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155-457: D-loops occur in a number of particular situations, including in DNA repair , in telomeres , and as a semi-stable structure in mitochondrial circular DNA molecules. Researchers at Caltech discovered in 1971 that the circular mitochondrial DNA from growing cells included a short segment of three strands which they called a displacement loop. They found the third strand was a replicated segment of

310-465: A Holliday junction . Following this, more DNA synthesis occurs on the invading strand (i.e., one of the original 3' overhangs), effectively restoring the strand on the homologous chromosome that was displaced during strand invasion. After the stages of resection, strand invasion and DNA synthesis, the DSBR and SDSA pathways become distinct. The DSBR pathway is unique in that the second 3' overhang (which

465-461: A nuclease domain, which cuts the single strand of DNA that emerges from the unzipping process. This unzipping continues until RecBCD encounters a specific nucleotide sequence (5'-GCTGGTGG-3') known as a Chi site . Upon encountering a Chi site, the activity of the RecBCD enzyme changes drastically. DNA unwinding pauses for a few seconds and then resumes at roughly half the initial speed. This

620-514: A D-loop. If the D-loop is cut, another swapping of strands forms a cross-shaped structure called a Holliday junction . Resolution of the Holliday junction by some combination of RuvABC or RecG can produce two recombinant DNA molecules with reciprocal genetic types, if the two interacting DNA molecules differ genetically. Alternatively, the invading 3’ end near Chi can prime DNA synthesis and form

775-511: A DNA damage. In one of the earliest steps, the stress-activated protein kinase, c-Jun N-terminal kinase (JNK) , phosphorylates SIRT6 on serine 10 in response to double-strand breaks or other DNA damage. This post-translational modification facilitates the mobilization of SIRT6 to DNA damage sites, and is required for efficient recruitment of poly (ADP-ribose) polymerase 1 (PARP1) to DNA break sites and for efficient repair of DSBs. PARP1 protein starts to appear at DNA damage sites in less than

930-456: A G[8,5-Me]T-modified plasmid in E. coli with specific DNA polymerase knockouts. Viability was very low in a strain lacking pol II, pol IV, and pol V, the three SOS-inducible DNA polymerases, indicating that translesion synthesis is conducted primarily by these specialized DNA polymerases. A bypass platform is provided to these polymerases by Proliferating cell nuclear antigen (PCNA). Under normal circumstances, PCNA bound to polymerases replicates

1085-468: A T-loop (Telomere-loop). This is a loop of both strands of the chromosome which are joined to an earlier point in the double-stranded DNA by the 3' strand end invading the strand pair to form a D-loop. The joint is stabilized by the shelterin protein POT1 . The T-loop, which is completed by the D-loop splice, protects the end of the chromosome from damage. When a double-stranded DNA molecule has suffered

1240-409: A barrier to all DNA-based processes that require recruitment of enzymes to their sites of action. To allow DNA repair, the chromatin must be remodeled . In eukaryotes, ATP dependent chromatin remodeling complexes and histone-modifying enzymes are two predominant factors employed to accomplish this remodeling process. Chromatin relaxation occurs rapidly at the site of a DNA damage. In one of

1395-407: A barrier to all DNA-based processes that require recruitment of enzymes to their sites of action. To allow homologous recombination (HR) DNA repair, the chromatin must be remodeled. In eukaryotes, ATP dependent chromatin remodeling complexes and histone-modifying enzymes are two predominant factors employed to accomplish this remodeling process. Chromatin relaxation occurs rapidly at the site of

1550-399: A break in both strands, one repair mechanism available in diploid eukaryotic cells is homologous recombination repair . This makes use of the intact chromosome homologous to the broken one as a template to bring the two double-stranded pieces into correct alignment for rejoining. Early in this process, one strand of one piece is matched to a strand of the intact chromosome and that strand

1705-443: A cell leaves it with an important decision: undergo apoptosis and die, or survive at the cost of living with a modified genome. An increase in tolerance to damage can lead to an increased rate of survival that will allow a greater accumulation of mutations. Yeast Rev1 and human polymerase η are members of Y family translesion DNA polymerases present during global response to DNA damage and are responsible for enhanced mutagenesis during

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1860-455: A cell undergoes division (see Hayflick limit ). In contrast, quiescence is a reversible state of cellular dormancy that is unrelated to genome damage (see cell cycle ). Senescence in cells may serve as a functional alternative to apoptosis in cases where the physical presence of a cell for spatial reasons is required by the organism, which serves as a "last resort" mechanism to prevent a cell with damaged DNA from replicating inappropriately in

2015-446: A cell's ability to carry out its function and appreciably increase the likelihood of tumor formation and contribute to tumor heterogeneity . The vast majority of DNA damage affects the primary structure of the double helix; that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in

2170-540: A collapsed replication fork and is fixed by several pathways of homologous recombination including the RecBCD pathway. In this pathway, a three-subunit enzyme complex called RecBCD initiates recombination by binding to a blunt or nearly blunt end of a break in double-strand DNA. After RecBCD binds the DNA end, the RecB and RecD subunits begin unzipping the DNA duplex through helicase activity. The RecB subunit also has

2325-599: A common global response. The probable explanation for this difference between yeast and human cells may be in the heterogeneity of mammalian cells. In an animal different types of cells are distributed among different organs that have evolved different sensitivities to DNA damage. In general global response to DNA damage involves expression of multiple genes responsible for postreplication repair , homologous recombination, nucleotide excision repair, DNA damage checkpoint , global transcriptional activation, genes controlling mRNA decay, and many others. A large amount of damage to

2480-420: A compaction state close to its pre-damage level after about 20 min. In vertebrates the locations at which recombination occurs are determined by the binding locations of PRDM9 , a protein which recognizes a specific sequence motif by its zinc finger array. At these sites, another protein, SPO11 catalyses recombination-initiating double strand breaks (DSBs), a subset of which are repaired by recombination with

2635-444: A different origin within the D-loop region and uses coupled-strand replication with simultaneous synthesis of both strands. Certain bases within the D-loop region are conserved, but large parts are highly variable and the region has proven to be useful for the study of the evolutionary history of vertebrates. The region contains promoters for the transcription of RNA from the two strands of mitochondrial DNA immediately adjacent to

2790-478: A gene can be prevented, and thus translation into a protein will also be blocked. Replication may also be blocked or the cell may die. In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when

2945-487: A gene necessary for the strand exchange reaction, a key step in homologous recombinational repair, there is functional homology from viruses to humans (i. e. uvsX in phage T4; recA in E. coli and other bacteria, and rad51 and dmc1 in yeast and other eukaryotes, including humans). Multiplicity reactivation has also been demonstrated in numerous pathogenic viruses. Coronaviruses are capable of genetic recombination when at least two viral genomes are present in

3100-417: A global response to DNA damage in eukaryotes. Experimental animals with genetic deficiencies in DNA repair often show decreased life span and increased cancer incidence. For example, mice deficient in the dominant NHEJ pathway and in telomere maintenance mechanisms get lymphoma and infections more often, and, as a consequence, have shorter lifespans than wild-type mice. In similar manner, mice deficient in

