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DNA Damage Repair in Plants
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DNA Damage Repair 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: closed (25 September 2020) | Viewed by 22184

Special Issue Editors

Dr. Jean Molinier

E-Mail Website
Guest Editor
Institut de Biologie Moleculaire des Plantes, Strasbourg, France
Interests: DNA repair; small RNA; genome-epigenome dynamics; abiotic stress
Special Issues, Collections and Topics in MDPI journals
Dr. Jose Manuel Gualberto

E-Mail Website
Guest Editor
Institut de Biologie Moleculaire des Plantes, Strasbourg, France
Interests: DNA repair; organellar genome; genome integrity maintenance

Special Issue Information

Dear Colleagues,

All living organisms have to cope with environmental stresses that affect the integrity of their genomes, interfering with genomic expression programs. It is therefore crucial to understand how the different DNA repair processes act to prevent deleterious genome alterations, while at the same time allowing the genome flexibility necessary for evolution.

Plants represent a material of choice to provide innovative knowledge in genome responses to DNA damage, due to their sessile life style, their phenotypic plasticity, and the availability of their large set of unique genetic resources. Deciphering the genomic responses to genotoxic stress also considerably improves our understanding of genome evolution.

This Special Issue calls for original articles, reviews, and perspectives that contribute to unveiling how DNA repair pathways act in the control of genome stability and plasticity in the plant cell.

Dr. Jean Molinier
Dr. Jose Manuel Gualberto
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 submissions that pass pre-check are 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 2600 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.

Keywords

  • excision repair
  • recombination
  • nucleus
  • organelles
  • evolution
  • genome plasticity
  • epigenome

Published Papers (6 papers)

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Research

Jump to: Review, Other

12 pages, 2960 KiB  
Article
CRISPR/Cas9 Induced Somatic Recombination at the CRTISO Locus in Tomato
by Ilan Ben Shlush, Aviva Samach, Cathy Melamed-Bessudo, Daniela Ben-Tov, Tal Dahan-Meir, Shdema Filler-Hayut and Avraham A. Levy
Genes 2021, 12(1), 59; https://doi.org/10.3390/genes12010059 - 31 Dec 2020
Cited by 23 | Viewed by 3428
Abstract
Homologous recombination (HR) in somatic cells is not as well understood as meiotic recombination and is thought to be rare. In a previous study, we showed that Inter-Homologous Somatic Recombination (IHSR) can be achieved by targeted induction of DNA double-strand breaks (DSBs). Here, [...] Read more.
Homologous recombination (HR) in somatic cells is not as well understood as meiotic recombination and is thought to be rare. In a previous study, we showed that Inter-Homologous Somatic Recombination (IHSR) can be achieved by targeted induction of DNA double-strand breaks (DSBs). Here, we designed a novel IHSR assay to investigate this phenomenon in greater depth. We utilized F1 hybrids from divergent parental lines, each with a different mutation at the Carotenoid isomerase (CRTISO) locus. IHSR events, namely crossover or gene conversion (GC), between the two CRTISO mutant alleles (tangerine color) can restore gene activity and be visualized as gain-of-function, wildtype (red) phenotypes. Our results show that out of four intron DSB targets tested, three showed DSB formation, as seen from non-homologous end-joining (NHEJ) footprints, but only one target generated putative IHSR events as seen by red sectors on tangerine fruits. F2 seeds were grown to test for germinal transmission of HR events. Two out of five F1 plants showing red sectors had their IHSR events germinally transmitted to F2, mainly as gene conversion. Six independent recombinant alleles were characterized: three had truncated conversion tracts with an average length of ~1 kb. Two alleles were formed by a crossover as determined by genotyping and characterized by whole genome sequencing. We discuss how IHSR can be used for future research and for the development of novel gene editing and precise breeding tools. Full article
(This article belongs to the Special Issue DNA Damage Repair in Plants)
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25 pages, 3798 KiB  
Article
The Importance of ATM and ATR in Physcomitrella patens DNA Damage Repair, Development, and Gene Targeting
by Martin Martens, Ralf Horres, Edelgard Wendeler and Bernd Reiss
Genes 2020, 11(7), 752; https://doi.org/10.3390/genes11070752 - 06 Jul 2020
Cited by 8 | Viewed by 3483
Abstract
Coordinated by ataxia-telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR), two highly conserved kinases, DNA damage repair ensures genome integrity and survival in all organisms. The Arabidopsis thaliana (A. thaliana) orthologues are well characterized and exhibit typical mammalian characteristics. We mutated the [...] Read more.
Coordinated by ataxia-telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR), two highly conserved kinases, DNA damage repair ensures genome integrity and survival in all organisms. The Arabidopsis thaliana (A. thaliana) orthologues are well characterized and exhibit typical mammalian characteristics. We mutated the Physcomitrella patens (P. patens) PpATM and PpATR genes by deleting functionally important domains using gene targeting. Both mutants showed growth abnormalities, indicating that these genes, particularly PpATR, are important for normal vegetative development. ATR was also required for repair of both direct and replication-coupled double-strand breaks (DSBs) and dominated the transcriptional response to direct DSBs, whereas ATM was far less important, as shown by assays assessing resistance to DSB induction and SuperSAGE-based transcriptomics focused on DNA damage repair genes. These characteristics differed significantly from the A. thaliana genes but resembled those in yeast (Saccharomyces cerevisiae). PpATR was not important for gene targeting, pointing to differences in the regulation of gene targeting and direct DSB repair. Our analysis suggests that ATM and ATR functions can be substantially diverged between plants. The differences in ATM and ATR reflect the differences in DSB repair pathway choices between A. thaliana and P. patens, suggesting that they represent adaptations to different demands for the maintenance of genome stability. Full article
(This article belongs to the Special Issue DNA Damage Repair in Plants)
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Review

