DNA Repair is a collection of processes in which cells identify and repair damage to DNA molecules that encode their genome. In human cells, normal metabolic activity and environmental factors such as radiation can cause DNA damage, which produces as many as 1 million molecular lesions per cell per day. Many of these lesions cause structural damage to DNA molecules and can alter or eliminate the ability of cells to transcribe the genes encoded in the affected DNA. Other lesions induce potentially harmful mutations in cell genes, affecting the survival of daughter cells after undergoing mitosis. As a result, the DNA repair process continues to be active because it responds to damage in the structure of DNA. When the normal repair process fails, and when cellular apoptosis does not occur, irreversible DNA damage can occur, including multiple strand breaks and DNA crosslinkages (interstrand crosslinks or ICLs). This may eventually lead to malignant tumors, or cancer corresponding to two hit hypotheses.
The rate of DNA repair depends on many factors, including cell type, cell age, and extracellular environment. Cells that have accumulated large amounts of DNA damage, or which are no longer effective at repairing damage to their DNA, may enter any of three possible conditions:
- irreversible dormancy state, known as senescence
- cell suicide, also known as apoptosis or programmed cell death
- unregulated cell division, which can lead to the formation of cancerous tumors
The ability to repair a cell's DNA is essential to its genome's integrity and thus to function normally from that organism. Many genes that initially prove to affect life span have been implicated in the repair and protection of DNA damage.
The Nobel Prize in Chemistry 2015 was awarded to Tomas Lindahl, Paul Modrich, and Aziz Sancar for their work on the molecular mechanism of DNA repair process. There are three types: nucleotide excision repair, base excision repair, and DNA mismatch repair.
Video DNA repair
Kerusakan DNA
DNA damage, due to environmental factors and normal metabolic processes within cells, occurs at levels of 10,000 to 1,000,000 molecular lesions per cell per day. Although this is only 0.000165% of the human genome of about 6 billion bases (3 billion base pairs), unrefined lesions in critical genes (such as tumor suppressor genes) can inhibit the ability of cells to perform their functions and increase the likelihood of tumors. formation and contribute to tumor heterogeneity.
Most of the DNA damage affects the main structure of the double helix; that is, the base itself is chemically modified. This modification can in turn interfere with the regular helical structure of the molecule by introducing non-native chemical bonds or large adducts that do not conform to the double helix standards. Unlike proteins and RNA, DNA usually does not have a tertiary structure and therefore damage or disturbance does not occur at that level. DNA, however, is supercoiled and wrapped around a "packing" protein called histones (in eukaryotes), and both superstructures are susceptible to the effects of DNA damage.
Source
DNA damage can be divided into two main types:
- endogenous damage such as attacks by reactive oxygen species resulting from normal metabolic byproducts (spontaneous mutations), especially oxidative deamination processes
- also includes a replication error
- exogenous damage caused by external agents such as
- ultraviolet [UV 200-400 nm] radiation from the sun
- other radiation frequencies, including x-rays and gamma rays
- hydrolysis or thermal disturbance
- Certain plant poison
- man-made mutagenic chemicals, especially aromatic compounds that act as DNA intercellation agents
- virus
Replication of damaged DNA before cell division can lead to incorrect incorporation of bases with damaged ones. The daughter cells that inherit this faulty base carry a mutation from which the original DNA sequence can not be recovered (except in rare cases of back mutations, for example, through gene conversion).
Type
There are several types of damage to DNA due to endogenous cellular processes:
- oxidation bases [ie. 8-oxo-7,8-dihydroguanine (8-oxoG)] and interrupt generation of strand DNA from reactive oxygen species,
- alkylation of base (usually methylation), such as the formation of 7-methylguanosine, 1-methyladenine, 6-O-Methylguanine
- hydrolysis from the base, such as deamination, depuration, and depyrimidination.
- "formation of large additions" (ie, benzo [a] dissolution of pyrene diol epoxide-dG, aromatactam I-dA adduct)
- mismatch bases, due to errors in DNA replication, in which incorrect DNA bases are stitched on newly formed DNA strands, or DNA bases are bypassed or incorrectly inserted./li>
- Monoadduct damage is caused by changes in a single nitrogen DNA base
- Get damage
Damage caused by exogenous agents comes in various forms. Some examples are:
- UV-B light causes crosslinking between the cytosine and adjacent thymine base to create pyrimidine dimer . This is called direct DNA damage.
- UV-A rays mostly create free radicals. The damage caused by free radicals is called indirect DNA damage.
- Ionizing radiation as created by radioactive decay or in cosmic rays causes the breaking of DNA strands. Medium-level ionisation radiation can cause irreversible DNA damage (causing replication and transcriptional errors necessary for neoplasia or may trigger viral interactions) leading to premature aging and cancer.
- Thermal Disorder at high temperatures increases depuration rate (loss of purine base from the DNA backbone) and single-strand break. For example, hydrolytic depurations are seen in thermophilic bacteria, which grow in hot springs at temperatures of 40-80 ° C. Depuration rates (300 purine residues per genome per generation) are too high in this species to be repaired by normal reparation machines, adaptive responses can not be ruled out.
- Industrial chemicals such as vinyl chloride and hydrogen peroxide, and environmental chemicals such as polycyclic aromatic hydrocarbons found in smoke, soot and tar create enormous diversity of the ethene-adduct, oxidized, alkylated phosphoteryriester and crosslinked DNA, just to name a few.
UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of induced damage. Spontaneous damage may include loss of base, deamination, wrinkling of sugar rings and tautomer shifts.