3255-555: A heterodimeric complex with DDB1 . This complex further complexes with the ubiquitin ligase protein CUL4A and with PARP1 . This larger complex rapidly associates with UV-induced damage within chromatin, with half-maximum association completed in 40 seconds. The PARP1 protein, attached to both DDB1 and DDB2, then PARylates (creates a poly-ADP ribose chain) on DDB2 that attracts the DNA remodeling protein ALC1 . Action of ALC1 relaxes

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3410-626: A highly complex form of DNA damage as clustered damage. It consists of different types of DNA lesions in various locations of the DNA helix. Some of these closely located lesions can probably convert to DSB by exposure to high temperatures. But the exact nature of these lesions and their interactions is not yet known Translesion synthesis (TLS) is a DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites . It involves switching out regular DNA polymerases for specialized translesion polymerases (i.e. DNA polymerase IV or V, from

3565-438: A homologous chromosome. The search process induces stretching of the DNA duplex, which enhances homology recognition (a mechanism termed conformational proofreading ). Upon finding such a sequence, the single-stranded nucleoprotein filament moves into the homologous recipient DNA duplex in a process called strand invasion . The invading 3' overhang causes one of the strands of the recipient DNA duplex to be displaced, to form

3720-517: A key repair and transcription protein that unwinds DNA helices have premature onset of aging-related diseases and consequent shortening of lifespan. However, not every DNA repair deficiency creates exactly the predicted effects; mice deficient in the NER pathway exhibited shortened life span without correspondingly higher rates of mutation. The maximum life spans of mice , naked mole-rats and humans are respectively ~3, ~30 and ~129 years. Of these,

3875-558: A large survival advantage early in life will be selected for even if they carry a corresponding disadvantage late in life. Defects in the NER mechanism are responsible for several genetic disorders, including: Homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may be also RNA in viruses ). Homologous recombination

4030-642: A last resort. Once the DNA damage is repaired or bypassed using polymerases or through recombination, the amount of single-stranded DNA in cells is decreased, lowering the amounts of RecA filaments decreases cleavage activity of LexA homodimer, which then binds to the SOS boxes near promoters and restores normal gene expression. Eukaryotic cells exposed to DNA damaging agents also activate important defensive pathways by inducing multiple proteins involved in DNA repair, cell cycle checkpoint control, protein trafficking and degradation. Such genome wide transcriptional response

4185-549: A model for recombination in meiosis which introduced key details of how the process can work, including the exchange of material between chromosomes through Holliday junctions . In 1983, Jack Szostak and colleagues presented a model now known as the DSBR pathway , which accounted for observations not explained by the Holliday model. During the next decade, experiments in Drosophila , budding yeast and mammalian cells led to

4340-505: A mutation. Three mechanisms exist to repair double-strand breaks (DSBs): non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and homologous recombination (HR): In an in vitro system, MMEJ occurred in mammalian cells at the levels of 10–20% of HR when both HR and NHEJ mechanisms were also available. The extremophile Deinococcus radiodurans has a remarkable ability to survive DNA damage from ionizing radiation and other sources. At least two copies of

4495-445: A population of cells composing a tissue with replicating cells, mutant cells will tend to be lost. However, infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is disadvantageous to the whole organism because such mutant cells can give rise to cancer. Thus, DNA damage in frequently dividing cells, because it gives rise to mutations,

4650-464: A protein called Spo11 makes a targeted double-strand break in DNA. These sites are non-randomly located on the chromosomes; usually in intergenic promoter regions and preferentially in GC-rich domains These double-strand break sites often occur at recombination hotspots , regions in chromosomes that are about 1,000–2,000 base pairs in length and have high rates of recombination. The absence of

4805-413: A recombination event may have been a critical step in the evolution of SARS-CoV-2's capability to infect humans. Recombination events are likely key steps in the evolutionary process that leads to the emergence of new human coronaviruses. During COVID-19 pandemic in 2020, many genomic sequences of Australian SARS‐CoV‐2 isolates have deletions or mutations (29742G>A or 29742G>U; "G19A" or "G19U")in

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4960-464: A recombination hotspot between two genes on the same chromosome often means that those genes will be inherited by future generations in equal proportion. This represents linkage between the two genes greater than would be expected from genes that independently assort during meiosis. Double-strand breaks can be repaired through homologous recombination, polymerase theta-mediated end joining (TMEJ) or through non-homologous end joining (NHEJ). NHEJ

5115-509: A replication fork. This type of resolution produces only one type of recombinant (non-reciprocal). Bacteria appear to use the RecF pathway of homologous recombination to repair single-strand gaps in DNA. When the RecBCD pathway is inactivated by mutations and additional mutations inactivate the SbcCD and ExoI nucleases, the RecF pathway can also repair DNA double-strand breaks. In the RecF pathway

5270-480: A ring-shaped ATPase , are loaded onto opposite sides of the Holliday junction, where they act as twin pumps that provide the force for branch migration. Between those two rings of RuvB, two sets of the RuvA protein assemble in the center of the Holliday junction such that the DNA at the junction is sandwiched between each set of RuvA. The strands of both DNA duplexes—the "donor" and the "recipient" duplexes—are unwound on

5425-431: A second, with half maximum accumulation within 1.6 seconds after the damage occurs. Next the chromatin remodeler Alc1 quickly attaches to the product of PARP1 action, a poly-ADP ribose chain, and Alc1 completes arrival at the DNA damage within 10 seconds of the occurrence of the damage. About half of the maximum chromatin relaxation, presumably due to action of Alc1, occurs by 10 seconds. This then allows recruitment of

5580-415: A second, with half maximum accumulation within 1.6 seconds after the damage occurs. PARP1 synthesizes polymeric adenosine diphosphate ribose (poly (ADP-ribose) or PAR) chains on itself. Next the chromatin remodeler ALC1 quickly attaches to the product of PARP1 action, a poly-ADP ribose chain, and ALC1 completes arrival at the DNA damage within 10 seconds of the occurrence of the damage. About half of

5735-854: A single person infected with a virus variant identical to the Wuhan WIV04 isolates, or simultaneously with another primary case infected with a virus containing the 11083G > T mutation. Linkage disequilibrium analysis confirmed that RNA recombination with the 11083G > T mutation also contributed to the increase of mutations among the viral progeny. The findings indicate that the 11083G > T mutation of SARS-CoV-2 spread during shipboard quarantine and arose through de novo RNA recombination under positive selection pressure. In addition, in three patients in this cruise, two mutations 29736G > T and 29751G > T ("G13" and "G28") were also located in Coronavirus 3′ stem-loop II-like motif (s2m) , as "G28"

5890-408: A specialized polymerase is needed to extend it; Pol ζ . Pol ζ is unique in that it can extend terminal mismatches, whereas more processive polymerases cannot. So when a lesion is encountered, the replication fork will stall, PCNA will switch from a processive polymerase to a TLS polymerase such as Pol ι to fix the lesion, then PCNA may switch to Pol ζ to extend the mismatch, and last PCNA will switch to

6045-502: A type of horizontal gene transfer in which DNA is transferred from one bacterium to another by a virus . Foreign, bacterial DNA is sometimes misincorporated in the capsid head of bacteriophage virus particles as DNA is packaged into new bacteriophages during viral replication. When these new bacteriophages infect other bacteria, DNA from the previous host bacterium is injected into the new bacterial host as double-strand DNA. The RecBCD enzyme then incorporates this double-strand DNA into

