File Name: dna repair mutagenesis and other responses to dna damage .zip
- Historical Perspective on the DNA Damage Response
- DNA Damage and Repair
- Mechanisms of DNA damage, repair and mutagenesis
- DNA damage (naturally occurring)
Historical Perspective on the DNA Damage Response
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction.
It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited.
However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis. Moreover, abnormalities in DNA repair which proved to be lethal for animal models are tolerated in plant genomes, although sensitivity to DNA damaging agents is retained. Due to the high conservation of DNA repair processes and factors mediating them among eukaryotes, genes and proteins that have been identified in model species may serve to identify homologous sequences in other species, including crop plants, in which these mechanisms are poorly understood.
Crop breeding programs have provided remarkable advances in food quality and yield over the last century. Breeding requires genetic diversity. The biological impact of any mutagenic agent used for the creation of genetic diversity depends on the chemical nature of the induced lesions and on the efficiency and accuracy of their repair.
More recent targeted mutagenesis procedures also depend on host repair processes, with different pathways yielding different products. Enhanced understanding of DNA repair processes in plants will inform and accelerate the engineering of crop genomes via both traditional and targeted approaches. Cellular DNA of living organisms normally suffers damage which may arise endogenously or can be induced by a variety of external genotoxins including ultraviolet light, ionizing radiation, and chemical mutagens.
The most frequently encountered injuries to the DNA- often induced through inevitable errors of internal metabolism- are modifications to nucleotides, intra- or inter-strand cross-links, and breaks of the phosphodiester bonds. If damaged DNA is not repaired it may have difficulties in being properly organized, replicated, or transcribed. The impairment of such essential molecular processes affects cellular functionality and may disturb the normal development of the whole organism Britt, ; Polyn et al.
Plants are particularly vulnerable to the DNA damaging factors present ubiquitously in the air, soil, and water. Hence, they have evolved a complex network of mechanisms of DNA damage detection and repair dedicated to ensure their genomic stability through removal of the DNA lesions and reconstitution of the original genetic information Bray and West, ; Yoshiyama et al. An intrinsic feature of certain DNA repair pathways is that they are not error-free, leading to potentially transmissible mutational alterations.
The error-prone nature of some DNA repair mechanisms, however, increases the genetic diversity and variability of the populations, thus contributing to the evolution of plant genomes Schuermann et al.
Chemical or radiation-induced mutagenesis has been a powerful tool for creation and improvement of economically important crop varieties Parry et al. The mutations occurring in the plant genome after particular mutagenic treatment are determined by both the spectrum of lesions generated by the mutagen and the specificity and efficiency of DNA repair pathways involved. Therefore, our understanding of DNA repair mechanisms and their regulation in plants is an essential requirement for the effective utilization of mutation technologies in future crop improvement.
It is generally accepted that the choice of a repair pathway and its action is primarily dependent on the type of the cell, its proliferation status, cell cycle stage, as well as on the type of the lesion and its genomic context Britt, Plants do not choose where they live and cannot escape unfavorable environmental impacts.
Therefore, they need strictly controlled but flexible DNA repair mechanisms responsive to the changing environment. Indeed, common external factors such as light regimes, temperature or water availability were shown to dictate the specific activation and efficiency of certain DNA repair pathways, such as recombination or photorepair in various plants Li et al.
Rapidly dividing and differentiated cells of different plant organs do not equally utilize the whole available repertoire of DNA repair mechanisms Kimura et al. Moreover, the capability of plants to maintain their genomic integrity was shown to decrease with plant age mainly due to a reduction in the efficiency and relative contribution of the employed DNA repair pathways Golubov et al. With some exceptions plants have been shown to possess all common DNA repair mechanisms which have been initially described to a greater extent in the other eukaryotic systems, such as yeast and mammals Britt, Photoreactivation of UV-induced DNA damage is one of the primary DNA repair mechanisms needed by plants on a daily basis because of their inherent necessity and exposure to solar light.
MMR has been implicated in the removal of incorrectly paired nucleotides and the UV-induced photolesions from the genome of higher plants Culligan and Hays, ; Lario et al. Some of the repair mechanisms as photoreactivation are highly specialized for a particular damage, however, others, like excision or recombination pathways may deal with a variety of lesions Ries et al.
