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
virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsk ...
es).
Homologous recombination is widely used by cells to accurately
DNA repair
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA da ...
harmful 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
Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately r ...
, the process by which
eukaryotes make
gamete
A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
cells, like
sperm and
egg cells
The egg cell, or ovum (plural ova), is the female reproductive cell, or gamete, in most anisogamous organisms (organisms that reproduce sexually with a larger, female gamete and a smaller, male one). The term is used when the female gamete is ...
in animals. These new combinations of DNA represent
genetic variation in offspring, which in turn enables populations to
adapt during the course of
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
.
Homologous recombination is also used in
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...
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 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
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide pentose-sugar-r ...
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); 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
virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsk ...
es, suggesting that it is a nearly universal biological mechanism. The discovery of genes for homologous recombination in
protist
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exc ...
s—a diverse group of eukaryotic
microorganisms—has been interpreted as evidence that meiosis emerged early in the evolution of eukaryotes. Since their dysfunction has been strongly associated with increased susceptibility to several types of
cancer
Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumors, which do not spread. Possible signs and symptoms include a lump, abnormal b ...
, the proteins that facilitate homologous recombination are topics of active research. Homologous recombination is also used in
gene targeting
Gene targeting (also, replacement strategy based on homologous recombination) is a genetic technique that uses homologous recombination to modify an endogenous gene. The method can be used to delete a gene, remove exons, add a gene and modify i ...
, a technique for introducing genetic changes into target organisms. For their development of this technique,
Mario Capecchi
Mario Ramberg Capecchi (born 6 October 1937) is an Italian-born molecular geneticist and a co-awardee of the 2007 Nobel Prize in Physiology or Medicine for discovering a method to create mice in which a specific gene is turned off, known as knock ...
,
Martin Evans
Sir Martin John Evans (born 1 January 1941) is an English biologist who, with Matthew Kaufman, was the first to culture mice embryonic stem cells and cultivate them in a laboratory in 1981. He is also known, along with Mario Capecchi and Olive ...
and
Oliver Smithies
Oliver Smithies (23 June 1925 – 10 January 2017) was a British-American geneticist and physical biochemist. He is known for introducing starch as a medium for gel electrophoresis in 1955, and for the discovery, simultaneously with Mario Cape ...
were awarded the 2007
Nobel Prize for Physiology or Medicine
The Nobel Prize in Physiology or Medicine is awarded yearly by the Nobel Assembly at the Karolinska Institute for outstanding discoveries in physiology or medicine. The Nobel Prize is not a single prize, but five separate prizes that, according ...
; Capecchi and Smithies independently discovered applications to mouse embryonic stem cells, however the highly conserved mechanisms underlying the DSB repair model, including uniform homologous integration of transformed DNA (gene therapy), were first shown in plasmid experiments by Orr-Weaver, Szostack 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
Illegitimate recombination, or nonhomologous recombination, is the process by which two unrelated double stranded segments of DNA are joined. This insertion of genetic material which is not meant to be adjacent tends to lead to genes being broken ...
is more frequent than in yeast.
History and discovery
In the early 1900s,
William Bateson
William Bateson (8 August 1861 – 8 February 1926) was an English biologist who was the first person to use the term genetics to describe the study of heredity, and the chief populariser of the ideas of Gregor Mendel following their rediscove ...
and
Reginald Punnett
Reginald Crundall Punnett FRS (; 20 June 1875 – 3 January 1967) was a British geneticist who co-founded, with William Bateson, the ''Journal of Genetics'' in 1910. Punnett is probably best remembered today as the creator of the Punnett ...
found an exception to one of the
principles of inheritance originally described by
Gregor Mendel
Gregor Johann Mendel, OSA (; cs, Řehoř Jan Mendel; 20 July 1822 – 6 January 1884) was a biologist, meteorologist, mathematician, Augustinian friar and abbot of St. Thomas' Abbey in Brünn (''Brno''), Margraviate of Moravia. Mendel was ...
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
Thomas Hunt Morgan (September 25, 1866 – December 4, 1945) was an American evolutionary biologist, geneticist, embryologist, and science author who won the Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that ...
suggested that "
crossovers" can occur between linked genes, where one of the linked genes physically crosses over to a different
chromosome
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
. Two decades later,
Barbara McClintock and
Harriet Creighton
Harriet Baldwin Creighton (27 June 1909 – January 9, 2004) was an American botanist, geneticist and educator.
Background
Born in Delavan, Illinois, Creighton graduated from Wellesley College in 1929, and went on to complete her Ph.D. at Cor ...
demonstrated that chromosomal crossover occurs during
meiosis
Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately r ...
,
the process of cell division by which
sperm and
egg cells
The egg cell, or ovum (plural ova), is the female reproductive cell, or gamete, in most anisogamous organisms (organisms that reproduce sexually with a larger, female gamete and a smaller, male one). The term is used when the female gamete is ...
are made. Within the same year as McClintock's discovery,
Curt Stern
Curt Stern (August 30, 1902 – October 23, 1981) was a German-born American geneticist.
Life
Curt Jacob Stern was born into a middle-class Jewish family in Hamburg, Germany on August 30, 1902. He was the first son of Earned S. Stern, born ...
showed that crossing over—later called "recombination"—could also occur in
somatic cells like
white blood cells and
skin cell
Skin is the layer of usually soft, flexible outer tissue covering the body of a vertebrate animal, with three main functions: protection, regulation, and sensation.