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33 pages, 4263 KiB  
Review
The Dark Side of UV-Induced DNA Lesion Repair
by Wojciech Strzałka, Piotr Zgłobicki, Ewa Kowalska, Aneta Bażant, Dariusz Dziga and Agnieszka Katarzyna Banaś
Genes 2020, 11(12), 1450; https://doi.org/10.3390/genes11121450 - 02 Dec 2020
Cited by 16 | Viewed by 4265
Abstract
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others [...] Read more.
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented. Full article
(This article belongs to the Special Issue DNA Damage Repair in Plants)
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18 pages, 1847 KiB  
Review
Plant Organellar DNA Polymerases Evolved Multifunctionality through the Acquisition of Novel Amino Acid Insertions
by Antolín Peralta-Castro, Paola L. García-Medel, Noe Baruch-Torres, Carlos H. Trasviña-Arenas, Víctor Juarez-Quintero, Carlos M. Morales-Vazquez and Luis G. Brieba
Genes 2020, 11(11), 1370; https://doi.org/10.3390/genes11111370 - 19 Nov 2020
Cited by 4 | Viewed by 2617
Abstract
The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative [...] Read more.
The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative DNAPs incorporate nucleotides with high fidelity and processivity, whereas TLS DNAPs are low-fidelity polymerases with distributive nucleotide incorporation. Plant organelles (mitochondria and chloroplast) are replicated by family-A DNA polymerases that are both replicative and TLS DNAPs. Furthermore, plant organellar DNA polymerases from the plant model Arabidopsis thaliana (AtPOLIs) execute repair of double-stranded breaks by microhomology-mediated end-joining and perform Base Excision Repair (BER) using lyase and strand-displacement activities. AtPOLIs harbor three unique insertions in their polymerization domain that are associated with TLS, microhomology-mediated end-joining (MMEJ), strand-displacement, and lyase activities. We postulate that AtPOLIs are able to execute those different functions through the acquisition of these novel amino acid insertions, making them multifunctional enzymes able to participate in DNA replication and DNA repair. Full article
(This article belongs to the Special Issue DNA Damage Repair in Plants)
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17 pages, 1210 KiB  
Review
All You Need Is Light. Photorepair of UV-Induced Pyrimidine Dimers
by Agnieszka Katarzyna Banaś, Piotr Zgłobicki, Ewa Kowalska, Aneta Bażant, Dariusz Dziga and Wojciech Strzałka
Genes 2020, 11(11), 1304; https://doi.org/10.3390/genes11111304 - 04 Nov 2020
Cited by 29 | Viewed by 5204
Abstract
Although solar light is indispensable for the functioning of plants, this environmental factor may also cause damage to living cells. Apart from the visible range, including wavelengths used in photosynthesis, the ultraviolet (UV) light present in solar irradiation reaches the Earth’s surface. The [...] Read more.
Although solar light is indispensable for the functioning of plants, this environmental factor may also cause damage to living cells. Apart from the visible range, including wavelengths used in photosynthesis, the ultraviolet (UV) light present in solar irradiation reaches the Earth’s surface. The high energy of UV causes damage to many cellular components, with DNA as one of the targets. Putting together the puzzle-like elements responsible for the repair of UV-induced DNA damage is of special importance in understanding how plants ensure the stability of their genomes between generations. In this review, we have presented the information on DNA damage produced under UV with a special focus on the pyrimidine dimers formed between the neighboring pyrimidines in a DNA strand. These dimers are highly mutagenic and cytotoxic, thus their repair is essential for the maintenance of suitable genetic information. In prokaryotic and eukaryotic cells, with the exception of placental mammals, this is achieved by means of highly efficient photorepair, dependent on blue/UVA light, which is performed by specialized enzymes known as photolyases. Photolyase properties, as well as their structure, specificity and action mechanism, have been briefly discussed in this paper. Additionally, the main gaps in our knowledge on the functioning of light repair in plant organelles, its regulation and its interaction between different DNA repair systems in plants have been highlighted. Full article
(This article belongs to the Special Issue DNA Damage Repair in Plants)
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Other