6200-447: A variety of repair strategies have evolved to restore lost information. If possible, cells use the unmodified complementary strand of the DNA or the sister chromatid as a template to recover the original information. Without access to a template, cells use an error-prone recovery mechanism known as translesion synthesis as a last resort. Damage to DNA alters the spatial configuration of the helix, and such alterations can be detected by

6355-586: Is p53 , as it is required for inducing apoptosis following DNA damage. The cyclin-dependent kinase inhibitor p21 is induced by both p53-dependent and p53-independent mechanisms and can arrest the cell cycle at the G1/S and G2/M checkpoints by deactivating cyclin / cyclin-dependent kinase complexes. The SOS response is the changes in gene expression in Escherichia coli and other bacteria in response to extensive DNA damage. The prokaryotic SOS system

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6510-516: Is widely used by cells to accurately repair harmful DNA breaks that occur on both strands of DNA, known as double-strand breaks (DSB), in a process called homologous recombinational repair (HRR). Homologous recombination also produces new combinations of DNA sequences during meiosis , the process by which eukaryotes make gamete cells, like sperm and egg cells in animals. These new combinations of DNA represent genetic variation in offspring, which in turn enables populations to adapt during

6665-429: Is a DNA repair mechanism which, unlike homologous recombination, does not require a long homologous sequence to guide repair. Whether homologous recombination or NHEJ is used to repair double-strand breaks is largely determined by the phase of cell cycle . Homologous recombination repairs DNA before the cell enters mitosis (M phase). It occurs during and shortly after DNA replication , in the S and G 2 phases of

6820-427: Is a major DNA repair process in bacteria. It is also important for producing genetic diversity in bacterial populations, although the process differs substantially from meiotic recombination, which repairs DNA damages and brings about diversity in eukaryotic genomes . Homologous recombination has been most studied and is best understood for Escherichia coli . Double-strand DNA breaks in bacteria are repaired by

6975-491: Is a nearly universal biological mechanism. The discovery of genes for homologous recombination in protists —a diverse group of eukaryotic microorganisms —has been interpreted as evidence that homologous recombination emerged early in the evolution of eukaryotes. Since their dysfunction has been strongly associated with increased susceptibility to several types of cancer , the proteins that facilitate homologous recombination are topics of active research. Homologous recombination

7130-614: Is a pair of large protein kinases belonging to the first group of PI3K-like protein kinases-the ATM ( Ataxia telangiectasia mutated ) and ATR (Ataxia- and Rad-related) kinases, whose sequence and functions have been well conserved in evolution. All DNA damage response requires either ATM or ATR because they have the ability to bind to the chromosomes at the site of DNA damage, together with accessory proteins that are platforms on which DNA damage response components and DNA repair complexes can be assembled. An important downstream target of ATM and ATR

7285-419: Is a prominent cause of cancer. In contrast, DNA damage in infrequently-dividing cells is likely a prominent cause of aging. Cells cannot function if DNA damage corrupts the integrity and accessibility of essential information in the genome (but cells remain superficially functional when non-essential genes are missing or damaged). Depending on the type of damage inflicted on the DNA's double helical structure,

7440-414: Is a special problem in non-dividing or slowly-dividing cells, where unrepaired damage will tend to accumulate over time. On the other hand, in rapidly dividing cells, unrepaired DNA damage that does not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell's survival. Thus, in

7595-420: Is about two million base pairs at the site of a DNA double-strand break. γH2AX does not, itself, cause chromatin decondensation, but within 30 seconds of irradiation, RNF8 protein can be detected in association with γH2AX. RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with CHD4 , a component of the nucleosome remodeling and deacetylase complex NuRD . DDB2 occurs in

7750-503: Is about two million base pairs at the site of a DNA double-strand break. γH2AX does not, itself, cause chromatin decondensation, but within 30 seconds of irradiation, RNF8 protein can be detected in association with γH2AX. RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with CHD4 , a component of the nucleosome remodeling and deacetylase complex NuRD . After undergoing relaxation subsequent to DNA damage, followed by DNA repair, chromatin recovers to

7905-414: Is also evidence for recombination in some RNA viruses , specifically positive-sense ssRNA viruses like retroviruses , picornaviruses , and coronaviruses . There is controversy over whether homologous recombination occurs in negative-sense ssRNA viruses like influenza . In RNA viruses, homologous recombination can be either precise or imprecise. In the precise type of RNA-RNA recombination, there

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8060-457: Is also used in gene targeting , a technique for introducing genetic changes into target organisms. For their development of this technique, Mario Capecchi , Martin Evans and Oliver Smithies were awarded the 2007 Nobel Prize for Physiology or Medicine ; Capecchi and Smithies independently discovered applications to mouse embryonic stem cells, however the highly conserved mechanisms underlying

8215-414: Is always highly conserved and one of the strongest short signals in the genome. The high information content of SOS boxes permits differential binding of LexA to different promoters and allows for timing of the SOS response. The lesion repair genes are induced at the beginning of SOS response. The error-prone translesion polymerases, for example, UmuCD'2 (also called DNA polymerase V), are induced later on as

8370-446: Is certain methylation of the bases cytosine and adenine. When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in

8525-440: Is clearly a bacterial adaptation for DNA transfer. In order for a bacterium to bind, take up and integrate donor DNA into its resident chromosome by homologous recombination, it must first enter a special physiological state termed competence . The RecA / Rad51 / DMC1 gene family plays a central role in homologous recombination during bacterial transformation as it does during eukaryotic meiosis and mitosis. For instance,

8680-450: Is controlled by the sequence context of the two recombining strands of RNA: sequences rich in adenine and uracil decrease crossover precision. Homologous recombination is important in facilitating viral evolution . For example, if the genomes of two viruses with different disadvantageous mutations undergo recombination, then they may be able to regenerate a fully functional genome. Alternatively, if two similar viruses have infected

8835-484: Is controlled by two master kinases , ATM and ATR . ATM responds to DNA double-strand breaks and disruptions in chromatin structure, whereas ATR primarily responds to stalled replication forks . These kinases phosphorylate downstream targets in a signal transduction cascade, eventually leading to cell cycle arrest. A class of checkpoint mediator proteins including BRCA1 , MDC1 , and 53BP1 has also been identified. These proteins seem to be required for transmitting

8990-485: Is critical for cell immortalization , a key feature of cancer. Most cancers maintain telomeres by upregulating telomerase. However, in several types of human cancer, a BIR-like pathway helps to sustain some tumors by acting as an alternative mechanism of telomere maintenance. This fact has led scientists to investigate whether such recombination-based mechanisms of telomere maintenance could thwart anti-cancer drugs like telomerase inhibitors . Homologous recombination

9145-526: Is cut on the crossing strand and the other Holliday junction is cut on the non-crossing strand (in Figure 5, along the horizontal purple arrowheads at one Holliday junction and along the vertical orange arrowheads at the other). Alternatively, if the two Holliday junctions are cut on the crossing strands (along the horizontal purple arrowheads at both Holliday junctions in Figure 5), then chromosomes without crossover will be produced. Homologous recombination via