Other animal coverings, such as the arthropod exoskeleton, have different de ...
s that divide through
mitosis.
In 1947, the microbiologist
Joshua Lederberg
Joshua () or Yehoshua ( ''Yəhōšuaʿ'', Tiberian: ''Yŏhōšuaʿ,'' lit. 'Yahweh is salvation') ''Yēšūaʿ''; syr, ܝܫܘܥ ܒܪ ܢܘܢ ''Yəšūʿ bar Nōn''; el, Ἰησοῦς, ar , يُوشَعُ ٱبْنُ نُونٍ '' Yūšaʿ ...
showed that bacteria—which had been assumed to reproduce only asexually through
binary fission
Binary may refer to:
Science and technology Mathematics
* Binary number, a representation of numbers using only two digits (0 and 1)
* Binary function, a function that takes two arguments
* Binary operation, a mathematical operation that ta ...
—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
The Nobel Prize in Physiology or Medicine is awarded yearly by the Nobel Assembly at the Karolinska Institute for outstanding discoveries in physiology or medicine. The Nobel Prize is not a single prize, but five separate prizes that, accord ...
. Building on studies in
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
, in 1964
Robin Holliday
Robin Holliday (6 November 1932 – 9 April 2014) was a British molecular biologist.
Holliday described a mechanism of DNA-strand exchange that attempted to explain gene-conversion events that occur during meiosis in fungi. That model first pro ...
proposed 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
Jack William Szostak (born November 9, 1952) is a Canadian American biologist of Polish British descent, Nobel Prize laureate, university professor at the University of Chicago, former Professor of Genetics at Harvard Medical School, and Alexan ...
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
''Drosophila'' () is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many speci ...
'',
budding yeast
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been ...
and mammalian cells led to 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
Patrick Sung is an American professor of structural biology and biochemistry at the University of Texas Health Science Center at San Antonio. He is known for his work on DNA repair.
Biography
Sung was born on May 24, 1959 in Hong Kong. In 1981, h ...
,
Stephen Kowalczykowski, and others.
In eukaryotes
Homologous recombination (HR) is essential to
cell division
Cell division is the process by which a parent cell divides into two daughter cells. Cell division usually occurs as part of a larger cell cycle in which the cell grows and replicates its chromosome(s) before dividing. In eukaryotes, there ar ...
in eukaryotes like plants, animals, fungi and protists. In cells that divide through
mitosis, 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
Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately r ...
to become specialized
gamete
A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
cells—
sperm or
egg cells
The egg cell, or ovum (plural ova), is the female reproductive cell, or gamete, in most anisogamous organisms (organisms that reproduce sexually with a larger, female gamete and a smaller, male one). The term is used when the female gamete is ...
in animals,
pollen or
ovule
In seed plants, the ovule is the structure that gives rise to and contains the female reproductive cells. It consists of three parts: the '' integument'', forming its outer layer, the ''nucellus'' (or remnant of the megasporangium), and the ...
s in plants, and
spores in
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
. It does so by facilitating
chromosomal crossover, in which regions of similar but not identical DNA are exchanged between
homologous chromosomes
A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during fertilization. Homologs have the same genes in the same loci where they provide points alon ...
.
This creates new, possibly beneficial combinations of genes, which can give offspring an evolutionary advantage. Chromosomal crossover often begins when 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 Recombination hotspots are regions in a genome that exhibit elevated rates of recombination relative to a neutral expectation. The recombination rate within hotspots can be hundreds of times that of the surrounding region. Recombination hotspots re ...
, regions in chromosomes that are about 1,000–2,000
base pairs in length and have high rates of recombination. The absence of 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.
Timing within the mitotic cell cycle
Double-strand breaks can be repaired through homologous recombination, polymerase theta-mediated end joining (TMEJ) or through
non-homologous end joining
Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology direc ...
(NHEJ). NHEJ 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
The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication) and some of its organelles, and sub ...
. Homologous recombination repairs DNA before the cell enters mitosis (M phase). It occurs during and shortly after
DNA replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
, in the
S and
G2 phases of the cell cycle, when
sister chromatids
A sister chromatid refers to the identical copies (chromatids) formed by the DNA replication of a chromosome, with both copies joined together by a common centromere. In other words, a sister chromatid may also be said to be 'one-half' of the dup ...
are more easily available. Compared to homologous chromosomes, which are similar to another chromosome but often have different
allele
An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution.
::"The chro ...
s, 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, the break is repaired via TMEJ in the
S and
G2 phases of the cell cycle. In contrast to homologous recombination and TMEJ, NHEJ is predominant in the
G1 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 the cell cycle vary widely between species.
Cyclin-dependent kinases (CDKs), which modify the activity of other proteins by adding
phosphate
In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthophosphoric acid .
The phosphate or orthophosphate ion is derived from phosph ...
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
Cyclin-dependent kinase 1 also known as CDK1 or cell division cycle protein 2 homolog is a highly conserved protein that functions as a serine/threonine protein kinase, and is a key player in cell cycle regulation. It has been highly studied in t ...
begins homologous recombination by phosphorylating the
Sae2 protein.
After being so activated by 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
Double-strand break repair protein MRE11 is an enzyme that in humans is encoded by the ''MRE11'' gene. The gene has been designated ''MRE11A'' to distinguish it from the pseudogene ''MRE11B'' that is nowadays named ''MRE11P1''.