Significant progress in elucidation of DNA damage repair in higher plants has been made mainly utilizing the small dicot Arabidopsis thaliana as a model Hays, The isolation and characterization of the first plant DNA repair genes involved in the photorepair, excision repair, HR and NHEJ have been initially based on the homologous sequence information available from other organisms Batschauer, ; Britt et al. During the last decade significant progress has also been made in the molecular characterization of the repair pathways and genes mediating these processes in important crop plants such as rice, spinach, cucumber, tomato, wheat, barley, etc.
The headlong progress of molecular technologies has expanded the number of sequenced crop genomes and thus contributed to the advancements made in the field of plant DNA repair as well Singh et al. In addition to Arabidopsis , rice is the other higher plant with relatively well characterized DNA repair mechanisms with respect to the influence of various developmental and environmental factors on their activation and efficiency, as well as regarding the identification and regulation of genes involved in the DNA repair and protection mechanisms Ueda and Nakamura, The sequence of the rice genome has been useful for the efficient identification of orthologous genes, regulatory regions and gene functions in other cereals Goff et al.
The intensive research performed on Arabidopsis and rice has enormously increased the current knowledge on the molecular nature and regulation of DNA damage and repair mechanisms in plants. However, such studies should be expanded to include a larger number of model and crop species if we want to have a clearer picture of the capacity of plant genomes to overcome the biological impacts of different genotoxins and to adapt to the changing environmental stress conditions.
DNA lesions are divided into two main categories: single- and double-stranded. Schematic representation of the major DNA lesions induced by various external and endogenous factors, and the types of DNA repair mechanisms employed to remove them from the eukaryotic genome. A major source of endogenous DNA lesions is the intracellular metabolism which increases the concentration of free radicals in the environment surrounding the DNA; in plants, ROS are especially ubiquitous in the chloroplasts and mitochondria Sharma et al.
AP sites may arise by spontaneous hydrolysis of the N-glycoside bond or as intermediates resulting from the repair of deaminated, alkylated or oxidized bases Cooke et al. Monofunctional alkylators such as MMS and EMS are the chemical agents most widely utilized to obtain mutagenized plants aimed at both crop improvement and reverse genetics studies Till et al. Bi- and polyfunctional alkylating agents as well as many carcinogenic compounds form intra-strand cross links between adjacent guanines or bulky adducts to nucleotides which significantly distort the conformation of the DNA molecule.
Psoralens and mitomycin C can also induce inter-strand cross-links connecting the two opposite DNA strands thus effectively blocking the replication and transcription machineries De Silva et al. Ionizing radiation in the form of gamma- and X-rays as well as ion-beams is another commonly employed DNA damaging agent with high mutagenic potential in plants van Harten, Oxidation products 8-oxoguanine, thymine glycols, etc.
Moreover, IR induces multiple damaged sites representing two or more closely localized lesions on the same or the opposite DNA strands Shikazono et al. Recent research shows that such a cluster might transform to DSB as a result of excision repair, but this probability depends on the local chromatin environment Cannan et al. It was generally thought that IR-induced DSBs are spread rather randomly in the genome; however, an accumulating body of evidence reveals the influence of chromatin organization and nuclear matrix proteins on DSB distribution Lavelle and Foray, Double-strand breaks are also produced by a variety of radiomimetic agents, so-called because of their ability to act on the DNA by mimicking the effects of IR.
The anticancer drug BLM which is frequently utilized in the studies of DSB formation and repair in mammalian cells has been shown to effectively generate DSB in many plant systems as well. BLMs are a family of glycopeptides which cannot diffuse freely through the cellular membranes due to their hydrophilic properties, but are transferred into the cell by a receptor-mediated endocytosis Chen and Stubbe, In addition, abasic sites with closely opposed SSB can also result from the BLM action in a frequency exceeding that expected by the coincidence of two independent damaging events.
The action of BLM is modulated by the local nucleosome structure and higher-order chromatin organization Smith et al. REs have a high clastogenic activity on the genomes of mammals and plants Obe et al. The unique selection ability of rare-cutting endonucleases has been used to develop highly specialized transgenic systems in order to monitor somatic HR in various plants such as Arabidopsis , tobacco and rice Puchta et al.