9300-564: Is damaged. This is followed by phosphorylation of the cell cycle checkpoint protein Chk1 , initiating its function, about 10 minutes after DNA is damaged. After DNA damage, cell cycle checkpoints are activated. Checkpoint activation pauses the cell cycle and gives the cell time to repair the damage before continuing to divide. DNA damage checkpoints occur at the G1 / S and G2 / M boundaries. An intra- S checkpoint also exists. Checkpoint activation

9455-416: Is found frequently in DNA, about once every 64 nucleotides. Before cutting, RuvC likely gains access to the Holliday junction by displacing one of the two RuvA tetramers covering the DNA there. Recombination results in either "splice" or "patch" products, depending on how RuvC cleaves the Holliday junction. Splice products are crossover products, in which there is a rearrangement of genetic material around

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9610-402: Is found, the recombinases facilitate invasion of the ssDNA end into the homologous dsDNA to form a D-loop. After strand exchange, homologous recombination intermediates are processed by either of two distinct pathways (see diagram) to form the final recombinant chromosomes. DNA repair DNA repair is a collection of processes by which a cell identifies and corrects damage to

9765-484: Is known to add the first adenine across the T^T photodimer using Watson-Crick base pairing and the second adenine will be added in its syn conformation using Hoogsteen base pairing . From a cellular perspective, risking the introduction of point mutations during translesion synthesis may be preferable to resorting to more drastic mechanisms of DNA repair, which may cause gross chromosomal aberrations or cell death. In short,

9920-496: Is likely because the slower RecB helicase unwinds the DNA after Chi, rather than the faster RecD helicase, which unwinds the DNA before Chi. Recognition of the Chi site also changes the RecBCD enzyme so that it cuts the DNA strand with Chi and begins loading multiple RecA proteins onto the single-stranded DNA with the newly generated 3' end. The resulting RecA-coated nucleoprotein filament then searches out similar sequences of DNA on

10075-452: Is located inside mitochondria organelles , exists in multiple copies, and is also tightly associated with a number of proteins to form a complex known as the nucleoid. Inside mitochondria, reactive oxygen species (ROS), or free radicals , byproducts of the constant production of adenosine triphosphate (ATP) via oxidative phosphorylation , create a highly oxidative environment that is known to damage mtDNA. A critical enzyme in counteracting

10230-731: Is more frequent than in yeast. In the early 1900s, William Bateson and Reginald Punnett found an exception to one of the principles of inheritance originally described by Gregor Mendel in the 1860s. In contrast to Mendel's notion that traits are independently assorted when passed from parent to child—for example that a cat's hair color and its tail length are inherited independent of each other—Bateson and Punnett showed that certain genes associated with physical traits can be inherited together, or genetically linked . In 1911, after observing that linked traits could on occasion be inherited separately, Thomas Hunt Morgan suggested that " crossovers " can occur between linked genes, where one of

10385-456: Is no difference between the two parental RNA sequences and the resulting crossover RNA region. Because of this, it is often difficult to determine the location of crossover events between two recombining RNA sequences. In imprecise RNA homologous recombination, the crossover region has some difference with the parental RNA sequences – caused by either addition, deletion, or other modification of nucleotides. The level of precision in crossover

10540-440: Is obligately dependent on energy absorbed from blue/UV light (300–500 nm wavelength ) to promote catalysis. Photolyase, an old enzyme present in bacteria , fungi , and most animals no longer functions in humans, who instead use nucleotide excision repair to repair damage from UV irradiation. Another type of damage, methylation of guanine bases, is directly reversed by the enzyme methyl guanine methyl transferase (MGMT),

10695-487: Is regulated by two key proteins: LexA and RecA . The LexA homodimer is a transcriptional repressor that binds to operator sequences commonly referred to as SOS boxes. In Escherichia coli it is known that LexA regulates transcription of approximately 48 genes including the lexA and recA genes. The SOS response is known to be widespread in the Bacteria domain, but it is mostly absent in some bacterial phyla, like

10850-402: Is the main recombination pathway used in many bacteria to repair double-strand breaks in DNA, and the proteins are found in a broad array of bacteria. These double-strand breaks can be caused by UV light and other radiation , as well as chemical mutagens . Double-strand breaks may also arise by DNA replication through a single-strand nick or gap. Such a situation causes what is known as

11005-492: Is then able to anneal to the other 3' overhang in the damaged chromosome through complementary base pairing. After the strands anneal, a small flap of DNA can sometimes remain. Any such flaps are removed, and the SDSA pathway finishes with the resealing, also known as ligation , of any remaining single-stranded gaps. During mitosis, the major homologous recombination pathway for repairing DNA double-strand breaks appears to be

11160-421: Is transferred between bacteria through direct cell-to-cell contact, homologous recombination helps integrate foreign DNA into the host genome via the RecBCD pathway. The RecBCD enzyme promotes recombination after DNA is converted from single-strand DNA–in which form it originally enters the bacterium–to double-strand DNA during replication. The RecBCD pathway is also essential for the final phase of transduction ,

11315-466: Is unique in that it does not require a separate similar or identical molecule of DNA, like the DSBR or SDSA pathways of homologous recombination. Instead, the SSA pathway only requires a single DNA duplex, and uses the repeat sequences as the identical sequences that homologous recombination needs for repair. The pathway is relatively simple in concept: after two strands of the same DNA duplex are cut back around

11470-552: Is used to form a D-loop at that point, displacing the intact chromosome's other strand. Various ligation and synthesis steps follow to effect the rejoining. In humans, the protein RAD51 is central to the homologous search and formation of the D-loop. In the bacterium Escherichia coli , a similar function is performed by the protein RecA . During meiosis , repair of double-strand damages, particularly double-strand breaks, occurs by

11625-473: Is very complex and tightly regulated, thus allowing coordinated global response to damage. Exposure of yeast Saccharomyces cerevisiae to DNA damaging agents results in overlapping but distinct transcriptional profiles. Similarities to environmental shock response indicates that a general global stress response pathway exist at the level of transcriptional activation. In contrast, different human cell types respond to damage differently indicating an absence of

11780-570: The Coronavirus 3′ stem-loop II-like motif (s2m) , an RNA motif in 3' untranslated region of viral genome, suggesting that RNA recombination events may have occurred in s2m of SARS-CoV-2. Based on computational analysis of 1319 Australia SARS‐CoV‐2 sequences using Recco algorithm ( https://recco.bioinf.mpi-inf.mpg.de/ ), 29742G("G19"), 29744G("G21"), and 29751G("G28") were predicted as recombination hotspots. The SARS-CoV-2 outbreak in Diamond Princess cruise most likely originated from either

11935-475: The DNA molecules that encode its genome . In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in tens of thousands of individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in

12090-627: The RecBCD pathway of homologous recombination. Breaks that occur on only one of the two DNA strands, known as single-strand gaps, are thought to be repaired by the RecF pathway . Both the RecBCD and RecF pathways include a series of reactions known as branch migration , in which single DNA strands are exchanged between two intercrossed molecules of duplex DNA, and resolution , in which those two intercrossed molecules of DNA are cut apart and restored to their normal double-stranded state. The RecBCD pathway