Nuclear versus mitochondria
In human cells, and eukaryotic cells in general, DNA is found in two cellular sites - within the nucleus and within the mitochondria. The nucleic DNA (nDNA) exists as chromatin during the non-replicative stage of the cell cycle and is condensed into an aggregate structure known as a chromosome during cell division. In both countries the DNA is very dense and ends around a manic-like protein called histones. Whenever a cell needs to express the genetic information encoded in its nDNA, the necessary chromosomal region decomposes, the genes located there are expressed, and then the region is condensed back to its resting conformation. Mitochondrial DNA (mtDNA) is located within the mitochondrial organelle, present in multiple copies, and is also closely related to a number of proteins to form a complex known as nucleotides. In mitochondria, reactive oxygen species (ROS), or free radicals, byproducts from the constant production of adenosine triphosphate (ATP) through oxidative phosphorylation, create a highly oxidative environment known to damage mtDNA. An important enzyme in counteracting the toxicity of this species is superoxide dismutase, which is present in both mitochondria and eukaryotic cell cytoplasm.
Senescence and apoptosis
Senescence, an irreversible process in which the cell no longer divides, is a protective response to the shortening of the ends of chromosomes. Telomere is a long area of ​​repetitive non-coded DNA that shuts off chromosomes and partial degradation every time the cell undergoes division (see Hayflick boundary). In contrast, quiescence is a reversible cellular dormancy state unrelated to genomic damage (see cell cycle). Senescence in cells can serve as a functional alternative to apoptosis in cases where the physical presence of cells for spatial reasons is required by the organism, which serves as a "last resort" mechanism to prevent cells with damaged DNA from replicating improperly in the absence of pro- growth. Unregulated cell division can lead to the formation of tumors (see cancer), which are potentially lethal to organisms. Therefore, the induction of aging and apoptosis is considered part of the cancer protection strategy.
Mutations
It is important to distinguish between DNA damage and mutations, two major types of errors in DNA. DNA damage and mutations are fundamentally different. Damage causes physical abnormalities in DNA, such as single and double strand breaks, 8-hydroxydeoxyguanosine residue, and stirred polycyclic aromatic hydrocarbons. DNA damage can be recognized by the enzyme, and thus can be corrected properly if excessive information, such as an undamaged sequence in a complementary strand of DNA or in homologous chromosomes, is available for copying. If cells maintain DNA damage, gene transcription can be prevented, and thus translation into proteins will also be blocked. Replication can also be blocked or cells can die.
In contrast to DNA damage, mutations are changes in the DNA base sequence. A mutation can not be recognized by an enzyme after a basic change is present on both strands of DNA, and thus mutations can not be repaired. At the cellular level, mutations can cause changes in protein function and regulation. Mutations are replicated when cells replicate. In cell populations, mutant cells will increase or decrease the frequency according to mutation effects on the cell's ability to survive and reproduce.
Although clearly distinct from one another, DNA damage and associated mutations due to DNA damage often lead to DNA synthesis errors during replication or repair; this error is the main source of mutation.
Given the nature of DNA damage and mutations, it can be seen that DNA damage is a particular problem in non-dividing cells or slowly dividing cells, where unfixed damage will tend to accumulate over time. On the other hand, in rapidly dividing cells, unfixed DNA damage that does not kill cells by blocking replication will tend to cause replication errors and thus mutations. Most mutations that are not neutral in their effects undermine cell survival. Thus, in populations of cells that make up tissues with replicating cells, mutant cells will tend to disappear. However, sparse mutations that provide survival benefits will tend to develop clonally at the expense of neighboring cells in the tissues. The advantage of these cells is unfavorable to all organisms, because such mutant cells can cause cancer. Thus, DNA damage to cells that often divide, because it causes mutations, is a prominent cause of cancer. In contrast, DNA damage in rare cells may be a major cause of aging.
Maps DNA repair
Mechanism
Cells can not work if DNA damage damages the integrity and accessibility of important information in the genome (but cells remain superficially when unnecessary genes are lost or damaged). Depending on the type of damage inflicted on the double helix structure of DNA, various remedial strategies have evolved to restore lost information. If possible, cells use unmodified complementary strands of DNA or chromatid sisters as templates to recover original information. Without access to templates, cells use an error-prone recovery mechanism known as transcission synthesis as a last resort.
DNA damage changes the helical spatial configuration, and the change can be detected by the cell. Once the damage is localized, certain DNA repair molecules bind to or near the site of damage, encouraging other molecules to bind and form complexes that allow actual repair to occur.
Direct reversal
Cells are known to remove three types of damage to their DNA by reversing them chemically. This mechanism does not require a template, because the type of damage they encounter can occur only in one of the four bases. Such direct reversal mechanisms are specific to the type of damage that occurs and do not involve damage to the phosphodiester backbone. The formation of pyrimidine dimers in irradiation with UV light results in an abnormal covalent bond between adjacent pyrimidine bases. The photoreactivation process instantly reverses this damage with the action of the photolyase enzyme, whose activation depends on the energy absorbed from blue/UV light (wavelength 300-500 nm) to induce catalysis. Photolyase, a long enzyme present in bacteria, fungi, and most animals no longer works in humans, which instead uses improved nucleotide excision to repair damage from UV radiation. Another type of damage, the methyl guanine methyl transferase (MGMT), is equivalent to a bacterium called ogt. This is an expensive process because every MGMT molecule can be used once; that is, the reaction is stoichiometric rather than catalytic. The general response to methylating agents in bacteria is known as adaptive response and provides resistance levels to alkylation agents on continuous exposure with increased regulation of alkylation improvements. The third type of DNA damage that the cell reverses is a particular methylation of the cytosine and adenine bases.
Single-strand damage
When only one of the two double helices has a defect, the other strand can be used as a template to guide damaged strands correction. To repair damage to one of two paired DNA molecules, there are a number of excision repair mechanisms that remove damaged nucleotides and replace them with an undamaged nucleotide appendix found in undamaged DNA strands.