Function
This ge ...
.
This allows a
protein complex
A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are distinct from multienzyme complexes, in which multiple catalytic domains are found in a single polypeptide chain.
Protein ...
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 role of chromatin
The packaging of eukaryotic DNA into chromatin presents 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
Histone-modifying enzymes are enzymes involved in the modification of histone substrates after protein translation and affect cellular processes including gene expression. To safely store the eukaryotic genome, DNA is wrapped around four core hi ...
are two predominant factors employed to accomplish this remodeling process.
Chromatin relaxation occurs rapidly at the site of a DNA damage.
In one of the earliest steps, the stress-activated protein kinase,
c-Jun N-terminal kinase (JNK), phosphorylates
SIRT6
Sirtuin 6 (SIRT6 or Sirt6) is a stress responsive protein deacetylase and mono-ADP ribosyltransferase enzyme encoded by the SIRT6 gene. In laboratory research, SIRT6 appears to function in multiple molecular pathways related to aging, including ...
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
Poly DP-ribosepolymerase 1 (PARP-1) also known as NAD+ ADP-ribosyltransferase 1 or poly DP-ribosesynthase 1 is an enzyme that in humans is encoded by the ''PARP1'' gene. It is the most abundant of the PARP family of enzymes, accounting for 90% o ...
protein starts to appear at DNA damage sites in less than 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 the DNA repair enzyme
MRE11
Double-strand break repair protein MRE11 is an enzyme that in humans is encoded by the ''MRE11'' gene. The gene has been designated ''MRE11A'' to distinguish it from the pseudogene ''MRE11B'' that is nowadays named ''MRE11P1''.
Function
This ge ...
, to initiate DNA repair, within 13 seconds.
γH2AX, the phosphorylated form of
H2AX
H2A histone family member X (usually abbreviated as H2AX) is a type of histone protein from the H2A family encoded by the ''H2AFX'' gene. An important phosphorylated form is γH2AX (S139), which forms when double-strand breaks appear.
In humans ...
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 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
E3 ubiquitin-protein ligase RNF8 is an enzyme that in humans is encoded by the ''RNF8'' gene. RNF8 has activity both in immune system functions and in DNA repair.
Function
The protein encoded by this gene contains a RING finger motif and an F ...
protein can be detected in association with γH2AX.
RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with
CHD4
Chromodomain-helicase-DNA-binding protein 4 is an enzyme that in humans is encoded by the ''CHD4'' gene.
Function
The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling ...
,
a component of the nucleosome remodeling and deacetylase complex
NuRD
In the field of molecular biology, the Mi-2/NuRD (Nucleosome Remodeling Deacetylase) complex, is a group of associated proteins with both ATP-dependent chromatin remodeling and histone deacetylase activities. , Mi-2/NuRD was the only known prot ...
.
After undergoing relaxation subsequent to DNA damage, followed by DNA repair, chromatin recovers to a compaction state close to its pre-damage level after about 20 min.
Homologous recombination during meiosis
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 the homologous chromosome. PRDM9 deposits both H3K4me3 and H3K36me3
histone methylation marks at the sites it binds, and this
methyltransferase
Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Ross ...
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 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.
Models
Two primary models for how homologous recombination repairs double-strand breaks in DNA are 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 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
Sgs1, also known as slow growth suppressor 1, is a DNA helicase protein found in ''Saccharomyces cerevisiae''. It is a homolog of the bacterial RecQ helicase. Like the other members of the RecQ helicase family, Sgs1 is important for DNA repair ...
helicase and the
Exo1
Exonuclease 1 is an enzyme that in humans is encoded by the ''EXO1'' gene.
This gene encodes a protein with 5' to 3' exonuclease activity as well as RNase activity (endonuclease activity cleaving RNA on DNA/RNA hybrid). It is similar to the Saccha ...
and
Dna2 nucleases. As a
helicase
Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...
, Sgs1 "unzips" the double-strand DNA, while 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
Affinity may refer to:
Commerce, finance and law
* Affinity (law), kinship by marriage
* Affinity analysis, a market research and business management technique
* Affinity Credit Union, a Saskatchewan-based credit union
* Affinity Equity Par ...
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
Meiotic recombination protein DMC1/LIM15 homolog is a protein that in humans is encoded by the ''DMC1'' gene.
Meiotic recombination protein Dmc1 is a homolog of the bacterial strand exchange protein RecA. Dmc1 plays the central role in homologous ...
, in meiosis) then forms a filament of nucleic acid and protein on the single strand of DNA coated with RPA. This
nucleoprotein
Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.
Structures
Nucleoproteins tend to be positively charged, facilitating int ...
filament then begins searching for DNA sequences similar to that of 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, the recipient DNA tends to be from a similar but not necessarily identical homologous chromosome.
A displacement loop (
D-loop
In molecular biology, a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. An R-loop is similar to a D-loop, but in this ca ...
) is formed during strand invasion between the invading 3' overhang strand and the homologous chromosome. After strand invasion, a
DNA polymerase
A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create ...
extends the end of the invading 3' strand by synthesizing new DNA. This changes the D-loop to a cross-shaped structure known as 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.
DSBR pathway
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 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
A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...
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 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 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.
SDSA pathway
Homologous recombination via 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 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
Ligation may refer to:
* Ligation (molecular biology), the covalent linking of two ends of DNA or RNA molecules
* In medicine, the making of a ligature (tie)
* Chemical ligation, the production of peptides from amino acids
* Tubal ligation, a meth ...