12245-518: The RecQ helicase unwinds the DNA and the RecJ nuclease degrades the strand with a 5' end, leaving the strand with the 3' end intact. RecA protein binds to this strand and is either aided by the RecF, RecO, and RecR proteins or stabilized by them. The RecA nucleoprotein filament then searches for a homologous DNA and exchanges places with the identical or nearly identical strand in the homologous DNA. Although

12400-637: The Spirochetes . The most common cellular signals activating the SOS response are regions of single-stranded DNA (ssDNA), arising from stalled replication forks or double-strand breaks, which are processed by DNA helicase to separate the two DNA strands. In the initiation step, RecA protein binds to ssDNA in an ATP hydrolysis driven reaction creating RecA–ssDNA filaments. RecA–ssDNA filaments activate LexA auto protease activity, which ultimately leads to cleavage of LexA dimer and subsequent LexA degradation. The loss of LexA repressor induces transcription of

12555-462: The cell cycle and is condensed into aggregate structures known as chromosomes during cell division . In either state the DNA is highly compacted and wound up around bead-like proteins called histones . Whenever a cell needs to express the genetic information encoded in its n-DNA the required chromosomal region is unraveled, genes located therein are expressed, and then the region is condensed back to its resting conformation. Mitochondrial DNA (mtDNA)

12710-465: The gene dosage of the gene SIR-2, which regulates DNA packaging in the nematode worm Caenorhabditis elegans , can significantly extend lifespan. The mammalian homolog of SIR-2 is known to induce downstream DNA repair factors involved in NHEJ, an activity that is especially promoted under conditions of caloric restriction. Caloric restriction has been closely linked to the rate of base excision repair in

12865-407: The heavy strand (or H-strand) of the molecule, which it displaced, and was hydrogen bonded to the light strand (or L-strand). Since then, it has been shown that the third strand is the initial segment generated by a replication of the heavy strand that has been arrested shortly after initiation and is often maintained for some period in that state. The D-loop occurs in the main non-coding area of

13020-552: The nuclease activity of Exo1 and Dna2 allows them to cut the single-stranded DNA produced by Sgs1. The RPA protein, which has high affinity for single-stranded DNA, then binds the 3' overhangs. With the help of several other proteins that mediate the process, the Rad51 protein (and Dmc1 , in meiosis) then forms a filament of nucleic acid and protein on the single strand of DNA coated with RPA. This nucleoprotein filament then begins searching for DNA sequences similar to that of

13175-471: The replication forks , are among known stimulation signals for a global response to DNA damage. The global response to damage is an act directed toward the cells' own preservation and triggers multiple pathways of macromolecular repair, lesion bypass, tolerance, or apoptosis . The common features of global response are induction of multiple genes , cell cycle arrest, and inhibition of cell division . The packaging of eukaryotic DNA into chromatin presents

13330-425: The toxicity of these species is superoxide dismutase , which is present in both the mitochondria and cytoplasm of eukaryotic cells. Senescence, an irreversible process in which the cell no longer divides , is a protective response to the shortening of the chromosome ends, called telomeres . The telomeres are long regions of repetitive noncoding DNA that cap chromosomes and undergo partial degradation each time

13485-399: The 3' overhang. After finding such a sequence, the single-stranded nucleoprotein filament moves into (invades) the similar or identical recipient DNA duplex in a process called strand invasion . In cells that divide through mitosis, the recipient DNA duplex is generally a sister chromatid, which is identical to the damaged DNA molecule and provides a template for repair. In meiosis, however,

13640-453: The BIR pathway remain unclear. Three proposed mechanisms have strand invasion as an initial step, but they differ in how they model the migration of the D-loop and later phases of recombination. The BIR pathway can also help to maintain the length of telomeres (regions of DNA at the end of eukaryotic chromosomes) in the absence of (or in cooperation with) telomerase . Without working copies of

13795-415: The D-loop structure that is associated with initiation of DNA replication. D-loop sequences are also of interest in the study of cancers. The function of the D-loop is not yet clear, but recent research suggests that it participates in the organization of the mitochondrial nucleoid . In 1999 it was reported that telomeres , which cap the end of chromosomes , terminate in a lariat -like structure termed

13950-622: The DNA repair enzyme MRE11 , to initiate DNA repair, within 13 seconds. γH2AX, the phosphorylated form of H2AX is also involved in the early steps leading to chromatin decondensation after DNA double-strand breaks. The histone variant H2AX constitutes about 10% of the H2A histones in human chromatin. γH2AX (H2AX phosphorylated on serine 139) can be detected as soon as 20 seconds after irradiation of cells (with DNA double-strand break formation), and half maximum accumulation of γH2AX occurs in one minute. The extent of chromatin with phosphorylated γH2AX

14105-400: The DNA, such as single- and double-strand breaks, 8-hydroxydeoxyguanosine residues, and polycyclic aromatic hydrocarbon adducts. DNA damage can be recognized by enzymes, and thus can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying. If a cell retains DNA damage, transcription of

14260-511: The DNA. At a site of lesion , PCNA is ubiquitinated, or modified, by the RAD6/ RAD18 proteins to provide a platform for the specialized polymerases to bypass the lesion and resume DNA replication. After translesion synthesis, extension is required. This extension can be carried out by a replicative polymerase if the TLS is error-free, as in the case of Pol η, yet if TLS results in a mismatch,

14415-463: The DSB repair model, including uniform homologous integration of transformed DNA (gene therapy), were first shown in plasmid experiments by Orr-Weaver, Szostak and Rothstein. Researching the plasmid-induced DSB, using γ-irradiation in the 1970s-1980s, led to later experiments using endonucleases (e.g. I-SceI) to cut chromosomes for genetic engineering of mammalian cells, where nonhomologous recombination

14570-425: The DSBR (double-strand break repair) pathway or the SDSA (synthesis-dependent strand annealing) pathway. Homologous recombination that occurs during DNA repair tends to result in non-crossover products, in effect restoring the damaged DNA molecule as it existed before the double-strand break. Homologous recombination is conserved across all three domains of life as well as DNA and RNA viruses , suggesting that it

14725-617: The Holliday junction moves along the linked DNA during the branch migration process. It is in this movement of the Holliday junction that base pairs between the two homologous DNA duplexes are exchanged. To catalyze branch migration, the RuvA protein first recognizes and binds to the Holliday junction and recruits the RuvB protein to form the RuvAB complex. Two sets of the RuvB protein, which each form

14880-545: The RecA protein is essential for transformation in Bacillus subtilis and Streptococcus pneumoniae , and expression of the RecA gene is induced during the development of competence for transformation in these organisms. As part of the transformation process, the RecA protein interacts with entering single-stranded DNA (ssDNA) to form RecA/ssDNA nucleofilaments that scan the resident chromosome for regions of homology and bring

15035-550: The SDSA pathway (rather than the DSBR pathway). The SDSA pathway produces non-crossover recombinants (Figure 5). During meiosis non-crossover recombinants also occur frequently and these appear to arise mainly by the SDSA pathway as well. Non-crossover recombination events occurring during meiosis likely reflect instances of repair of DNA double-strand damages or other types of DNA damages. The single-strand annealing (SSA) pathway of homologous recombination repairs double-strand breaks between two repeat sequences . The SSA pathway

