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Homologous recombination is a type of
genetic recombination Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, ph ...
in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded
nucleic acid Nucleic acids are biopolymer Biopolymers are natural polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecule ...

nucleic acid
s (usually
DNA Deoxyribonucleic acid (; DNA) is a molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically Electricity is the set of physical ...

DNA
as in cellular organisms but may be also
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

RNA
in
virus A virus is a submicroscopic infectious agent In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecu ...

virus
es). It is widely used by cells to accurately
repair The technical meaning of maintenance involves functional checks, servicing, repairing or replacing of necessary devices, equipment, machinery, building infrastructure, and supporting utilities in industrial, business, and residential installati ...

repair
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 (; , because it is a reductional division) is a special type of of in organisms used to produce the , such as or . It involves two rounds of division that ultimately result in four cells with only one copy of each (). Additionall ...

meiosis
, the process by which
eukaryote Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...

eukaryote
s make
gamete A gamete ( /ˈɡæmiːt/; from Ancient Greek Ancient Greek includes the forms of the Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply ...
cells, like
sperm Sperm is the male reproductive Cell (biology), cell, or gamete, in anisogamous forms of sexual reproduction (forms in which there is a larger, female reproductive cell and a smaller, male one). Animals produce motile sperm with a tail known as ...

sperm
and
egg cells Diagram of a chicken egg in its 9th day. Membranes: allantois, chorion, amnion, and vitellus/ yolk. An egg is the organic vessel containing the zygote A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγο ...

egg cells
in animals. These new combinations of DNA represent
genetic variation thumb File:Genetic Variation and Inheritance.svg, Parents have similar gene coding in this specific situation where they reproduce and variation in the offspring is seen. Offspring containing the variation also reproduce and passes down traits t ...

genetic variation
in offspring, which in turn enables populations to
adapt
adapt
during the course of
evolution Evolution is change in the heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, ...

evolution
. 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 A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
to exchange genetic material between different strains and species of bacteria and viruses. Although homologous recombination varies widely among different organisms and cell types, for double-stranded DNA (
dsDNA Deoxyribonucleic acid (; DNA) is a molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically Electricity is the set of physical ...
) 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 Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divide ...
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 In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecu ...

virus
es, suggesting that it is a nearly universal biological mechanism. The discovery of genes for homologous recombination in
protist A protist () is any eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are c ...
s—a diverse group of eukaryotic
microorganisms A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes ...

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 tumor A benign tumor is a mass of cells Cell most often refers to: * Cell (biolo ...

cancer
, the proteins that facilitate homologous recombination are topics of active research. Homologous recombination is also used in
gene targeting mouse gene targeted for the agouti coat color gene, with its offspring Gene targeting (also, replacement strategy based on homologous recombination) is a genetics, genetic technique that uses homologous recombination to modify an endogenous Endo ...
, a technique for introducing genetic changes into target organisms. For their development of this technique,
Mario Capecchi Mario Ramberg Capecchi (6 October 1937) is an Italian-born molecular geneticist and a co-winner 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 knockout mou ...
,
Martin Evans Sir Martin John Evans (born 1 January 1941) is a British biologist who, with Matthew Kaufman Matthew H. Kaufman (29 September 1942 – 11 August 2013) was a British biologist. He was Professor Emeritus at University of Edinburgh having be ...
and
Oliver Smithies Oliver Smithies (23 June 1925 – 10 January 2017) was a British-American geneticist and physical biochemistry, physical biochemist. He is known for introducing starch as a medium for gel electrophoresis in 1955, and for the discovery, simultaneou ...
were awarded the 2007
Nobel Prize for Physiology or Medicine The Nobel Prize in Physiology or Medicine is awarded yearly by the Nobel Assembly , native_name_lang = , image = Nobel Assembly at Karolinska Institutet.jpeg , size = , motto = , formation = 190113 March 1978(as a formal ...
; 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 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 A biologist is a professional who has specialized knowledge in the field of biology Biology is the natural science that studies life and living organisms, ...

