dramatic changes in (epi)genome structure. Therefore, plants may have taken an evolutionary benefit of combining genome and epigenome surveillance processes, to efficiently deal with the deleterious effects of UV radiation. This review will present the different mechanisms activated upon UV exposure that contribute to maintain genome and epigenome integrities.

 

Working Title: A 26S proteasome subunit RPT5A is essential for normal leaf development through the alleviation of DNA damage under zinc deficiency

Putative Authors: Naoyuki Sotta1,†, Takuya Sakamoto2,†, Sachihiro Matsunaga2, Toru Fujiwara1,* 

Affiliations1Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
2Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan†These authors equally contributed to this work

†These authors equally contributed to this work

*Corresponding author

Abstract: Leaf development in plant is tightly regulated, including control of dorsoventral (adaxial/abaxial) patterning. It has been reported that some 26S proteasome subunits are required for the proper adaxial/abaxial polarity establishment. In the present study, we revealed that in Arabidopsis thaliana, a mutation in RPT5A, a subunit of 26S proteasome, causes abnormally narrow true leaves in a combination with low zinc conditions. qRT-PCR revealed that DNA damage marker genes in leaves were induced by zinc deficiency. Among them, PARP1 was more strongly induced by zinc deficiency in rpt5a mutants compared to wild type, suggesting that accumulation of single strand break is responsible for the abnormal leaf development. Treatment with DNA damage causing reagent, Zeocin, induced the development of the narrow leaves, even in the wild type under sufficient zinc conditions, which established that DNA damage is sufficient to induce the development of the abnormally narrow true leaves. These findings demonstrate that RPT5A is essential for alleviation of DNA damage accumulation under zinc deficiency, and that controlling DNA damage is critical for normal leaf development.

 

Working Title: Scaffolding for repair: Understanding molecular functions of the structural maintenance of chromosomes SMC5/6 complex in plants

Putative Authors: Mariana Diaz1 and Ales Pecinka1,*

Affiliations1Centre of Plants Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences v.v.i., Šlechtitelů 31, 783 71 Olomouc - Holice, Czechia

*Corresponding author

Abstract: Chromosomes need to be continuously reorganized into different functional domains and repaired during various cellular processes. The key factors involved in large-scale chromatin organization are the structural maintenance of chromosomes (SMC) complexes, where cohesin connects the sister chromatids, condensin compacts the chromosomes and SMC5/6 preserves genome integrity. Here, we provide overview on the current knowledge of SMC5/6 complex functions in plants. The SMC5/6 complex consists of the heterodimeric SMC backbone and six additional non-SMC elements (NSE). All plant components share homology with the fungal and animal orthologs, except for the ASAP1 and SNI1, which are plant-specific proteins structurally similar to the yeast NSE5 and NSE6, respectively. The SMC5/6 functions are essential and strong effect mutations in non-duplicated subunits result in lethality. There is solid evidence that SMC5/6 facilitates DNA damage repair in plant somatic and meiotic cells, but neither the underlying mechanism nor the critical damage type are known. Recent studies suggest that SMC5/6 complex is involved in a number of other processes including suppression of immune responses, stress resistance, control of flowering time and seed development. We envision that the future plant SMC5/6 research will focus on addressing both the canonical and the non-canonical functions, characterizing molecular activity and interacting partners of individual subunits and integrate the complex into molecular pathways.

 

Working Title: DNA Damage Repair System in Plants: A Worldwide Research Update

Putative Authors: Gimenez, E.1 and Manzano, F.1

Affiliations: 1 Research Central Services. University of Almeria. Crta. Sacramento s/n. 04120 Almeria, Spain.

Abstract: Living organism are usually exposed to varying DNA damaging agents. So mechanisms to detect and repair diverse DNA lesions have been developed in all organisms with the aim to maintain genome integrity. Defects in DNA repair machinery contributing to cancer, certain diseases and aging. Therefore, conserving genomic sequence in organisms is key for the perpetuation of life. The machinery of DNA damage repair (DDR) in prokaryotes and eukaryotes are similar. Plants also share mechanisms to DNA repair with animals, although they differ in other important details. Plants have been surprisingly less investigated than other living organisms in this context, despite numerous lethal mutations in animals are viable in plants. In this article, a historical review of the DDR systems is made, reviewing the current literature on this subject, and carry out a bibliometric analysis of DDR research in plants. The bibliometric analyses prove that the first study about DDR system in plants (1987) was published thirteen years later than in other living organisms (1975). Despite the increase in number of papers about DDR mechanism in plants during last decades, nowadays number of articles published by year about DDR system in plants only represents 10% of total number of articles about DDR. As expected, percentage of studies published about DDR system in plants increases in the subject area Agricultural and Biological Sciences and diminishes in Medicine with respect to DDR studies in other living organisms. In order to study the evolution of research about DDR system in plants, in this article the authors make a historical review of the DDR systems, review the current literature on this subject, and carry out a bibliometric analysis of DDR research in plants.

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