The more recently developed chimeric nucleases designed to target particular genomic locations and introduce DSB at specific DNA sequences have the potential to broaden the studies of DSB rejoining in plant genomes see later. Ultraviolet radiation, being a component of sunlight, is the most common genome-damaging agent ubiquitously found on earth Britt, It belongs to the electromagnetic radiation spectrum with wavelengths ranging from to nm.
UV light generates two major types of lesions in DNA — CPDs and PPs, whose relative proportion and non-random distribution within the eukaryotic genome depends on the sequence composition and chromatin structure Pfeifer, ; Kwon and Smerdon, ; Law et al.
The presence of CPDs has the potential to block the transcribing complexes thus completely altering the relative expression pattern of genes Tornaletti et al.
During replication, however, dimers can be bypassed by specialized translesion DNA polymerases which increase the cellular tolerance to UV damage, also in plants Britt, ; Curtis and Hays, ; Nakagawa et al.
UV radiation may also induce oxidative DNA damage, mediated predominantly, but not exclusively, by endogenous photosensitizers that generate free radicals upon their activation. As in plants pyrimidine dimers are primarily repaired by photoreactivation, it might be speculated that oxidative DNA damage, known to be eliminated by the error-prone excision repair, could also contribute to the UV-associated mutagenicity and plant genomic instability.
Photoreactivation is a rare example of a simple and error-free pathway for the reversal, rather than the removal of DNA damage. It is performed by a single, lesion-specific enzyme called photolyase.
Two different types of photolyase enzymes have been established in plants which are specialized to reverse selectively the photoproducts photolyase type or the CPD class II photolyase. Photolyases bind to their specific damage-substrate within the double-stranded DNA in a light-independent manner. However, in order to get energy for correcting the lesion they need to be excited by photons from the blue or near UV-A spectrum Brettel and Byrdin, Figure 2.
The exact chemistry of the photorepair reactions differ between the two photolyase types, however, the final products are monomerized pyrimidine bases and unchanged nucleotide sequence Yi and He, The error-free nature of photoreactivation makes it the preferable and most effective mechanism utilized by plants to quickly reduce the negative effects of DNA photodimers generated upon their normal exposure to solar radiation Dany et al.
However, inability of the cell to photorepair may lead to a switch in the transcriptional response of UV stressed plants activating the completely different DNA repair pathway such as HR Molinier et al. Schematic representation of the photoreactivation mechanism utilized by plants to repair UV-induced pyrimidine dimers. On the right is presented a hypothetical mode of CPD photoreactivation, which might operate within the open DNA regions generated during transcription, replication and repair processes.
Future research is needed to prove or reject such an intriguing concept. Effective light-dependent repair of DNA photolesions has been demonstrated in all plants investigated so far and the lesion-specific photolyases identified in Arabidopsis Pang and Hays, ; Chen et al.
In view of the importance of the photorepair mechanism for plant growth and development under UV exposure it is not surprising that the CPD photolyase has become one of the most intensively studied DNA repair genes in higher plants.
Plant CPD photolyases analyzed so far, particularly the Arabidopsis and rice enzymes, show similar chromophore compositions, consisting of both a reduced FADH and a pterin-like cofactor Waterworth et al. The cryptochromes work mainly as photoreceptors regulating plant development as they do not possess the standard photorepair activity characteristic of the photolyase proteins. These intriguing observations have inspired the hypothesis that DASH-type cryptochromes might be involved in the repair of the locally unwound DNA regions generated by the active matrix processes such as replication, transcription, and DNA repair Selby and Sancar, ; Pokorny et al.
Chromatin organization affects not only the formation, but also the repair of UV-induced pyrimidine dimers. In yeast the access of photolyase proteins to the UV-damaged DNA was inhibited in the compacted chromatin, whereas the local nucleosome unpacking and repositioning facilitated photoreactivation Thoma, It has been recently shown that histone-binding proteins of the ASF group are essential for CPD repair in Arabidopsis specifically under light conditions Lario et al.