'', of any remaining single-stranded gaps.
During mitosis, the major homologous recombination pathway for repairing DNA double-strand breaks appears to be 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.
SSA pathway
The single-strand annealing (SSA) pathway of homologous recombination repairs double-strand breaks between two
repeat sequences
Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. In many organisms, a significant fraction of the genom ...
. The SSA pathway 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 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
RAD52 homolog (S. cerevisiae), also known as RAD52, is a protein which in humans is encoded by the ''RAD52'' gene.
Function
The protein encoded by this gene shares similarity with ''Saccharomyces cerevisiae'' Rad52, a protein important for DNA ...
then binds each of the repeat sequences on either side of 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 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.
BIR pathway
During
DNA replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
, double-strand breaks can sometimes be encountered at
replication fork
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
s as
DNA helicase
Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...
unzips the template strand. These defects are repaired in the ''break-induced replication'' (BIR) pathway of homologous recombination. The precise molecular mechanisms of 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
A telomere (; ) is a region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes. Although there are different architectures, telomeres, in a broad sense, are a widespread genetic feature mos ...
(regions of DNA at the end of eukaryotic chromosomes) in the absence of (or in cooperation with)
telomerase
Telomerase, also called terminal transferase, is a ribonucleoprotein that adds a species-dependent telomere repeat sequence to the 3' end of telomeres. A telomere is a region of repetitive sequences at each end of the chromosomes of most euka ...
. Without working copies of the enzyme telomerase, telomeres typically shorten with each cycle of mitosis, which eventually blocks
cell division
Cell division is the process by which a parent cell divides into two daughter cells. Cell division usually occurs as part of a larger cell cycle in which the cell grows and replicates its chromosome(s) before dividing. In eukaryotes, there ar ...
and leads to
senescence. In
budding yeast
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been ...
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 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.
In bacteria
Homologous recombination 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
Eukaryotes () are organisms whose Cell (biology), cells have a cell nucleus, nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the ...
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
s. Homologous recombination has been most studied and is best understood for ''
Escherichia coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...
''. Double-strand DNA breaks in bacteria are repaired by the
RecBCD
Exodeoxyribonuclease V (EC 3.1.11.5, RecBCD, Exonuclease V, ''Escherichia coli'' exonuclease V, ''E. coli'' exonuclease V, gene recBC endoenzyme, RecBC deoxyribonuclease, gene recBC DNase, gene recBCD enzymes) is an enzyme of ''E. coli'' that ini ...
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 The RecF pathway, also called the RecFOR pathway, is a pathway of homologous recombination that repairs DNA in bacteria. It repairs breaks that occur on only one of DNA's two strands, known as single-strand gaps. The RecF pathway can also repair ...
. 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.
RecBCD pathway
The RecBCD pathway 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
Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nm (with a corresponding frequency around 30 PHz) to 400 nm (750 THz), shorter than that of visible light, but longer than X-rays. UV radiation i ...
and other
radiation, as well as chemical
mutagens. Double-strand breaks may also arise by
DNA replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
through a single-strand nick or gap. Such a situation causes what is known as a collapsed
replication fork
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
and is fixed by several pathways of homologous recombination including the RecBCD pathway.
In this pathway, a three-subunit
enzyme complex called
RecBCD
Exodeoxyribonuclease V (EC 3.1.11.5, RecBCD, Exonuclease V, ''Escherichia coli'' exonuclease V, ''E. coli'' exonuclease V, gene recBC endoenzyme, RecBC deoxyribonuclease, gene recBC DNase, gene recBCD enzymes) is an enzyme of ''E. coli'' that ini ...
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
Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...
activity. The RecB subunit also has 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
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecule ...
sequence (5'-GCTGGTGG-3') known as a
Chi site
Chi or CHI may refer to:
Greek
*Chi (letter), the Greek letter (uppercase Χ, lowercase χ);
Chinese
* ''Chi'' (length) (尺), a traditional unit of length, about ⅓ meter
* Chi (mythology) (螭), a dragon
* Chi (surname) (池, pinyin: ''chí ...
.
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 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
RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homolog ...
proteins onto the single-stranded DNA with the newly generated 3' end. The resulting RecA-coated
nucleoprotein
Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.
Structures
Nucleoproteins tend to be positively charged, facilitating int ...
filament then searches out similar sequences of DNA on a homologous chromosome. The search process induces stretching of the DNA duplex, which enhances homology recognition (a mechanism termed
conformational proofreading
Conformational proofreading or conformational selection is a general mechanism of molecular recognition systems in which introducing a structural mismatch between a molecular recognizer and its target, or an energetic barrier, enhances the recogn ...
). 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 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 a replication fork. This type of resolution produces only one type of recombinant (non-reciprocal).
RecF pathway
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 the
RecQ
RecQ helicase is a family of helicase enzymes initially found in ''Escherichia coli'' that has been shown to be important in genome maintenance. They function through catalyzing the reaction ATP + H2O → ADP + P and thus driving the unwind ...
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 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.
Branch migration
Immediately after strand invasion, 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 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 the surface of RuvA as they are guided by the protein from one duplex to the other.
Resolution
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
Degeneracy, degenerate, or degeneration may refer to:
Arts and entertainment
* Degenerate (album), ''Degenerate'' (album), a 2010 album by the British band Trigger the Bloodshed
* Degenerate art, a term adopted in the 1920s by the Nazi Party i ...
sequence 5'-(A/T)TT(G/C)-3'. The sequence 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 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.