William Bateson
and
Reginald Punnett Reginald Crundall Punnett FRS FRS may also refer to: Government and politics * Facility Registry System, a centrally managed Environmental Protection Agency database that identifies places of environmental interest in the United States * Fa ...
found an exception to one of the
principles of inheritance
principles of inheritance
originally described by
Gregor Mendel Gregor Johann Mendel (; cs, Řehoř Jan Mendel; 20 July 1822 – 6 January 1884) was a meteorologist, mathematician, biologist, AugustinianAugustinian may refer to: *Augustinians Augustinians are members of Christian religious orders th ...

Gregor Mendel
in the 1860s. In contrast to Mendel's notion that traits are
independently assorted
independently assorted
when passed from parent to child—for example that a cat's hair color and its tail length are
inherited
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 t ...

Thomas Hunt Morgan
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 genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by Chaperone (protein), chaperone proteins, bind to and ...

chromosome
. Two decades later,
Barbara McClintock Barbara McClintock (June 16, 1902 – September 2, 1992) was an American scientist and cytogeneticist Cytogenetics is essentially a branch of genetics, but is also a part of cell biology/cytology (a subdivision of human anatomy), that is conce ...
and Harriet Creighton demonstrated that chromosomal crossover occurs during
meiosis Meiosis (; , because it is a reductional division) is a special type of of in organisms used to produce the , such as or . It involves two rounds of division that ultimately result in four cells with only one copy of each (). Additionall ...

meiosis
, the process of cell division by which
sperm Sperm is the male reproductive Cell (biology), cell, or gamete, in anisogamous forms of sexual reproduction (forms in which there is a larger, female reproductive cell and a smaller, male one). Animals produce motile sperm with a tail known as ...

sperm
and
egg cells Diagram of a chicken egg in its 9th day. Membranes: allantois, chorion, amnion, and vitellus/ yolk. An egg is the organic vessel containing the zygote A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγο ...

egg cells
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 18 ...
showed that crossing over—later called "recombination"—could also occur in
somatic cell A somatic cell (from Ancient Greek Ancient Greek includes the forms of the Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply as Greek (, ...
s like
white blood cell White blood cells (WBCs), also called leukocytes or leucocytes, are the cells of the immune system The immune system is a network of biological processes that protects an organism In biology, an organism (from Ancient Greek, Greek: ...
s and
skin cell Skin is the layer of usually soft, flexible outer tissue covering the body of a vertebrate Vertebrates () comprise all species of animal Animals (also called Metazoa) are multicellular eukaryotic organisms that form the Kingdom (biolo ...
s that divide through
mitosis In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical proce ...

mitosis
. In 1947, the microbiologist
Joshua Lederberg Joshua Lederberg, ForMemRS Fellowship of the Royal Society (FRS, ForMemRS and HonFRS) is an award granted by the judges of the Royal Society The Royal Society, formally The Royal Society of London for Improving Natural Knowledge, is a l ...

Joshua Lederberg
showed that bacteria—which had been assumed to reproduce only asexually through
binary fission Binary may refer to: Science and technology Mathematics * Binary number In mathematics and digital electronics Digital electronics is a field of electronics The field of electronics is a branch of physics and electrical engineeri ...

binary fission
—are capable of genetic recombination, which is more similar to sexual reproduction. This work established '''' as a
model organism A model organism (often shortened to model) is a non-human species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is ...
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 , native_name_lang = , image = Nobel Assembly at Karolinska Institutet.jpeg , size = , motto = , formation = 190113 March 1978(as a forma ...
. Building on studies in
fungi A fungus (plural The plural (sometimes abbreviated An abbreviation (from Latin ''brevis'', meaning ''short'') is a shortened form of a word or phrase, by any method. It may consist of a group of letters, or words taken from the full ...

fungi
, 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 junction A Holliday junction is a branched nucleic acid Nucleic acids are biopolymer Biopolymers are natural polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material c ...

Holliday junction
s. In 1983,
Jack Szostak Jack William Szostak (born November 9, 1952) is a Canadian American biologist Francesco Redi, the founder of biology, is recognized to be one of the greatest biologists of all time A biologist is a professional who has specialized knowledge ...
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 fly, flies, belonging to the family (biology), family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the character ...