- Basic excision repair (BER) fixes damage to a single nitrogen base by exerting an enzyme called glycosylase. These enzymes remove one single nitrogen base to make apurinic or apyrimidinic sites (AP sites). An enzyme called endonucleases AP nick the damaged DNA backbone on the AP site. DNA polymerase then removes damaged areas using 5 'to 3' exonuclease activities and correctly synthesizes new strands using complementary strands as a template.
- Nucleotide excision repair (NER) fixes damaged DNA that usually consists of major damage, helical-distortion, such as the dimerization of pyrimidine caused by UV light. The damaged areas will be removed in 12-24 long-nucleotide strands in a three-step process consisting of damage recognition, damaged DNA excision both upstream and downstream damage by endonuclease, and resynthesis of the released DNA region. NER is a highly evolutionary improvement mechanism that is preserved and used in virtually all eukaryotic and prokaryotic cells. In prokaryotes, NER is mediated by the Uvr protein. In eukaryotes, many proteins are involved, although the strategy is generally the same.
- The error repair system appears basically all cells to correct errors that are not corrected by proofreading. This system consists of at least two proteins. One detects mismatch, and the other recruits endonuclease that cuts the newly synthesized DNA strand to the area of ​​destruction. In E. coli , the proteins involved are Mut class proteins. This is followed by removal of areas damaged by exonuclease, resintesis by DNA polymerase, and nickel insertion by DNA ligase.
Break two lines
The break of two strands, in which the two strands in the double helix are decided, are very harmful to the cell because they can cause a genome rearrangement. PVN Acharya noted that the double-stranded break and "cross-linking connecting the two strands at the same point can not be repaired because the two strands can serve as templates for improvement.The cells will die at the next mitosis or in some rare, mutated instances." There are three mechanisms for correcting double-strand breaks (DSBs): non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and homologous recombination (HR). In the in vitro system, MMEJ occurs in mammalian cells at 10-20% of HR levels when both HR and NHEJ mechanisms are available.
In NHEJ, DNA Ligase IV, a special DNA ligase that forms a complex with an XRCC4 cofactor, instantly joins both ends. To guide accurate repair, NHEJ relies on a short homologous sequence called microhomology that exists at the single strand end of the DNA end to be joined. If this overhang is compatible, the fix is ​​usually accurate. NHEJ may also introduce mutations during repair. The loss of damaged nucleotides at the rest site can lead to deletion, and merge with nonmatching termini forms of insertion or translocation. NHEJ is essential before cells have replicated its DNA, since no template is available for repair with homologous recombination. There is a "back up" of the NHEJ line in the higher eukaryotes. In addition to its role as a genome interceptor, NHEJ is needed to join the hairpin-capped double-strand break induced during recombination V (D), a process that produces the diversity of B cells and T cell receptors in the vertebrate immune system.
Homologous recombination requires an identical or nearly identical sequence to be used as a template to correct the gap. The enzymatic machinery responsible for this repair process is almost identical to the machine responsible for the crossover chromosome during meiosis. This pathway allows the damaged chromosome to be repaired by using sibling chromatids (available in G2 after DNA replication) or homologous chromosomes as a template. DSBs caused by replicating machines that attempt to synthesize across single-strand breaks or unfixed lesions lead to collapse of replication forks and are usually fixed by recombination.
The MMEJ starts with a short-range resection by MRE11 nuclease on both sides of a double-strand break to reveal the microhomology area. In the next step, Poly (ADP-ribose) polymerase 1 (PARP1) is required and may be the first step in the MMEJ. There is a pair from the microhomology area followed by the recruitment of the specific flap structure of endonucleases 1 (FEN1) to remove the hanging flap. This is followed by the recruitment of XRCC1-LIG3 to the site to bind the ends of the DNA, which leads to intact DNA. MMEJ is always accompanied by removal, so the MMEJ is a mutagenic pathway for DNA repair.
The extremophile Deinococcus radiodurans has a remarkable ability to withstand DNA damage from ionizing radiation and other sources. At least two copies of the genome, with randomly damaged DNA, can form DNA fragments through annealing. Some overlapping fragments are then used to synthesis the homologous region via a moving D-loop that can continue the extension until they find a complementary strand. In the final step there is a crossover by recombinating Homologous recA-dependent.
Topoisomerase introduces both single and double strand breaks in the course of changing the state of supercoiling DNA, which is very common in areas near open replication forks. Such breaks are not considered DNA damage because they are natural intermediates in the biochemical mechanism of topoisomerase and are immediately repaired by the enzyme that created them.