15190-401: The SDSA pathway occurs in cells that divide through mitosis and meiosis and results in non-crossover products. In this model, the invading 3' strand is extended along the recipient DNA duplex by a DNA polymerase, and is released as the Holliday junction between the donor and recipient DNA molecules slides in a process called branch migration . The newly synthesized 3' end of the invading strand

15345-432: The SOS genes and allows for further signal induction, inhibition of cell division and an increase in levels of proteins responsible for damage processing. In Escherichia coli , SOS boxes are 20-nucleotide long sequences near promoters with palindromic structure and a high degree of sequence conservation. In other classes and phyla, the sequence of SOS boxes varies considerably, with different length and composition, but it

15500-691: The Y Polymerase family), often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides. The polymerase switching is thought to be mediated by, among other factors, the post-translational modification of the replication processivity factor PCNA . Translesion synthesis polymerases often have low fidelity (high propensity to insert wrong bases) on undamaged templates relative to regular polymerases. However, many are extremely efficient at inserting correct bases opposite specific types of damage. For example, Pol η mediates error-free bypass of lesions induced by UV irradiation , whereas Pol ι introduces mutations at these sites. Pol η

15655-493: The absence of pro-growth cellular signaling . Unregulated cell division can lead to the formation of a tumor (see cancer ), which is potentially lethal to an organism. Therefore, the induction of senescence and apoptosis is considered to be part of a strategy of protection against cancer. It is important to distinguish between DNA damage and mutation, the two major types of error in DNA. DNA damage and mutation are fundamentally different. Damage results in physical abnormalities in

15810-503: The addition of a phosphate, Sae2 causes a clean cut to be made near a double-strand break in DNA. It is unclear if the endonuclease responsible for this cut is Sae2 itself or another protein, Mre11 . This allows a protein complex including Mre11, known as the MRX complex , to bind to DNA, and begins a series of protein-driven reactions that exchange material between two DNA molecules. The packaging of eukaryotic DNA into chromatin presents

15965-463: The bacterial equivalent of which is called ogt . This is an expensive process because each MGMT molecule can be used only once; that is, the reaction is stoichiometric rather than catalytic . A generalized response to methylating agents in bacteria is known as the adaptive response and confers a level of resistance to alkylating agents upon sustained exposure by upregulation of alkylation repair enzymes. The third type of DNA damage reversed by cells

16120-601: The break is cut back. This happens in two distinct steps: first the MRX complex recruits the Sae2 protein, and these two proteins trim back the 5' ends on either side of the break to create short 3' overhangs of single-strand DNA; in the second step, 5'→3' resection is continued by the Sgs1 helicase and the Exo1 and Dna2 nucleases. As a helicase , Sgs1 "unzips" the double-strand DNA, while

16275-435: The break is repaired via TMEJ in the S and G 2 phases of the cell cycle. In contrast to homologous recombination and TMEJ, NHEJ is predominant in the G 1 phase of the cell cycle, when the cell is growing but not yet ready to divide. It occurs less frequently after the G 1 phase, but maintains at least some activity throughout the cell cycle. The mechanisms that regulate homologous recombination and NHEJ throughout

16430-475: The break, and aligns them to enable the two complementary repeat sequences to anneal. After annealing is complete, leftover non-homologous flaps of the 3' overhangs are cut away by a set of nucleases, known as Rad1/Rad10 , which are brought to the flaps by the Saw1 and Slx4 proteins. New DNA synthesis fills in any gaps, and ligation restores the DNA duplex as two continuous strands. The DNA sequence between

16585-429: The capacity of the cell to repair it, the accumulation of errors can overwhelm the cell and result in early senescence, apoptosis, or cancer. Inherited diseases associated with faulty DNA repair functioning result in premature aging, increased sensitivity to carcinogens and correspondingly increased cancer risk (see below ). On the other hand, organisms with enhanced DNA repair systems, such as Deinococcus radiodurans ,

16740-496: The cell cycle vary widely between species. Cyclin-dependent kinases (CDKs), which modify the activity of other proteins by adding phosphate groups to (that is, phosphorylating ) them, are important regulators of homologous recombination in eukaryotes. When DNA replication begins in budding yeast, the cyclin-dependent kinase Cdc28 begins homologous recombination by phosphorylating the Sae2 protein. After being so activated by

16895-433: The cell cycle, when sister chromatids are more easily available. Compared to homologous chromosomes, which are similar to another chromosome but often have different alleles , sister chromatids are an ideal template for homologous recombination because they are an identical copy of a given chromosome. When no homologous template is available or when the template cannot be accessed due to a defect in homologous recombination,

17050-492: The cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damage and mutation are related because DNA damage often causes errors of DNA synthesis during replication or repair; these errors are a major source of mutation. Given these properties of DNA damage and mutation, it can be seen that DNA damage

17205-566: The cell type, the age of the cell, and the extracellular environment. A cell that has accumulated a large amount of DNA damage or can no longer effectively repair its DNA may enter one of three possible states: The DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal functionality of that organism. Many genes that were initially shown to influence life span have turned out to be involved in DNA damage repair and protection. The 2015 Nobel Prize in Chemistry

17360-475: The cell's genome, which affect the survival of its daughter cells after it undergoes mitosis . As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur. This can eventually lead to malignant tumors, or cancer as per the two-hit hypothesis . The rate of DNA repair depends on various factors, including

17515-404: The cell. Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind and form a complex that enables the actual repair to take place. Cells are known to eliminate three types of damage to their DNA by chemically reversing it. These mechanisms do not require a template, since the types of damage they counteract can occur in only one of

17670-690: The checkpoint activation signal to downstream proteins. DNA damage checkpoint is a signal transduction pathway that blocks cell cycle progression in G1, G2 and metaphase and slows down the rate of S phase progression when DNA is damaged. It leads to a pause in cell cycle allowing the 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 group, two serine/threonine(S/T) kinases and their adaptors. Central to all DNA damage induced checkpoints responses

17825-441: The chromatin at the site of UV damage to DNA. This relaxation allows other proteins in the nucleotide excision repair pathway to enter the chromatin and repair UV-induced cyclobutane pyrimidine dimer damages. After rapid chromatin remodeling , cell cycle checkpoints are 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

17980-439: The course of evolution . Homologous recombination is also used in horizontal gene transfer to exchange genetic material between different strains and species of bacteria and viruses. Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria. Although homologous recombination varies widely among different organisms and cell types, for double-stranded DNA ( dsDNA ) most forms involve

18135-560: The course of changing the DNA's state of supercoiling , which is especially common in regions near an open replication fork. Such breaks are not considered DNA damage because they are a natural intermediate in the topoisomerase biochemical mechanism and are immediately repaired by the enzymes that created them. Another type of DNA double-strand breaks originates from the DNA heat-sensitive or heat-labile sites. These DNA sites are not initial DSBs. However, they convert to DSB after treating with elevated temperature. Ionizing irradiation can induces

18290-412: The double-strand break repair (DSBR) pathway (sometimes called the double Holliday junction model ) and the synthesis-dependent strand annealing (SDSA) pathway. The two pathways are similar in their first several steps. After a double-strand break occurs, the MRX complex ( MRN complex in humans) binds to DNA on either side of the break. Next a resection takes place, in which DNA around the 5' ends of