Drosophila
'',
budding yeast ''Saccharomyces cerevisiae'' () is a species of yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are ...
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, Stephen Kowalczykowski, and others.


In eukaryotes

Homologous recombination (HR) is essential to
cell division Cell division is the process by which a parent cell (biology), cell divides into two or more daughter cells. Cell division usually occurs as part of a larger cell cycle. In eukaryotes, there are two distinct types of cell division; a vegetative ...

cell division
in eukaryotes like plants, animals, fungi and protists. In cells that divide through
mitosis In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical proce ...

mitosis
, homologous recombination repairs double-strand breaks in DNA caused by
ionizing radiation Ionizing radiation (or ionising radiation), including nuclear radiation, consists of s or s that have sufficient to s or s by detaching s from them. The particles generally travel at a speed that is greater than 1% of , and the electromagnetic w ...
or DNA-damaging chemicals. Left unrepaired, these double-strand breaks can cause large-scale rearrangement of chromosomes in
somatic cell A somatic cell (from Ancient Greek Ancient Greek includes the forms of the Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply as Greek (, ...
s, which can in turn lead to cancer. In addition to repairing DNA, homologous recombination also helps produce
genetic diversity Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species In biology, a species is the basic unit of biological classificati ...
when cells divide in
meiosis Meiosis (; , because it is a reductional division) is a special type of of in organisms used to produce the , such as or . It involves two rounds of division that ultimately result in four cells with only one copy of each (). Additionall ...

meiosis
to become specialized
gamete A gamete ( /ˈɡæmiːt/; from Ancient Greek Ancient Greek includes the forms of the Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply ...
cells—
sperm Sperm is the male reproductive Cell (biology), cell, or gamete, in anisogamous forms of sexual reproduction (forms in which there is a larger, female reproductive cell and a smaller, male one). Animals produce motile sperm with a tail known as ...

sperm
or
egg cells Diagram of a chicken egg in its 9th day. Membranes: allantois, chorion, amnion, and vitellus/ yolk. An egg is the organic vessel containing the zygote A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγο ...

egg cells
in animals,
pollen Pollen is a powdery substance consisting of pollen grains which are microsporophytes of seed plants The spermatophytes (; ), also known as phanerogams (taxon Phanerogamae) or phaenogams (taxon Phaenogamae), comprise those plant Plant ...

pollen
or
ovule In seed plant A seed is an embryonic ''Embryonic'' is the twelfth studio album by experimental rock band the Flaming Lips released on October 13, 2009, on Warner Bros. Records, Warner Bros. The band's first double album, it was released ...

ovule
s in plants, and
spore In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...
s in
fungi A fungus (plural The plural (sometimes abbreviated An abbreviation (from Latin ''brevis'', meaning ''short'') is a shortened form of a word or phrase, by any method. It may consist of a group of letters, or words taken from the full ...

fungi
. It does so by facilitating
chromosomal crossover Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction Sexual reproduction is a type of reproduction Reproduction (or procreation or breeding) is the biological process Biological pro ...
, 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 locus (genetics), loci where they pr ...
. This creates new, possibly beneficial combinations of genes, which can give offspring an evolutionary advantage. Chromosomal crossover often begins when a protein called
Spo11 Spo11 is a protein that in humans is encoded by the ''SPO11'' gene. Spo11, in a complex with mTopVIB, creates double strand breaks to initiate meiotic genetic recombination, recombination. Its active site contains a tyrosine which ligates and diss ...
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 pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids Nucleic acids are biopolymer Biopolymers are natural polymers produced by the cells of Organism, living organisms. Biopolymers consist of monomeric units that are Covalent_ ...
s 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 Linkage may refer to: *Linkage (album), ''Linkage'' (album), by J-pop singer Mami Kawada, released in 2010 *Linkage (graph theory), the maximum min-degree of any of its subgraphs *Linkage (horse), an American Thoroughbred racehorse *Hierarchical cl ...
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 directe ...
(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 In , DNA replication is the of pro ...

cell cycle
. Homologous recombination repairs DNA before the cell enters mitosis (M phase). It occurs during and shortly after
DNA replication In molecular biology Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, mo ...