Transcription synthesis
Translesion synthesis (TLS) is a process of DNA damage tolerance that allows the DNA replication machine to replicate past DNA lesions such as thymine dimers or AP sites. This involves switching out regular DNA polymerases for special transleased polymerases (ie IV or V polymerase DNA, from Y Polymerase families), often with larger active sites that can facilitate the insertion of bases that are opposed to damaged nucleotides. The transition of the polymerase is considered mediated by, among other factors, the post-translational modification of PCNA replication process factors. Transiion polymerase synthesis often has a low fidelity (high tendency to incorporate an incorrect base) in an undamaged template relative to the usual polymerase. However, many are very efficient at inserting the correct base opposite certain types of damage. For example, Pol? mediate the error-free bypass of lesions caused by UV radiation, while Pol? introduce mutations on these sites. Pol? is known to add the first adenine across the T ^ T photodimer using a Watson-Crick base pair and a second adenine will be added in a syn conformation using a Hoogsteen base pairing. From a cellular perspective, risking the introduction of point mutations during transcendic synthesis may be better for using a more drastic mechanism of DNA repair, which can lead to chronic gross aberrations or cell death. In short, this process involves a special polymerase either passing through or repairing a lesion at a stopping DNA replication site. For example, DNA polymerase Human eta can bypass complex DNA lesions such as intra-strand crosslinked guanine-thymine, G [8.5-Me] T, although it can lead to targeted and semi-targeted mutations. Paromita Raychaudhury and Ashis Basu studied the toxicity and mutagenesis of the same lesions in Escherichia coli by replicating G [8.5-Me] T-modified plasmid in E. coli with KOase Specific DNA polymerase. Very low viability of less pol, II, pol IV, and pol V strains, three SOS-induced DNA polymerases, indicates that trans- port synthesis is performed primarily by this particular DNA polymerase. The bypass platform is provided for this polymerase by Proliferating cell nuclear antigen (PCNA). Under normal circumstances, PCNA is bound to polymerase replicating DNA. In lesion sites, PCNA is ubiquitinated, or modified, by RAD6/RAD18 proteins to provide a platform for specific polymerases to cut lesions and to continue DNA replication. After transcelient synthesis, extension is required. This extension can be done by replicative polymerase if TLS is error free, as in Pol case, but if TLS result is in non-conformity, special polymerase is required to extend it; Pol? Pol? is unique in that it can extend terminal mismatch, whereas a more progressive polymerase can not. So when the les is found, the replication fork will jam, will PCNA switch from processive polymerase to TLS polymerase like Pol? to fix the lesion, then PCNA can switch to Pol? to expand the mismatch, and the last PCNA will switch to polymerase process to continue replication.
Global response to DNA damage
Cells exposed to ionizing radiation, ultraviolet light or chemicals are susceptible to acquiring multiple sites of large DNA lesions and multiple strand breaks. In addition, DNA-damaging agents can damage other biomolecules such as proteins, carbohydrates, lipids, and RNA. Accumulated damage, to be specific, double-strand breaks or adducts forbid replication forks, are among the known stimulation signals for a global response to DNA damage. The global response to damage is an act directed against the preservation of the cell itself and triggers several pathways of macromolecular repair, bypass lesions, tolerance, or apoptosis. Common features of global response are the induction of several genes, cell cycle capture, and inhibition of cell division.
First step
Packaging eukaryotic DNA into chromatin presents a barrier to all DNA-based processes that require enzyme recruitment to their workplace. To enable DNA repair, chromatin should be modified. In eukaryotes, chromatin-dependent remodeling complexes depend on ATP and histone-modifying enzymes are the two main factors used to complete this remodeling process.
The release of chromatin occurs rapidly at the site of DNA damage. In one of the earliest steps, stress-activated protein kinase, c-Jun N-terminal kinase (JNK), phosphorylates SIRT6 in serine 10 in response to multiple strand breaks or other DNA damage. This post-translational modification facilitates the mobilization of SIRT6 into DNA damage sites, and is required for efficient polymer (1) ADP-ribose (PARP1) recruitment into DNA break sites and for efficient DSB repair. PARP1 proteins begin to appear on the site of DNA damage in less than a second, with half the maximum accumulation in 1.6 seconds after the damage occurs. PARP1 synthesizes polymeric adenosine diphosphate ribose (poly (ADP-ribose) or PAR) on itself. Furthermore, chromatin remodeler ALC1 quickly attaches to the action product PARP1, a ribose poly-ADP chain, and ALC1 completes the onset of DNA damage within 10 seconds of damage. About half of the maximum chromatin relaxation, probably because of the action of ALC1, occurs 10 seconds. This then allows the recruitment of MRE11 DNA repair enzymes, to initiate DNA repair, within 13 seconds.
? H2AX, a phosphorylated form of H2AX is also involved in early steps leading to chromatin decondensation after the breaking of the DNA strand. Histone H2ax variants represent about 10% of histone H2A in human chromatin. ? H2AX (H2AX phosphorylated at serine 139) can be detected immediately after 20 seconds after cell irradiation (with multiple strands of DNA strand formation), and half the maximum accumulation? H2AX takes place in one minute. The extent of chromatin with phosphorylated? H2AX is about two million base pairs in the location of a double strands of DNA strand. ? H2AX does not, by itself, cause chromatin decondensation, but within 30 seconds of irradiation, the RNF8 protein can be detected in association with? H2AX. RNF8 mediates the decompensation of chromatin extensively, through subsequent interactions with CHD4, a component of nucleosome renodeling and the NuRD deacetylase complex.
DDB2 occurs in a heterodimeric complex with DDB1. The complex is increasingly complex with ubiquitin ligase protein CUL4A and with PARP1. This larger complex is rapidly associated with UV-induced damage in chromatin, with the half-maximal association being completed in 40 seconds. The PARP1 protein, attached to DDB1 and DDB2, then PARUMAT (creating a ribose poly-ADP chain) in DDB2 attracts the DNA protein remodeling ALC1. Action ALC1 relaxes chromatin at the site of UV damage to DNA. This relaxation allows other proteins in the nucleotide excision repair pathway to enter chromatin and to repair UV-induced UV-induced cyclobutane peptidin damage.
After rapid chromatin remodeling, the cell cycle checkpoint is activated to allow DNA repair to occur before the cell cycle progresses. First, two kinases, ATM and ATR are activated within 5 or 6 minutes after DNA damage. This is followed by the phosphorylation of the Chromos1 cell cycle checkpoint protein, starting its function, about 10 minutes after DNA damage.
DNA damage check point
After DNA damage, cell cycle checkpoints are activated. Checkpoint activation stops the cell cycle and gives the cell time to repair the damage before proceeding to split. DNA damage checkpoints occur at the boundary G1/S and G2/M. An intra-S checkpoint also exists. Activation of checkpoints is controlled by two master kinase, ATM and ATR. The ATM responds to the breaking of the DNA double strand and disturbance in the chromatin structure, whereas the ATR primarily responds to a jammed replication fork. This kinase phosphorylates the downstream target in the signal transduction cascade, which eventually leads to cell cycle capture. A class of mediator checkpoint proteins including BRCA1, MDC1, and 53BP1 have also been identified. This protein seems to be necessary to transmit the checkpoint activation signal to the downstream protein.