Facilitating genetic transfer
Homologous recombination is an important method of integrating donor DNA into a recipient organism's genome in
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...
, the process by which an organism incorporates foreign DNA from another organism without being 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 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, a type of horizontal gene transfer in which DNA is transferred from one bacterium to another by a
virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsk ...
. Foreign, bacterial DNA is sometimes misincorporated in the
capsid
A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or ma ...
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 the genome of the new bacterial host.
Bacterial transformation
Natural bacterial
transformation
Transformation may refer to:
Science and mathematics
In biology and medicine
* Metamorphosis, the biological process of changing physical form after birth or hatching
* Malignant transformation, the process of cells becoming cancerous
* Tran ...
involves the transfer of
DNA from a donor bacterium to a recipient bacterium, where both donor and recipient are ordinarily of the same
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
. Transformation, unlike bacterial conjugation and transduction, depends on numerous bacterial gene products that specifically interact to perform this process. Thus transformation 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
RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homolog ...
''/
''Rad51''/
''DMC1'' gene family plays a central role in homologous recombination during bacterial transformation as it does during eukaryotic meiosis and mitosis. For instance, 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 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
Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately r ...
.
In viruses
Homologous recombination occurs in several
groups
A group is a number of persons or things that are located, gathered, or classed together.
Groups of people
* Cultural group, a group whose members share the same cultural identity
* Ethnic group, a group whose members share the same ethnic ide ...
of viruses. In
DNA virus
A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and ...
es such as
herpesvirus
''Herpesviridae'' is a large family of DNA viruses that cause infections and certain diseases in animals, including humans. The members of this family are also known as herpesviruses. The family name is derived from the Greek word ''ἕρπειν ...
, recombination occurs through a break-and-rejoin mechanism like in bacteria and eukaryotes.
There is also evidence for recombination in some
RNA viruses, specifically
positive-sense ssRNA virus
Positive-strand RNA viruses (+ssRNA viruses) are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated in ...
es like
retroviruses,
picornavirus
Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm ...
es, and
coronaviruses. There is controversy over whether homologous recombination occurs in
negative-sense ssRNA virus
Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a dis ...
es like
influenza.
[ ]
In RNA viruses, homologous recombination can be either precise or imprecise. In the precise type of RNA-RNA recombination, there 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 is controlled by the sequence context of the two recombining strands of RNA: sequences rich in
adenine
Adenine () ( symbol A or Ade) is a nucleobase (a purine derivative). It is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The three others are guanine, cytosine and thymine. Its deri ...
and
uracil
Uracil () (symbol U or Ura) is one of the four nucleobases in the nucleic acid RNA. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced b ...
decrease crossover precision.
Homologous recombination is important in facilitating
viral evolution
Viral evolution is a subfield of evolutionary biology and virology that is specifically concerned with the evolution of viruses. Viruses have short generation times, and many—in particular RNA viruses—have relatively high mutation rates (on the ...
.
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 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
Human herpesvirus 6 (HHV-6) is the common collective name for '' human betaherpesvirus 6A'' (HHV-6A) and '' human betaherpesvirus 6B'' (HHV-6B). These closely related viruses are two of the nine known herpesviruses that have humans as their prim ...
'' 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 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
RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homolog ...
'' in E. coli and other bacteria, and ''
rad51'' and ''
dmc1
Meiotic recombination protein DMC1/LIM15 homolog is a protein that in humans is encoded by the ''DMC1'' gene.
Meiotic recombination protein Dmc1 is a homolog of the bacterial strand exchange protein RecA. Dmc1 plays the central role in homologous ...
'' in yeast and other eukaryotes, including humans).
Multiplicity reactivation has also been demonstrated in numerous pathogenic viruses.
Coronavirus
Coronaviruses are capable of
genetic recombination when at least two viral
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
s are present in 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 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 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 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
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is h ...
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" was predicted as recombination hotspots in Australian SARS-CoV-2 mutants. Although s2m is considered an RNA motif highly conserved among many coronavirus species, this result also suggests that s2m of SARS-CoV-2 is rather a RNA recombination/mutation hotspot.
Effects of dysfunction
Without proper homologous recombination, chromosomes often incorrectly align for the first phase of cell division in meiosis
Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately r ...
. This causes chromosomes to fail to properly segregate in a process called nondisjunction
Nondisjunction is the failure of homologous chromosomes or sister chromatids to separate properly during cell division (mitosis/meiosis). There are three forms of nondisjunction: failure of a pair of homologous chromosomes to separate in meiosis ...
. In turn, nondisjunction can cause sperm and ova
, abbreviated as OVA and sometimes as OAV (original animation video), are Japanese animated films and series made specially for release in home video formats without prior showings on television or in theaters, though the first part of an OVA s ...
to have too few or too many chromosomes. Down's syndrome
Down syndrome or Down's syndrome, also known as trisomy 21, is a genetic disorder caused by the presence of all or part of a third copy of chromosome 21. It is usually associated with physical growth delays, mild to moderate intellectual disa ...
, which is caused by an extra copy of chromosome 21
Chromosome 21 is one of the 23 pairs of chromosomes in humans. Chromosome 21 is both the smallest human autosome and chromosome, with 48 million base pairs (the building material of DNA) representing about 1.5 percent of the total DNA in cells. M ...