DNA replication
, in the S and G2 phases of the cell cycle, when
sister chromatids A sister chromatid refers to the identical copies (chromatid In the diagram, (1) refers to a chromatid: 1-half of two identical threadlike strands of a replicated sister chromatid pair") are joined at the region called the centromere">ister_chr ...
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 one of two, or more, forms of a given gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance ...
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 G1 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 kinase Cyclin-dependent kinases (CDKs) are the families of s first discovered for their role in regulating the . They are also involved in regulating , mRNA processing, and the differentiation of nerve cells. They are present in all known , and their re ...
s (CDKs), which modify the activity of other proteins by adding
phosphate In chemistry, a phosphate is an anion, salt (chemistry), salt, functional group or ester derived from a phosphoric acids and phosphates, phosphoric acid. It most commonly means orthophosphate, a derivative of phosphoric acid, orthophosphoric a ...

phosphate
groups to (that is,
phosphorylating In chemistry, phosphorylation of a molecule is the attachment of a phosphoryl group. This process and its inverse, dephosphorylation, are critical for many cellular processes in biology. Protein phosphorylation is especially important for their fu ...

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 Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckt ...
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 Endonucleases are enzymes that cleave the phosphodiester bond A phosphodiester bond occurs when exactly two of the hydroxyl groups A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen atom ...
responsible for this cut is Sae2 itself or another protein,
Mre11 Double-strand break repair protein MRE11 is an enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry) ...
. This allows a
protein complex A protein complex or multiprotein complex is a group of two or more associated polypeptide chain Peptides (from Greek language Greek (modern , romanized: ''Elliniká'', Ancient Greek, ancient , ''Hellēnikḗ'') is an independent branch of ...
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 Chromatin remodeling is the dynamic modification of chromatin Chromatin is a complex of DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, w ...
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 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 Poly DP-ribosepolymerase 1 (PARP-1) also known as NAD+ ADP-ribosyltransferase 1 or poly DP-ribosesynthase 1 is an enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The m ...
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 Chromodomain-helicase-DNA-binding protein 1-like (ALC1) is an enzyme that in humans is encoded by the ''CHD1L'' gene. It has been implicated in chromatin remodeling and DNA relaxation process required for DNA replication, repair and transcription. T ...
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 Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry) ...
, 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 In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes ...
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 Enzymes () are s that act as s (biocatalysts). Catalysts accelerate . The molecules upon which enzymes may act are called , and the enzyme converts the substrates into different molecules known ...
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 Enzymes () are s that act as s (biocatalysts). Catalysts accelerate . The molecules upon which enzymes may act are called , and the enzyme converts the substrates into different mole ...
, 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 adenosine triphosphate, ATP-dependent chromatin remodeling and histone deacetylase activities. , Mi-2/NuRD was ...
. 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 Spo11 is a protein that in humans is encoded by the ''SPO11'' gene. Spo11, in a complex with mTopVIB, creates double strand breaks to initiate meiotic genetic recombination, recombination. Its active site contains a tyrosine which ligates and diss ...
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 Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes. Methylation of histones can either increase or decreas ...
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 Rossm ...
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 The MRN complex (MRX complex in yeast) is a protein complex A protein complex or multiprotein complex is a group of two or more associated polypeptide chain Peptides (from Greek language Greek (modern , romanized: ''Elliniká'', Ancient Gr ...
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 Helicases are a class of enzyme Enzymes () are s that act as s (biocatalysts). Catalysts accelerate . The molecules upon which enzymes may act are called , and the enzyme c ...

Sgs1
helicase and the
Exo1 Exonuclease 1 is an enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one locati ...
and Dna2 nucleases. As a
helicase Helicases are a class of enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one ...

helicase
, Sgs1 "unzips" the double-strand DNA, while the
nuclease A nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids. Nucleases variously affect nick (DNA), single and double-strand break, do ...
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) In law and in cultural anthropology Cultural anthropology is a branch of anthropology Anthropology is the scientific study of human Humans (''Homo sapiens' ...
for single-stranded DNA, then binds the 3' overhangs. With the help of several other proteins that mediate the process, the
Rad51 DNA repair protein RAD51 homolog 1 is a protein encoded by the gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molec ...
protein (and
Dmc1 Meiotic recombination protein DMC1/LIM15 homolog is a protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and ...