DNA damage check point is a signal transduction pathway that blocks cell cycle progression in G1, G2 and metaphase and slows the rate of phase S development when DNA is damaged. This causes a pause in the cell cycle that allows cell time to repair the damage before continuing to divide.
Checkpoint Proteins can be separated into four groups: phosphatidylinositol 3-kinase (PI3K) -like protein kinase, proliferating cell nuclear antigen (PCNA) -like groups, two serine/threonine (S/T) kinases and their adapters. The center for all DNA damage induced by checkpoints is a pair of large protein kinases belonging to the first group of protein kinases such as PI3K-ATM (Ataxia telangiectasia mutated) and ATR (Ataxia- and Rad-related) kinase, whose sequence and function have been well preserved in evolution. All DNA damage responses require ATM or ATR because they have the ability to bind chromosomes at the site of DNA damage, along with accessory proteins that are platforms where the DNA damage response components and complex DNA repair can be assembled.
An important downstream target of ATM and ATR is p53, as it is necessary to induce apoptosis after DNA damage. The kinase-dependent kinase inhibitor p21 is induced by both p53-dependent and p53-independent mechanisms and can capture cell cycles in G1/S and G2/M checkpoints by disabling the cyclin/cyclin-dependent kinase complex.
Prokaryotic SOS response
The SOS response is a change in gene expression in Escherichia coli and other bacteria in response to extensive DNA damage. The prokaryotic SOS system is governed by two major proteins: LexA and RecA. LexA homodimer is a transcriptional receptor that binds to the order of operators commonly referred to as SOS boxes. In Escherichia coli it is known that LexA regulates the transcription of about 48 genes including the lexA and recA genes. The SOS response is widely known in the Bacteria domain, but most do not exist in some bacterial phyla, such as Spirochetes. The most common cellular signal that activates the SOS response is a single-stranded (ssDNA) DNA region, which arises from a jammed or double-stranded replication fork, which is processed by DNA helicase to separate two DNA strands. At the initiation step, the RecA protein binds to ssDNA in an ATP hydrolysis reaction resulting in a RecA-ssDNA filament. The RecA-ssDNA filament activates the Lexa autoprotease activity, which ultimately leads to LexA dimer splits and subsequent LexA degradation. The loss of a LexA repressor induces transcription of the SOS gene and allows further signal induction, inhibition of cell division and an increase in the level of protein responsible for the processing of the damage.
In Escherichia coli , the SOS box is a 20-nucleotide sequence near the promoter with a palindromic structure and a high-order conservation level. In other classes and phyla, the SOS box sequence varies, with different lengths and compositions, but is always highly sustainable and one of the strongest short signals in the genome. The high information content of the SOS box allows the LexA differential binding to different promoters and allows for SOS response time. The lesion repair gene was induced early in the SOS response. The error-prone transcriptional polymers, for example, UmuCD'2 (also called DNA polymerase V), were induced later as a last resort. After DNA damage is repaired or bypassed using polymerase or via recombination, the number of single strands of DNA in the cell decreases, decreasing the number of recA filaments decreases the LexA homodimer division activity, which then binds to the SOS box near the promoter and restores normal gene expression.
Response of eukaryotic transcription to DNA damage
Eukaryotic cells exposed to DNA-damaging agents also activate important defense pathways by inducing some proteins involved in DNA repair, cell cycle check control, protein trade and degradation. The broad genome's transcription response is highly complex and tightly regulated, allowing a coordinated global response to damage. Saccharomyces cerevisiae yeast exposure to a DNA destroyer produces an overlapping but distinct transcription profile. The similarity with the environmental shock response indicates that the common global voltage response path is at the level of transcriptional activation. In contrast, different types of human cells responding to different damage show no general global response. A possible explanation for the difference between yeast and human cells may be in the heterogeneity of mammalian cells. In animals, different types of cells are distributed among various organs that have evolved different sensitivity to DNA damage.
In general, the global response to DNA damage involves the expression of genes responsible for postreplication improvement, homologous recombination, nucleotide excision repair, DNA damage checks, global transcriptional activation, genes that control mRNA decay, and many others. A large amount of damage to cells leaves it with an important decision: undergo apoptosis and die, or survive on living expenses with a modified genome. Increased tolerance to damage can lead to an increase in survival rates that will allow for the accumulation of larger mutations. Rev1 yeast and human polymerase? is a member of [Y family translesion DNA polymerases present during a global response to DNA damage and is responsible for enhancing mutagenesis during a global response to DNA damage in eukaryotes.
Aging
Pathological effects of poor DNA repair
Animals with genetic deficiencies in DNA repair often show decreased life span and increased incidence of cancer. For example, mice lacking the dominant NHEJ pathways and in telomere maintenance mechanisms acquire more frequent lymphomas and infections, and, consequently, have a shorter life span than wild-type mice. In the same way, the deficient mice in key repair and transcriptional proteins that release helical DNA have an early onset of aging-related disease and shorten the life span. However, not every deficiency of DNA repair creates a predictable effect; the shortage of rats in the NER path showed a shortened life span without a higher mutation rate.
If the extent of DNA damage exceeds the capacity of cells to repair it, accumulation of errors can overwhelm the cells and cause premature aging, apoptosis, or cancer. Inherited diseases associated with incorrect DNA repair functions cause premature aging, increase sensitivity to carcinogens, and also increase the risk of cancer (see below). On the other hand, organisms with improved DNA repair systems, such as Deinococcus radiodurans , the most radiation resistant organisms, exhibit tremendous resistance to the double division effect of radioactivity, possibly due to increased efficiency of DNA repair and especially NHEJ.