18445-487: The earliest steps, the stress-activated protein kinase, c-Jun N-terminal kinase (JNK) , phosphorylates SIRT6 on serine 10 in response to double-strand breaks or other DNA damage. This post-translational modification facilitates the mobilization of SIRT6 to DNA damage sites, and is required for efficient recruitment of poly (ADP-ribose) polymerase 1 (PARP1) to DNA break sites and for efficient repair of DSBs. PARP1 protein starts to appear at DNA damage sites in less than

18600-1316: The emergence of other models of homologous recombination, called SDSA pathways , which do not always rely on Holliday junctions. Much of the later work identifying proteins involved in the process and determining their mechanisms has been performed by a number of individuals including James Haber , Patrick Sung , Stephen Kowalczykowski , and others. Homologous recombination (HR) is essential to cell division in eukaryotes like plants, animals, fungi and protists. Homologous recombination repairs double-strand breaks in DNA caused by ionizing radiation or DNA-damaging chemicals. Left unrepaired, these double-strand breaks can cause large-scale rearrangement of chromosomes in somatic cells , which can in turn lead to cancer. In addition to repairing DNA, homologous recombination also helps produce genetic diversity when cells divide in meiosis to become specialized gamete cells— sperm or egg cells in animals, pollen or ovules in plants, and spores in fungi . It does so by facilitating chromosomal crossover , in which regions of similar but not identical DNA are exchanged between homologous chromosomes . This creates new, possibly beneficial combinations of genes, which can give offspring an evolutionary advantage. Chromosomal crossover often begins when

18755-466: The entering ssDNA to the corresponding region, where strand exchange and homologous recombination occur. Thus the process of homologous recombination during bacterial transformation has fundamental similarities to homologous recombination during meiosis . Homologous recombination occurs in several groups of viruses. In DNA viruses such as herpesvirus , recombination occurs through a break-and-rejoin mechanism like in bacteria and eukaryotes. There

18910-401: The enzyme telomerase, telomeres typically shorten with each cycle of mitosis, which eventually blocks cell division and leads to senescence . In budding yeast cells where telomerase has been inactivated through mutations, two types of "survivor" cells have been observed to avoid senescence longer than expected by elongating their telomeres through BIR pathways. Maintaining telomere length

19065-412: The four bases. Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone. The formation of pyrimidine dimers upon irradiation with UV light results in an abnormal covalent bond between adjacent pyrimidine bases. The photoreactivation process directly reverses this damage by the action of the enzyme photolyase , whose activation

19220-406: The genome of the new bacterial host. Natural bacterial transformation involves the transfer of DNA from a donor bacterium to a recipient bacterium, where both donor and recipient are ordinarily of the same species . Transformation, unlike bacterial conjugation and transduction, depends on numerous bacterial gene products that specifically interact to perform this process. Thus transformation

19375-432: The genome, with random DNA breaks, can form DNA fragments through annealing . Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue extension until complementary partner strands are found. In the final step, there is crossover by means of RecA -dependent homologous recombination . Topoisomerases introduce both single- and double-strand breaks in

19530-449: The homologous chromosome. PRDM9 deposits both H3K4me3 and H3K36me3 histone methylation marks at the sites it binds, and this methyltransferase activity is essential for its role in DSB positioning. Following their formation, DSB sites are processed by resection, resulting in single-stranded DNA (ssDNA) that becomes decorated with DMC1. From mid-zygotene to early pachytene, as part of the recombinational repair process, DMC1 dissociates from

19685-550: The incorporation of wrong bases opposite damaged ones. Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable (except in the rare case of a back mutation , for example, through gene conversion ). There are several types of damage to DNA due to endogenous cellular processes: Damage caused by exogenous agents comes in many forms. Some examples are: UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of induced damage. Spontaneous damage can include

19840-511: The linked genes physically crosses over to a different chromosome . Two decades later, Barbara McClintock and Harriet Creighton demonstrated that chromosomal crossover occurs during meiosis , the process of cell division by which sperm and egg cells are made. Within the same year as McClintock's discovery, Curt Stern showed that crossing over—later called "recombination"—could also occur in somatic cells like white blood cells and skin cells that divide through mitosis . In 1947,

19995-455: The loss of a base, deamination, sugar ring puckering and tautomeric shift. Constitutive (spontaneous) DNA damage caused by endogenous oxidants can be detected as a low level of histone H2AX phosphorylation in untreated cells. In human cells, and eukaryotic cells in general, DNA is found in two cellular locations – inside the nucleus and inside the mitochondria . Nuclear DNA (n-DNA) exists as chromatin during non-replicative stages of

20150-698: The maximum chromatin relaxation, presumably due to action of ALC1, occurs by 10 seconds. This then allows recruitment of the DNA repair enzyme MRE11 , to initiate DNA repair, within 13 seconds. γH2AX, the phosphorylated form of H2AX is also involved in the early steps leading to chromatin decondensation after DNA double-strand breaks. The histone variant H2AX constitutes about 10% of the H2A histones in human chromatin. γH2AX (H2AX phosphorylated on serine 139) can be detected as soon as 20 seconds after irradiation of cells (with DNA double-strand break formation), and half maximum accumulation of γH2AX occurs in one minute. The extent of chromatin with phosphorylated γH2AX

20305-492: The microbiologist Joshua Lederberg showed that bacteria—which had been assumed to reproduce only asexually through binary fission —are capable of genetic recombination, which is more similar to sexual reproduction. This work established E. coli as a model organism in genetics, and helped Lederberg win the 1958 Nobel Prize in Physiology or Medicine . Building on studies in fungi , in 1964 Robin Holliday proposed

20460-408: The mitochondrial DNA molecule, a segment called the control region or D-loop region. Replication of the mitochondrial DNA can occur in two different ways, both starting in the D-loop region. One way continues replication of the heavy strand through a substantial part (e.g. two-thirds) of the circular molecule, and then replication of the light strand begins. The more recently reported mode starts at

20615-420: The most radiation-resistant known organism, exhibit remarkable resistance to the double-strand break-inducing effects of radioactivity , likely due to enhanced efficiency of DNA repair and especially NHEJ. A number of individual genes have been identified as influencing variations in life span within a population of organisms. The effects of these genes is strongly dependent on the environment, in particular, on

20770-460: The nuclear DNA of rodents, although similar effects have not been observed in mitochondrial DNA. The C. elegans gene AGE-1, an upstream effector of DNA repair pathways, confers dramatically extended life span under free-feeding conditions but leads to a decrease in reproductive fitness under conditions of caloric restriction. This observation supports the pleiotropy theory of the biological origins of aging , which suggests that genes conferring

20925-434: The offspring of that organism. Homologous recombination requires incoming DNA to be highly similar to the recipient genome, and so horizontal gene transfer is usually limited to similar bacteria. Studies in several species of bacteria have established that there is a log-linear decrease in recombination frequency with increasing difference in sequence between host and recipient DNA. In bacterial conjugation , where DNA

21080-756: The organism's diet. Caloric restriction reproducibly results in extended lifespan in a variety of organisms, likely via nutrient sensing pathways and decreased metabolic rate . The molecular mechanisms by which such restriction results in lengthened lifespan are as yet unclear (see for some discussion); however, the behavior of many genes 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 constitutive level of mTOR signaling, an evidence of reduction of metabolic activity , and concurrently to reduce constitutive level of DNA damage induced by endogenously generated reactive oxygen species. For example, increasing