, is one of many abnormalities that result from such a failure of homologous recombination in meiosis.
Deficiencies in homologous recombination have been strongly linked to cancer formation in humans. For example, each of the cancer-related diseases Bloom syndrome
Bloom syndrome (often abbreviated as BS in literature) is a rare autosomal recessive genetic disorder characterized by short stature, predisposition to the development of cancer, and genomic instability. BS is caused by mutations in the '' BLM'' ge ...
, Werner syndrome
Werner syndrome (WS) or Werner's syndrome, also known as "adult progeria",James, William; Berger, Timothy; Elston, Dirk (2005). ''Andrews' Diseases of the Skin: Clinical Dermatology''. (10th ed.). Saunders. . is a rare, autosomal recessive disorder ...
and Rothmund–Thomson syndrome
Rothmund–Thomson syndrome (RTS) is a rare autosomal recessive skin condition.
There have been several reported cases associated with osteosarcoma. A hereditary basis, mutations in the DNA helicase ''RECQL4'' gene, causing problems during initi ...
are caused by malfunctioning copies of RecQ
RecQ helicase is a family of helicase enzymes initially found in ''Escherichia coli'' that has been shown to be important in genome maintenance. They function through catalyzing the reaction ATP + H2O → ADP + P and thus driving the unwind ...
helicase genes involved in the regulation
Regulation is the management of complex systems according to a set of rules and trends. In systems theory, these types of rules exist in various fields of biology and society, but the term has slightly different meanings according to context. Fo ...
of homologous recombination: '' BLM'', '' WRN'' and '' RECQL4'', respectively. In the cells of Bloom's syndrome patients, who lack a working copy of the BLM protein, there is an elevated rate of homologous recombination. Experiments in mice deficient in BLM have suggested that the mutation gives rise to cancer through a loss of heterozygosity
Loss of heterozygosity (LOH) is a type of genetic abnormality in diploid organisms in which one copy of an entire gene and its surrounding chromosomal region are lost. Since diploid cells have two copies of their genes, one from each parent, a sing ...
caused by increased homologous recombination. A loss in heterozygosity refers to the loss of one of two versions—or alleles
An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution.
::"The chrom ...
—of a gene. If one of the lost alleles helps to suppress tumors, like the gene for the retinoblastoma protein
The retinoblastoma protein (protein name abbreviated pRb; gene name abbreviated ''Rb'', ''RB'' or ''RB1'') is a proto-oncogenic tumor suppressor protein that is dysfunctional in several major cancers. One function of pRb is to prevent excessive ...
for example, then the loss of heterozygosity can lead to cancer.
Decreased rates of homologous recombination cause inefficient DNA repair, which can also lead to cancer. This is the case with BRCA1
Breast cancer type 1 susceptibility protein is a protein that in humans is encoded by the ''BRCA1'' () gene. Orthologs are common in other vertebrate species, whereas invertebrate genomes may encode a more distantly related gene. ''BRCA1'' is a ...
and BRCA2, two similar tumor suppressor genes
A tumor suppressor gene (TSG), or anti-oncogene, is a gene that regulates a cell during cell division and replication. If the cell grows uncontrollably, it will result in cancer. When a tumor suppressor gene is mutated, it results in a loss or red ...
whose malfunctioning has been linked with considerably increased risk for breast
The breast is one of two prominences located on the upper ventral region of a primate's torso. Both females and males develop breasts from the same embryological tissues.
In females, it serves as the mammary gland, which produces and sec ...
and ovarian cancer
Ovarian cancer is a cancerous tumor of an ovary. It may originate from the ovary itself or more commonly from communicating nearby structures such as fallopian tubes or the inner lining of the abdomen. The ovary is made up of three different c ...
. Cells missing BRCA1 and BRCA2 have a decreased rate of homologous recombination and increased sensitivity to ionizing radiation, suggesting that decreased homologous recombination leads to increased susceptibility to cancer. Because the only known function of BRCA2 is to help initiate homologous recombination, researchers have speculated that more detailed knowledge of BRCA2's role in homologous recombination may be the key to understanding the causes of breast and ovarian cancer.
Tumours with a homologous recombination deficiency (including BRCA defects) are described as HRD-positive.
Evolutionary conservation
While the pathways can mechanistically vary, the ability of organisms to perform homologous recombination is universally conserved across all domains of life. Based on the similarity of their amino acid sequences, homologs of a number of proteins can be found in multiple domains of life indicating that they evolved a long time ago, and have since diverged from common ancestral proteins.
RecA recombinase family members are found in almost all organisms with RecA
RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homolog ...
in bacteria, Rad51 and DMC1
Meiotic recombination protein DMC1/LIM15 homolog is a protein that in humans is encoded by the ''DMC1'' gene.
Meiotic recombination protein Dmc1 is a homolog of the bacterial strand exchange protein RecA. Dmc1 plays the central role in homologous ...
in eukaryotes, RadA in archaea, and UvsX in T4 phage.
Related single stranded binding proteins that are important for homologous recombination, and many other processes, are also found in all domains of life.
Rad54, Mre11
Double-strand break repair protein MRE11 is an enzyme that in humans is encoded by the ''MRE11'' gene. The gene has been designated ''MRE11A'' to distinguish it from the pseudogene ''MRE11B'' that is nowadays named ''MRE11P1''.
Function
This ge ...
, Rad50
DNA repair protein RAD50, also known as RAD50, is a protein that in humans is encoded by the ''RAD50'' gene.