Longevity and calorie restrictions
A number of individual genes have been identified as affecting the variation in the life span within the population of the organism. The effects of these genes are highly dependent on the environment, in particular, on organism diets. Reproductive calorie restriction results in extended life in various organisms, possibly through nutrient sensing pathways and decreased metabolic rates. The molecular mechanism by which such restriction produces a long life span is unclear (see for some discussions); However, the behavior of many genes that are known to be involved in DNA repair is altered under conditions of caloric restriction. Several agents reported to have anti-aging properties have been shown to attenuate the constitutive level of mTOR signaling, evidence of reduction in metabolic activity, and simultaneously to reduce the constitutive rate of DNA damage caused by endogenous reactive oxygen species produced.
For example, increasing the dose of genes from the SIR-2 gene, which regulates packing of DNA in the nematode worm Caenorhabditis elegans , can extend the lifespan significantly. The mammalian homolog of SIR-2 is known to induce the downstream DNA repair factors involved in NHEJ, an activity that is specifically promoted under caloric restriction conditions. Caloric restriction has been closely related to the rate of repair of base excision in mouse core DNA, although similar effects have not been observed in mitochondrial DNA.
The AGE-1 gene, an upstream effector of the DNA repair pathway, dramatically prolongs life under free-eating conditions but leads to a decrease in reproductive fitness under conditions of calorie restriction. This observation supports the pleiotropy theory of the biological origins of aging, which suggests that genes that provide substantial survival benefits early in life will be chosen because even if they carry related losses in old age.
Medicine and DNA repair modulation
Hereditary DNA repair disorder
Defects in the mechanism of NSAID are responsible for several genetic disorders, including:
- Xeroderma pigmentosum: hypersensitivity to sun/UV, resulting in increased incidence of skin cancer and premature aging
- Cockayne syndrome: hypersensitivity to UV and chemical agents
- Trichothiodystrophy: sensitive skin, brittle hair and nails
Mental retardation often accompanies the last two disorders, indicating increased susceptibility to developmental neurons.
Other DNA repair disorders include:
- Werner's syndrome: premature aging and stunted growth
- Bloom syndrome: sunlight hypersensitivity, high incidence of malignancy (especially leukemia).
- Ataxia telangiectasia: sensitivity to ionizing radiation and some chemical agents
All of the above diseases are often called "segmental progerias" because their victims look old and suffer from age-related illnesses that are not normal, while not manifesting all the symptoms of old age.
Other diseases associated with reduced DNA repair function include Fanconi anemia, Hereditary breast cancer and colon cancer.
Cancer
Due to inherent limitations in DNA repair mechanisms, if humans live long enough, they will all eventually develop cancer. There are at least 34 mutations of human DNA genes repaired that increase the risk of cancer. Many of these mutations cause DNA repair to be less effective than usual. Specifically, Hereditary nonpolyposis colorectal cancer (HNPCC) is strongly associated with specific mutations in the DNA mismatch repair path. BRCA1 and BRCA2 , two important genes whose mutations have an increased risk of breast cancer in the career are both associated with a large number of DNA repair pathways, especially NHEJ and homologous recombination.
Cancer therapy procedures such as chemotherapy and radiotherapy work by flooding cell capacity to repair DNA damage, resulting in cell death. The most rapidly dividing cells - most of the cancer cells - are particularly affected. Side effects are other non-cancerous cells but rapidly divide as progenitor cells in the intestine, skin, and hematopoietic systems are also affected. Modern cancer treatments seek to localize DNA damage to cancer-related cells and tissues either by physical means (concentrating therapeutic agents in the tumor region) or by biochemical means (exploiting unique features for cancer cells in the body)....; in the context of therapy that targets DNA damage response genes, the latter approach has been called 'synthetic lethality'.
Perhaps the most famous of these 'deadly synthetic' drugs is poly (ADP-ribose) polymerase 1 (PARP1) olaparib inhibitor, approved by the Food and Drug Administration in 2015 for treatment of women from BRCA-cancer-defective ovaries. Tumor cells with partial loss of DNA damage response (in particular, improvement of homologous recombination) are dependent on other mechanisms - the improvement of single-strand stops - a mechanism consisting, in part, of the PARP1 gene product. Olaparib is combined with chemotherapeutics to inhibit single-strand break repair caused by DNA damage caused by chemotherapy given together. The tumor cells that rely on this mechanism of DNA remediation can not repair the damage and therefore can not survive and proliferate, whereas normal cells can repair the damage by a functioning homologous recombination mechanism.
Many other drugs used to fight the mechanisms of repair of other residual DNA commonly found in cancer are currently under investigation. However, the therapeutic approach of synthetic lethality has been questioned because of the evidence emerging from the acquired resistance, achieved through the rewiring of DNA damage response pathways and return of previously impeded defects.
fix DNA defects in cancer
It has become clear over the last few years that DNA damage response acts as a barrier to the malignant prenoplastic cell transformation. Previous research has demonstrated an increased DNA damage response in cell culture models with oncogen activation and prenoplastic colon adenoma. Mechanisms of DNA damage response trigger cell-cycle capture, and attempts to repair DNA lesions or increase cell death/aging if repairs are not possible. Stress replication is observed in prenoplastic cells because of increased proliferative signaling of oncogenic mutations. Stress replication is characterized by: increased initiation of replication/firing of origin; increased transcription and complex collisions of transcription-replication; nucleotide deficiency; increased species of reactive oxygen (ROS).