21235-502: The process involves specialized polymerases either bypassing or repairing lesions at locations of stalled DNA replication. For example, Human DNA polymerase eta can bypass complex DNA lesions like guanine-thymine intra-strand crosslink, G[8,5-Me]T, although it can cause targeted and semi-targeted mutations. Paromita Raychaudhury and Ashis Basu studied the toxicity and mutagenesis of the same lesion in Escherichia coli by replicating

21390-412: The processive polymerase to continue replication. Cells exposed to ionizing radiation , ultraviolet light or chemicals are prone to acquire multiple sites of bulky DNA lesions and double-strand breaks. Moreover, DNA damaging agents can damage other biomolecules such as proteins , carbohydrates , lipids , and RNA . The accumulation of damage, to be specific, double-strand breaks or adducts stalling

21545-541: The proteins and specific mechanisms involved in their initial phases differ, the two pathways are similar in that they both require single-stranded DNA with a 3' end and the RecA protein for strand invasion. The pathways are also similar in their phases of branch migration , in which the Holliday junction slides in one direction, and resolution , in which the Holliday junctions are cleaved apart by enzymes. The alternative, non-reciprocal type of resolution may also occur by either pathway. Immediately after strand invasion,

21700-405: The recipient DNA tends to be from a similar but not necessarily identical homologous chromosome. A displacement loop ( D-loop ) is formed during strand invasion between the invading 3' overhang strand and the homologous chromosome. After strand invasion, a DNA polymerase extends the end of the invading 3' strand by synthesizing new DNA. This changes the D-loop to a cross-shaped structure known as

21855-417: The recombination process outlined in the accompanying diagram. As shown in the diagram, a D-loop plays a central role in meiotic recombinational repair of such damages. During this process, Rad51 and Dmc1 recombinases bind the 3’ single-strand DNA (ssDNA) tails to form helical nucleoprotein filaments that perform a search for intact homologous double-stranded DNA (dsDNA). Once the homologous sequence

22010-447: The repeats is always lost, as is one of the two repeats. The SSA pathway is considered mutagenic since it results in such deletions of genetic material. During DNA replication , double-strand breaks can sometimes be encountered at replication forks as DNA helicase unzips the template strand. These defects are repaired in the break-induced replication (BIR) pathway of homologous recombination. The precise molecular mechanisms of

22165-448: The same basic steps. After a double-strand break occurs, sections of DNA around the 5' ends of the break are cut away in a process called resection . In the strand invasion step that follows, an overhanging 3' end of the broken DNA molecule then "invades" a similar or identical DNA molecule that is not broken. After strand invasion, the further sequence of events may follow either of two main pathways discussed below (see Models );

22320-800: The same host cell, homologous recombination can allow those two viruses to swap genes and thereby evolve more potent variations of themselves. Homologous recombination is the proposed mechanism whereby the DNA virus human herpesvirus-6 integrates into human telomeres. When two or more viruses, each containing lethal genomic damage, infect the same host cell, the virus genomes can often pair with each other and undergo homologous recombinational repair to produce viable progeny. This process, known as multiplicity reactivation, has been studied in several bacteriophages , including phage T4 . Enzymes employed in recombinational repair in phage T4 are functionally homologous to enzymes employed in bacterial and eukaryotic recombinational repair. In particular, with regard to

22475-714: The same infected cell. RNA recombination appears to be a major driving force in determining (1) genetic variability within a CoV species, (2) the capability of a CoV species to jump from one host to another, and (3) infrequently, the emergence of novel CoVs. The mechanism of recombination in CoVs likely involves template switching during genome replication. Recombination in RNA viruses appears to be an adaptation for coping with genome damage. The pandemic SARS-CoV-2's entire receptor binding motif appears to have been introduced through recombination from coronaviruses of pangolins . Such

22630-399: The shortest lived species, mouse, expresses DNA repair genes, including core genes in several DNA repair pathways, at a lower level than do humans and naked mole rats. Furthermore several DNA repair pathways in humans and naked mole-rats are up-regulated compared to mouse. These observations suggest that elevated DNA repair facilitates greater longevity . If the rate of DNA damage exceeds

22785-436: The site of recombination. Patch products, on the other hand, are non-crossover products in which there is no such rearrangement and there is only a "patch" of hybrid DNA in the recombination product. Homologous recombination is an important method of integrating donor DNA into a recipient organism's genome in horizontal gene transfer , the process by which an organism incorporates foreign DNA from another organism without being

22940-478: The site of the double-strand break, the two resulting 3' overhangs then align and anneal to each other, restoring the DNA as a continuous duplex. As DNA around the double-strand break is cut back, the single-stranded 3' overhangs being produced are coated with the RPA protein, which prevents the 3' overhangs from sticking to themselves. A protein called Rad52 then binds each of the repeat sequences on either side of

23095-463: The ssDNA and counts decrease until all breaks (except those on the XY chromosomes) are repaired at late pachytene. Several other proteins are involved in this process, including ZCWPW1, the first protein directly positioned by PRDM9's dual histone marks. ZCWPW1 is important for homologous DSB repair, not positioning. Two primary models for how homologous recombination repairs double-strand breaks in DNA are

23250-452: The standard double helix. Unlike proteins and RNA , DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage. DNA damage can be subdivided into two main types: The replication of damaged DNA before cell division can lead to

23405-498: The surface of RuvA as they are guided by the protein from one duplex to the other. In the resolution phase of recombination, any Holliday junctions formed by the strand invasion process are cut, thereby restoring two separate DNA molecules. This cleavage is done by RuvAB complex interacting with RuvC, which together form the RuvABC complex. RuvC is an endonuclease that cuts the degenerate sequence 5'-(A/T)TT(G/C)-3'. The sequence

23560-498: The undamaged DNA strand. Double-strand breaks, in which both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements . In fact, when a double-strand break is accompanied by a cross-linkage joining the two strands at the same point, neither strand can be used as a template for the repair mechanisms, so that the cell will not be able to complete mitosis when it next divides, and will either die or, in rare cases, undergo

23715-490: Was awarded to Tomas Lindahl , Paul Modrich , and Aziz Sancar for their work on the molecular mechanisms of DNA repair processes. DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day. While this constitutes at most only 0.0003125% of the human genome's approximately 3.2 billion bases, unrepaired lesions in critical genes (such as tumor suppressor genes ) can impede

23870-464: Was not involved in strand invasion) also forms a Holliday junction with the homologous chromosome. The double Holliday junctions are then converted into recombination products by nicking endonucleases , a type of restriction endonuclease which cuts only one DNA strand. The DSBR pathway commonly results in crossover, though it can sometimes result in non-crossover products; the ability of a broken DNA molecule to collect sequences from separated donor loci

24025-462: Was shown in mitotic budding yeast using plasmids or endonuclease induction of chromosomal events. Because of this tendency for chromosomal crossover, the DSBR pathway is a likely model of how crossover homologous recombination occurs during meiosis. Whether recombination in the DSBR pathway results in chromosomal crossover is determined by how the double Holliday junction is cut, or "resolved". Chromosomal crossover will occur if one Holliday junction

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