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6 pages, 826 KiB  
Commentary
Effects of mitoTALENs-Directed Double-Strand Breaks on Plant Mitochondrial Genomes
by Shin-ichi Arimura
Genes 2021, 12(2), 153; https://doi.org/10.3390/genes12020153 - 25 Jan 2021
Cited by 7 | Viewed by 2334
Abstract
Mitochondrial genomes in flowering plants differ from those in animals and yeasts in several ways, including having large and variable sizes, circular, linear and branched structures, long repeat sequences that participate in homologous recombinations, and variable genes orders, even within a species. Understanding [...] Read more.
Mitochondrial genomes in flowering plants differ from those in animals and yeasts in several ways, including having large and variable sizes, circular, linear and branched structures, long repeat sequences that participate in homologous recombinations, and variable genes orders, even within a species. Understanding these differences has been hampered by a lack of genetic methods for transforming plant mitochondrial genomes. We recently succeeded in disrupting targeted genes in mitochondrial genomes by mitochondria-targeted transcription activator-like effector nucleases (mitoTALENs) in rice, rapeseed, and Arabidopsis. Double-strand breaks created by mitoTALENs were repaired not by non-homologous end-joining (NHEJ) but by homologous recombination (HR) between repeats near and far from the target sites, resulting in new genomic structures with large deletions and different configurations. On the other hand, in mammals, TALENs-induced DSBs cause small insertions or deletions in nuclear genomes and degradation of mitochondrial genomes. These results suggest that the mitochondrial and nuclear genomes of plants and mammals have distinct mechanisms for responding to naturally occurring DSBs. The different responses appear to be well suited to differences in size and copy numbers of each genome. Full article
(This article belongs to the Special Issue DNA Damage Repair in Plants)
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