Stress replication, along with selection to deactivate mutations in DNA damage response genes in tumor evolution, leads to downregulation and/or loss of some DNA damage response mechanisms, and hence lost repair of programmed cell/programmed DNA and/or aging. In the experimental mouse model, loss of DNA damage in response-mediated cell senescence was observed after short hairpin RNA (shRNA) to inhibit the double-strand break kinase ataxia telangiectasia (ATM) response, which led to an increase in tumor size and invasion. Humans born with congenital defects in DNA repair mechanisms (eg, Li-Fraumeni syndrome) have a higher cancer risk.
The prevalence of DNA mutation response mutations varies across all types of cancer; for example, 30% of breast invasive carcinomas have mutations in genes involved in homologous recombination. In cancer, downregulation is observed in all mechanisms of DNA damage response (basic excision repair (BER), nucleotide excision repair (NER), DNA mismatch improvement (MMR), improvement of homologous recombination (HR), non-homologous end incorporation (NHEJ) DNA synthesis (TLS). Like mutations to DNA repair repair genes, mutations also appear in genes responsible for capturing cell cycles to allow sufficient time for DNA repair to occur, and some of the genes involved in repairing DNA damage and checkpoint control of cell cycle , eg ATM and checkpoint kinase 2 (CHEK2) - tumor suppressors that are often absent or regulated in non-small cell lung cancer.
Table: Genes involved in DNA damage and mutation pathways often mutated in cancer (HR = homologous recombination NHEJ = non-homologous endpoints; SSA = single-strand annealing; FA = fanconi anemia path; BER = repair of base excision; NER = nucleotides) excision repair; MMR = mismatch repair)
Repair of epigenetic DNA damage to cancer
Classically, cancer has been seen as a series of diseases that are driven by progressive genetic disorders that include mutations in tumor suppressor genes and oncogenes, and chromosome aberrations. However, it has become clear that cancer is also driven by epigenetic changes.
Epigenetic changes refer to functionally relevant modifications to the genome that do not involve changes to the nucleotide sequence. Examples of such modifications are changes in DNA methylation (hypermethylation and hypometilation) and histone modification, changes in chromosome architecture (caused by improper protein expression such as HMGA2 or HMGA1) and changes caused by microRNAs. Each of these epigenetic changes serves to regulate gene expression without altering the underlying DNA sequence. This change usually remains through cell division, persisting for several generations of cells, and can be considered as epimutasi (equivalent to mutation).
While a large number of epigenetic changes are found in cancer, epigenetic changes in DNA repair genes, which lead to reduced expression of DNA repair proteins, appear to be very important. This kind of change is thought to occur early in the development of cancer and is a likely cause of the characteristics of genetic instability of the cancer.
Reduced expression of DNA repair gene leads to poor DNA repair. When DNA repair deficiencies of damaged DNA remain in cells at a higher level than normal and this excessive damage causes an increase in the frequency of mutations or epimutations. The rate of mutation increases substantially in the damaged cells in repair of DNA mismatch or improvement of homologous recombination (HRR). Rearranging chromosomes and aneuploidy also increases the damaged cells of HRR.
Higher levels of DNA damage not only cause an increase in mutations, but also cause an increase in epimutation. During repair of double strand DNA damage, or repair of other DNA damage, repair sites that are not repaired can cause silencing of epigenetic genes.
The protein deficient expression of DNA repair due to inherited mutations can lead to an increased risk of cancer. Individuals with inherited disorders in one of 34 DNA repair genes (see article DNA repair-deficient disorder) have an increased risk of cancer, with some defects causing up to 100% chance of a cancer lifetime (eg p53 mutations). However, germline mutations (which cause very penetrant cancer syndrome) are the cause of only about 1 percent of cancer.
The frequency of epilatoration in DNA repair genes
Deficiencies in DNA repair enzymes are sometimes caused by somatic mutations emerging in DNA repair genes, but are much more often caused by epigenetic changes that reduce or silence the expression of DNA repair genes. For example, when 113 colorectal cancers were examined sequentially, only four had missense mutations in the MGMT DNA repair genes, while the majority had reduced MGMT expression due to methylation of the MGMT promoter region (epigenetic changes). Five different studies found that between 40% and 90% of colorectal cancers have reduced the expression of MGMT due to MGMT region promoter methylation.
Similarly, out of 119 cases of colorectal cancer that did not improve mectatch improvements that did not have expression of PMS2 gene gene repair, PMS2 deficiency at 6 due to mutations in the PMS2 gene, while in 103 cases PMS2 expression deficiency because the partner pair MLH1 is suppressed due to promoter PMS2 is unstable in the absence of MLH1). In the other 10 cases, the loss of PMS2 expression is likely due to epigenetic overexpression of the microRNA, miR-155, which decreases-regulates MLH1.
In a further example (tabulated in Table 4 of this reference), epigenetic defects were found at frequencies ranging from 13% -100% for DNA repair genes BRCA1, WRN, FANCB, FANCF, MGMT, MLH1, MSH2, MSH4, ERCC1, XPF, NEIL1 and ATM. This epigenetic defect occurs in different types of cancer (eg breast, ovary, colorectal and head and neck). Two or three deficiencies in the expression of ERCC1, XPF or PMS2 occur simultaneously in most of the 49 colon cancers evaluated by Facista et al.
The chart in this section shows some DNA-damaging agents, examples of DNA lesions they cause, and pathways that deal with this DNA damage. At least 169 enzymes are directly used in DNA repair or affect the process of DNA repair. Of these, 83 are directly used in repairing 5 types of DNA damage illustrated in the chart.
Some of the better-studied genes that are central to this improvement process are shown in the chart. The determination of genes shown in red, gray or cyan genes suggests genes are often epigenetically altered in many types of cancers. The Wikipedia article on each of the genes highlighted by red, gray or cyan describes the epigenetic (s) and cancer (s) changes in which these epimutations are found. Two review articles, and two extensive experimental survey articles also documented most of the deficiencies in epigenetic DNA repair in cancer.