Dmc1
, in meiosis) then forms a filament of nucleic acid and protein on the single strand of DNA coated with RPA. This
nucleoprotein Nucleoproteins are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ ...
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) 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 enzyme Enzymes () are s that act as s (biocatalysts). Catalysts accelerate . The molecules upon which enzymes may act are called , and the enzyme converts the substrates into different molecules ...

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 a
Holliday junction A Holliday junction is a branched nucleic acid Nucleic acids are biopolymer Biopolymers are natural polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material c ...

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 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 Annealing (biology)#Annealing, 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 ''DNA ligase, ligation'', 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 Repeated sequence (DNA), repeat sequences. 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 then binds each of the repeat sequences on either side of the break, and aligns them to enable the two Complementarity (molecular biology), 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 Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, mo ...

DNA replication
, double-strand breaks can sometimes be encountered at replication forks as Helicase, 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 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 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 (biology), cell divides into two or more daughter cells. Cell division usually occurs as part of a larger cell cycle. In eukaryotes, there are two distinct types of cell division; a vegetative ...

cell division
and leads to Senescence#Cellular senescence, senescence. In
budding yeast ''Saccharomyces cerevisiae'' () is a species of yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are ...
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 Biological immortality#Cell lines, cell immortalization, a key feature of cancer. Most cancers maintain telomeres by upregulate, 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 Enzyme inhibitor, 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 meiosis, 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 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 Homologous recombination#RecF pathway, 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.


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 Ultraviolet, UV light and other Ionizing radiation, radiation, as well as chemical mutagens. Double-strand breaks may also arise by
DNA replication In molecular biology Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, mo ...

DNA replication
through a single-strand nick or gap. Such a situation causes what is known as a collapsed replication fork and is fixed by several pathways of homologous recombination including the RecBCD pathway. In this pathway, a three-subunit Multiprotein complex, enzyme complex called RecBCD initiates recombination by binding to a DNA end#Variations in double-stranded molecules, blunt or nearly blunt end of a break in double-strand DNA. After RecBCD binds the DNA end, the RecB and RecD Protein subunit, subunits begin unzipping the DNA duplex through
helicase Helicases are a class of enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one ...

helicase
activity. The RecB subunit also has a endonuclease, 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 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 Nucleoproteins are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ ...
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). 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 A Holliday junction is a branched nucleic acid Nucleic acids are biopolymer Biopolymers are natural polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material c ...

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 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 pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids Nucleic acids are biopolymer Biopolymers are natural polymers produced by the cells of Organism, living organisms. Biopolymers consist of monomeric units that are Covalent_ ...
s between the two homologous DNA duplexes are exchanged. To catalyze branch migration, the RuvABC, RuvA protein first recognizes and binds to the Holliday junction and recruits the RuvABC, 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 Endonucleases are enzymes that cleave the phosphodiester bond A phosphodiester bond occurs when exactly two of the hydroxyl groups A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen atom ...
that cuts the Codon#Degeneracy of the genetic code, degenerate 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 A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
, 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 Semi-log graph, 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 (genetics), 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 In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecu ...

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 the genome of the new bacterial host.


Bacterial transformation

Natural bacterial Transformation (genetics), transformation involves the transfer of
DNA Deoxyribonucleic acid (; DNA) is a molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically Electricity is the set of physical ...

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 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 Natural competence, competence. The ''RecA''/RAD51, ''Rad51''/DMC1 (gene), ''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 Homologous chromosome, 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 (; , because it is a reductional division) is a special type of of in organisms used to produce the , such as or . It involves two rounds of division that ultimately result in four cells with only one copy of each (). Additionall ...

meiosis
.


In viruses

Homologous recombination occurs in several Viral classification, groups of viruses. In DNA viruses such as herpesvirus, 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 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 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 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 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 Escherichia virus T4, 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'' 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.