Moreover, chromatin factors and histone acetylation have been important prerequisites for UV damage removal in both Arabidopsis and maize, suggesting an important role of chromatin restructuring for the effective photorepair process also in plants Campi et al.
Currently the data obtained in different plant species concerning the distribution of photolyase proteins and their activities within the intracellular compartments are rather controversial.
A number of studies have shown that CPD photolyase is present exclusively in the nucleus thus implying that extranuclear DNA in plant mitochondria and chloroplasts cannot be photoreactivated. Indeed, fractionated extracts from spinach chloroplasts were found to be free of the photolyase activity otherwise contained in whole leave preparations Hada et al. The lack of CPD repair from spinach organelles confirmed the earlier findings showing that young Arabidopsis seedlings were able to remove CPD only from the nuclear genome, but not from the chloroplast and mitochondrial DNA sequences Chen et al.
In line with the idea, in Arabidopsis it was demonstrated that the CPD photolyase protein is transported only into the nucleus, but not in the chloroplasts Kaiser et al. On the other hand, light-dependent repair with varying efficiency was found in the individual soybean and maize genes localized not only in the nucleus but also in the chloroplast and mitochondrial genomes Cannon et al. The fully developed Arabidopsis leaves also repaired CPDs and PPs in the nuclear and chloroplast DNA upon prolonged blue light exposure and restored the replication of both nuclear and organellar genomes.
These observations illustrate that young and mature plants may differ in their DNA repair capacity, which in turn may affect their overall tolerance to UV stress Draper and Hays, Moreover, data obtained in rice reveal that CPD photolyase is localized not only in the nucleus, but is also active in the mitochondria and plastids.
DNA Damage and Repair
Living organisms are continuously exposed to a myriad of DNA damaging agents that can impact health and modulate disease-states. However, robust DNA repair and damage-bypass mechanisms faithfully protect the DNA by either removing or tolerating the damage to ensure an overall survival. Deviations in this fine-tuning are known to destabilize cellular metabolic homeostasis, as exemplified in diverse cancers where disruption or deregulation of DNA repair pathways results in genome instability. Because routinely used biological, physical and chemical agents impact human health, testing their genotoxicity and regulating their use have become important. Preserving genomic sequence information in living organisms is important for the perpetuation of life.
The integrity of the genome is essential to the health of the individual and to the reproductive success of a species. Transmission of genetic information is in a selective balance between two opposing forces, the maintenance of genetic stability versus elimination of mutational change and loss of evolutionary potential. Caenorhabditis elegans provides many advantages for the study of DNA surveillance and repair in a multicellular organism. Several genes have been identified by mutagenesis and RNA interference that affect DNA damage checkpoint and repair functions. Many of these DNA damage response genes also play essential roles in DNA replication, cell cycle control, development, meiosis and mitosis.
response to DNA damage, is activated to get rid of cells. with extensive genome Exogenous DNA damage, on the other hand, occurs when.
Mechanisms of DNA damage, repair and mutagenesis
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity.
DNA damage (naturally occurring)
Damage to cellular DNA is involved in mutagenesis and the development of cancer. The DNA in a human cell undergoes several thousand to a million damaging events per day, generated by both external exogenous and internal metabolic endogenous processes. Changes to the cellular genome can generate errors in the transcription of DNA and ensuing translation into proteins necessary for signaling and cellular function.
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Martin L. Smith, Young R. The regulation of DNA excision repair pathways by p53 and its downstream genes is an emerging body of literature, largely distinct and separable from the more-studied cell cycle arrest and apoptosis responses regulated by p Regulation of nucleotide excision repair of UV-damage by p53 and its downstream genes Gadd45 and p48XPE has been well-documented, but much remains to be done in elucidating mechanisms.
Genome integrity is challenged by DNA damage from both endogenous and environmental sources. This damage must be repaired to allow both RNA and DNA polymerases to accurately read and duplicate the information in the genome. These kinases improve the efficiency of DNA repair by phosphorylating repair proteins to modify their activities, by initiating a complex series of changes in the local chromatin structure near the damage site, and by altering the overall cellular environment to make it more conducive to repair.
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. Other lesions induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and DNA crosslinkages interstrand crosslinks or ICLs. The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular environment.