The genes marked red are often reduced or silenced by the epigenetic mechanisms in various cancers. When these genes have low or absent expression, DNA damage can accumulate. Past replication errors of this damage (see transcircle synthesis) can lead to increased mutation and, ultimately, cancer. Epigenetic repression of DNA repair genes in an accurate DNA repair pathway seems to be central to carcinogenesis.
Two gray-highlighted genes RAD51 and BRCA2 are required for the repair of homologous recombination. They are sometimes expressed epigenetically and are sometimes less expressed in certain cancers. As shown in the Wikipedia article on RAD51 and BRCA2, such cancers usually have epigenetic deficiencies in other DNA repair genes. Repairing this deficiency is likely to cause an increase in DNA damage that is not repaired. The excessive expression RAD51 and BRCA2 seen in this cancer may reflect selective pressures for RAD51 compensation or BRCA2 above - expression and an improvement in homologous recolational improvement at least partially overcome the excess DNA damage. In cases where RAD51 or BRCA2 is under-expressed, this alone will cause an increase in DNA damage that is not corrected. Past replication errors (see transthesis synthesis) can lead to increased mutations and cancer, so expression under RAD51 or BRCA2 will be carcinogenic in its own right.
Cyan-highlighted genes are on the pathway of microhomology-mediated end (MMEJ) and are regulated in cancer. The MMEJ is an additional repair path that does not have an inaccurate error for double-strand breaks. In the MMEJ repair of the double-strand break, a homology of 5-25 complementary base pairs between the two strands paired is sufficient to align the strands, but the flap end is usually present. The MMEJ eliminates the extra nucleotides (flaps) in which the strands join, and then binds the strands to make the double helix of the DNA intact. MMEJ almost always involves at least a small removal, so it is a mutagenic pathway. FEN1, the flon endonuclease in the MMEJ, is epigenetically increased by hypomethylation promoters and is overexpressed in the majority of breast, prostate, stomach, neuroblastoma, pancreatic, and lung cancers. PARP1 is also overexpressed when its epigenetric-promoter ETS sites are hypomethylated, and this contributes to the development of endometrial cancer, BRCA-mutated ovarian cancer, and ovarian BRCA-mutated serous malignancies. Other genes in the MMEJ pathway are also overexpressed in a number of cancers (see MMEJ for a summary), and are also shown in cyan.
Genome-wide distribution of DNA repair in human somatic cells
The differential activity of DNA repair pathways in different regions of the human genome causes mutations to be very uneven in the tumor genome. In particular, genomic regions of early genetic and replicating genes exhibit lower mutation frequencies than heterochromatin with poorly-replicated genes. One such underlying mechanism involves modification of histone H3K36me3, which can recruit unsuitable repair proteins, thereby lowering the rate of mutation in the region marked H3K36me3. Another important mechanism concerns the repair of nucleotide excision, which can be recruited by transcriptional machinery, lowering the rate of somatic mutation in the active gene and other open chromatin areas.
Evolution
The basic process of DNA repair is highly sustainable between prokaryotes and eukaryotes and even among bacteriophages (viruses that infect bacteria); However, more complex organisms with more complex genomes have more complex repair mechanisms. The ability of a large number of structural motives of proteins to catalyze relevant chemical reactions has played an important role in the elaboration of mechanism improvements during evolution. For a very detailed review of hypotheses related to the evolution of DNA repair, see.
The fossil record shows that single cell life began to multiply on the planet at some point during the Pre-Cambrian period, though exactly when the first recognized modern life emerged was unclear. Nucleic acid is the only and universal tool of encoding genetic information, requiring DNA repair mechanisms that in its basic form have been inherited by all life forms that still exist from their common ancestors. The emergence of Earth's oxygen-rich atmosphere (known as "oxygen calamity") due to photosynthetic organisms, and the presence of potentially damaging free radicals in cells due to oxidative phosphorylation, necessitates the evolution of specific DNA repair mechanisms. to fight the type of damage caused by oxidative stress.
Level of evolutionary change
On some occasions, DNA damage is not repaired, or corrected by an error-prone mechanism that results in a change from the original sequence. When this happens, mutations may propagate into the genome of the cell's descendants. If such an event occurs in germinal line cells that will ultimately produce gametes, mutations have the potential to be passed on to the offspring of the organism. The rate of evolution in certain species (or, in certain genes) is a function of the rate of mutation. As a result, the degree and accuracy of DNA repair mechanisms has an influence on evolutionary change processes. Protection and repair of DNA damage does not affect the level of adaptation by gene regulation and by recombination and selection of alleles. On the other hand, repair and protection of DNA damage affects the level of irreversible accumulation, benefit, code development, inherited mutations, and slow the evolutionary mechanism for the expansion of the organism's genomes with new functionality. The tension between evolvability and repair and mutation protection needs further investigation.
Technology
A technology called repetitive clusters that periodically insert palindromic replicates (abbreviated to CRISPR-Cas9) were discovered in 2012. This new technology allows anyone with a molecular biology training to alter the genes of each species appropriately. Cheaper, more efficient, and more precise than any other technology. With the help of CRISPR-Cas9, parts of the genome can be edited by scientists by removing, adding, or altering parts in the DNA sequence.
See also
References
External links
- Roswell Park Cancer Institute DNA Repair Lectures
- A complete list of Human DNA Repair Genes
- 3D structure of some DNA repair enzymes
- Humans repair DNA disease
- DNA fixes special interest groups
- DNA Repair
- DNA Damage and DNA Repair
- Segmental Progeria
- Repair DNA damage; the good, the bad, and the ugly
Source of the article : Wikipedia
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