Function
The protein encoded by this gene is highly similar to ''Saccharomyces cerevisiae'' Rad50, a protein involved in DNA double- ...
, and a number of other proteins are also found in both archaea and eukaryotes.
The RecA recombinase family
The proteins of the RecA recombinase family of proteins are thought to be descended from a common ancestral recombinase. The RecA recombinase family contains RecA
RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homolog ...
protein from bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
, the Rad51 and Dmc1
Meiotic recombination protein DMC1/LIM15 homolog is a protein that in humans is encoded by the ''DMC1'' gene.
Meiotic recombination protein Dmc1 is a homolog of the bacterial strand exchange protein RecA. Dmc1 plays the central role in homologous ...
proteins from eukaryotes, and RadA from archaea, and the recombinase paralog proteins. Studies modeling the evolutionary relationships between the Rad51, Dmc1 and RadA proteins indicate that they are monophyletic, or that they share a common molecular ancestor. Within this protein family, Rad51 and Dmc1 are grouped together in a separate clade from RadA. One of the reasons for grouping these three proteins together is that they all possess a modified helix-turn-helix
Helix-turn-helix is a DNA-binding protein (DBP). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of ...
motif, which helps the proteins bind to DNA, toward their N-terminal end
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...
s. An ancient gene duplication event of a eukaryotic RecA gene and subsequent mutation has been proposed as a likely origin of the modern RAD51 and DMC1 genes.
The proteins generally share a long conserved region known as the RecA/Rad51 domain. Within this protein domain are two sequence motifs, Walker A motif and Walker B motif. The Walker A and B motifs allow members of the RecA/Rad51 protein family to engage in ATP binding and ATP hydrolysis
ATP hydrolysis is the catabolic reaction process by which chemical energy that has been stored in the high-energy phosphoanhydride bonds in adenosine triphosphate (ATP) is released after splitting these bonds, for example in muscles, by prod ...
.
Meiosis-specific proteins
The discovery of Dmc1 in several species of '' Giardia'', one of the earliest protists to diverge as a eukaryote, suggests that meiotic homologous recombination—and thus meiosis itself—emerged very early in eukaryotic evolution. In addition to research on Dmc1, studies on the Spo11 protein have provided information on the origins of meiotic recombination. Spo11, a type II topoisomerase
Type II topoisomerases are topoisomerases that cut both strands of the DNA helix simultaneously in order to manage DNA tangles and supercoils. They use the hydrolysis of ATP, unlike Type I topoisomerase. In this process, these enzymes change th ...
, can initiate homologous recombination in meiosis by making targeted double-strand breaks in DNA. Phylogenetic trees based on the sequence of genes similar to SPO11 in animals, fungi, plants, protists and archaea have led scientists to believe that the version Spo11 currently in eukaryotes emerged in the last common ancestor
In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA) or concestor, of a set of organisms is the most recent individual from which all the organisms of the set are descended. The ...
of eukaryotes and archaea.
Technological applications
Gene targeting
Many methods for introducing DNA sequences into organisms to create recombinant DNA
Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) that bring together genetic material from multiple sources, creating sequences that would not otherwise be fo ...
and genetically modified organisms use the process of homologous recombination. Also called gene targeting
Gene targeting (also, replacement strategy based on homologous recombination) is a genetic technique that uses homologous recombination to modify an endogenous gene. The method can be used to delete a gene, remove exons, add a gene and modify i ...
, the method is especially common in yeast
Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constit ...
and mouse genetics. The gene targeting method in knockout mice uses mouse embryonic stem cells to deliver artificial genetic material (mostly of therapeutic interest), which represses the target gene of the mouse by the principle of homologous recombination. The mouse thereby acts as a working model to understand the effects of a specific mammalian gene. In recognition of their discovery of how homologous recombination can be used to introduce genetic modifications in mice through embryonic stem cells, Mario Capecchi
Mario Ramberg Capecchi (born 6 October 1937) is an Italian-born molecular geneticist and a co-awardee of the 2007 Nobel Prize in Physiology or Medicine for discovering a method to create mice in which a specific gene is turned off, known as knock ...
, Martin Evans
Sir Martin John Evans (born 1 January 1941) is an English biologist who, with Matthew Kaufman, was the first to culture mice embryonic stem cells and cultivate them in a laboratory in 1981. He is also known, along with Mario Capecchi and Olive ...
and Oliver Smithies
Oliver Smithies (23 June 1925 – 10 January 2017) was a British-American geneticist and physical biochemist. He is known for introducing starch as a medium for gel electrophoresis in 1955, and for the discovery, simultaneously with Mario Cape ...
were awarded the 2007 Nobel Prize for Physiology or Medicine
The Nobel Prize in Physiology or Medicine is awarded yearly by the Nobel Assembly at the Karolinska Institute for outstanding discoveries in physiology or medicine. The Nobel Prize is not a single prize, but five separate prizes that, according ...
.
Advances in gene targeting technologies which hijack the homologous recombination mechanics of cells are now leading to the development of a new wave of more accurate, isogenic human disease models
Isogenic human disease models are a family of cells that are selected or engineered to accurately model the genetics of a specific patient population, ''in vitro''. They are provided with a genetically matched 'normal cell' to provide an isogenic s ...
. These engineered human cell models are thought to more accurately reflect the genetics of human diseases than their mouse model predecessors. This is largely because mutations of interest are introduced into endogenous genes, just as they occur in the real patients, and because they are based on human genomes rather than rat genomes. Furthermore, certain technologies enable the knock-in of a particular mutation rather than just knock-outs associated with older gene targeting technologies.
Protein engineering
Protein engineering with homologous recombination develops chimeric proteins by swapping fragments between two parental proteins. These techniques exploit the fact that recombination can introduce a high degree of sequence
In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is calle ...
diversity while preserving a protein's ability to fold into its tertiary structure
Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may i ...
, or three-dimensional shape. This stands in contrast to other protein engineering techniques, like random point mutagenesis
Mutagenesis () is a process by which the genetic information of an organism is changed by the production of a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using lab ...
, in which the probability of maintaining protein function declines exponentially with increasing amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...
substitutions. The chimeras produced by recombination techniques are able to maintain their ability to fold because their swapped parental fragments are structurally and evolutionarily conserved. These recombinable "building blocks" preserve structurally important interactions like points of physical contact between different amino acids in the protein's structure. Computational methods like SCHEMA
The word schema comes from the Greek word ('), which means ''shape'', or more generally, ''plan''. The plural is ('). In English, both ''schemas'' and ''schemata'' are used as plural forms.
Schema may refer to:
Science and technology
* SCHEMA ...
and statistical coupling analysis can be used to identify structural subunits suitable for recombination.
Techniques that rely on homologous recombination have been used to engineer new proteins. In a study published in 2007, researchers were able to create chimeras of two enzymes involved in the biosynthesis of isoprenoids, a diverse class of compounds including hormone
A hormone (from the Greek participle , "setting in motion") is a class of signaling molecules in multicellular organisms that are sent to distant organs by complex biological processes to regulate physiology and behavior. Hormones are require ...
s, visual pigments and certain pheromones. The chimeric proteins acquired an ability to catalyze an essential reaction in isoprenoid biosynthesis—one of the most diverse pathways of biosynthesis found in nature—that was absent in the parent proteins. Protein engineering through recombination has also produced chimeric enzymes with new function in members of a group of proteins known as the cytochrome P450
Cytochromes P450 (CYPs) are a superfamily of enzymes containing heme as a cofactor that functions as monooxygenases. In mammals, these proteins oxidize steroids, fatty acids, and xenobiotics, and are important for the clearance of various co ...
family, which in humans is involved in detoxifying foreign compounds like drugs, food additives and preservatives.
Cancer therapy
Homologous recombination proficient (HRP) cancer cells are able to repair the DNA damage, which is caused by chemotherapy such as cisplatin. Thus, HRP cancers are difficult to treat. Studies suggest that homologous recombination can be targeted via c-Abl inhibition. Cancer cells with BRCA mutations have deficiencies in homologous recombination, and drugs to exploit those deficiencies have been developed and used successfully in clinical trials. Olaparib
Olaparib, sold under the brand name Lynparza, is a medication for the maintenance treatment of BRCA-mutated advanced ovarian cancer in adults. It is a PARP inhibitor, inhibiting poly ADP ribose polymerase (PARP), an enzyme involved in DNA repair ...
, a PARP1 inhibitor, shrunk or stopped the growth of tumors from breast
The breast is one of two prominences located on the upper ventral region of a primate's torso. Both females and males develop breasts from the same embryological tissues.
In females, it serves as the mammary gland, which produces and sec ...
, ovarian
The ovary is an organ in the female reproductive system that produces an ovum. When released, this travels down the fallopian tube into the uterus, where it may become fertilized by a sperm. There is an ovary () found on each side of the body ...
and prostate cancers caused by mutations in the BRCA1
Breast cancer type 1 susceptibility protein is a protein that in humans is encoded by the ''BRCA1'' () gene. Orthologs are common in other vertebrate species, whereas invertebrate genomes may encode a more distantly related gene. ''BRCA1'' is a ...
or BRCA2 genes, which are necessary for HR. When BRCA1 or BRCA2 is absent, other types of DNA repair mechanisms must compensate for the deficiency of HR, such as base-excision repair
Base excision repair (BER) is a cellular mechanism, studied in the fields of biochemistry and genetics, that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from t ...
(BER) for stalled replication forks or non-homologous end joining
Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology direc ...
(NHEJ) for double strand breaks. By inhibiting BER in an HR-deficient cell, olaparib applies the concept of synthetic lethality
Synthetic lethality is defined as a type of genetic interaction where the combination of two genetic events results in cell death or death of an organism. Although the foregoing explanation is wider than this, it is common when referring to synthet ...
to specifically target cancer cells. While PARP1 inhibitors represent a novel approach to cancer therapy, researchers have cautioned that they may prove insufficient for treating late-stage metastatic
Metastasis is a pathogenic agent's spread from an initial or primary site to a different or secondary site within the host's body; the term is typically used when referring to metastasis by a cancerous tumor. The newly pathological sites, then, ...
cancers. Cancer cells can become resistant to a PARP1 inhibitor if they undergo deletions of mutations in BRCA2, undermining the drug's synthetic lethality by restoring cancer cells' ability to repair DNA by HR.
See also
* Chromosomal crossover
* Homology directed repair
References
External links
Animations – homologous recombination
Animations showing several models of homologous recombination
Animation of the bacterial RecBCD pathway of homologous recombination
{{DEFAULTSORT:Homologous Recombination
DNA repair
Modification of genetic information
Telomeres