Coronavirus

Coronaviruses are capable of
genetic recombination Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, ph ...
when at least two viral genomes are present in the same infected cell.
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

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.Su S, Wong G, Shi W, Liu J, Lai ACK, Zhou J, Liu W, Bi Y, Gao GF. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends Microbiol. 2016 Jun;24(6):490-502. doi: 10.1016/j.tim.2016.03.003. Epub 2016 Mar 21. Review. PMID 27012512 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.Barr JN, Fearns R. How RNA viruses maintain their genome integrity. J Gen Virol. 2010 Jun;91(Pt 6):1373-87. doi: 10.1099/vir.0.020818-0. Epub 2010 Mar 24. Review. PMID 20335491 The pandemic SARS-CoV-2's entire receptor binding motif appears to have been introduced through genetic recombination, recombination from coronaviruses of pangolins.Li X, Giorgi EE, Marichannegowda MH, Foley B, Xiao C, Kong XP, Chen Y, Gnanakaran S, Korber B, Gao F. Emergence of SARS-CoV-2 through recombination and strong purifying selection. Sci Adv. 2020 Jul 1;6(27):eabb9153. doi: 10.1126/sciadv.abb9153. PMID 32937441 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 (ship), 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 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 (; , because it is a reductional division) is a special type of of in organisms used to produce the , such as or . It involves two rounds of division that ultimately result in four cells with only one copy of each (). Additionall ...

meiosis
. This causes chromosomes to fail to properly segregate in a process called nondisjunction. In turn, nondisjunction can cause
sperm Sperm is the male reproductive Cell (biology), cell, or gamete, in anisogamous forms of sexual reproduction (forms in which there is a larger, female reproductive cell and a smaller, male one). Animals produce motile sperm with a tail known as ...

sperm
and Ovum, ova to have too few or too many chromosomes. Down's syndrome, which is caused by an extra copy of chromosome 21, 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 tumorigenesis, cancer formation in humans. For example, each of the cancer-related diseases Bloom's syndrome, Werner's syndrome and Rothmund-Thomson syndrome are caused by malfunctioning copies of RecQ helicase genes involved in the Regulation of gene expression, regulation of homologous recombination: ''BLM (gene), BLM'', ''WRN (gene), 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 caused by increased homologous recombination. A loss in heterozygosity refers to the loss of one of two versions—or alleles—of a gene. If one of the lost alleles helps to suppress tumors, like the gene for the retinoblastoma protein 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 and BRCA2, two similar tumor suppressor genes whose malfunctioning has been linked with considerably increased risk for Breast cancer, breast and ovarian cancer. Cells missing BRCA1 and BRCA2 have a decreased rate of homologous recombination and increased sensitivity to
ionizing radiation Ionizing radiation (or ionising radiation), including nuclear radiation, consists of s or s that have sufficient to s or s by detaching s from them. The particles generally travel at a speed that is greater than 1% of , and the electromagnetic w ...
, 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 Homology (biology)#Homology of sequences in genetics, 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 in bacteria, Rad51 and DMC1 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 Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry) ...
, Rad50, 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 protein from bacteria, the Rad51 and Dmc1 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 motif, which helps the proteins bind to DNA, toward their N-terminal ends. 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 sequence, conserved region known as the RecA/Rad51 domain. Within this protein domain are two sequence motifs, Walker 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.


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 Spo11 is a protein that in humans is encoded by the ''SPO11'' gene. Spo11, in a complex with mTopVIB, creates double strand breaks to initiate meiotic genetic recombination, recombination. Its active site contains a tyrosine which ligates and diss ...
protein have provided information on the origins of meiotic recombination. Spo11, a type II topoisomerase, 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 of eukaryotes and archaea.


Technological applications


Gene targeting

Many methods for introducing DNA sequences into organisms to create recombinant DNA and genetically modified organisms use the process of homologous recombination. Also called
gene targeting mouse gene targeted for the agouti coat color gene, with its offspring Gene targeting (also, replacement strategy based on homologous recombination) is a genetics, genetic technique that uses homologous recombination to modify an endogenous Endo ...
, the method is especially common in budding yeast, yeast and mus musculus, mouse genetics. The gene targeting method in Knockout mouse, 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 (6 October 1937) is an Italian-born molecular geneticist and a co-winner 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 knockout mou ...
,
Martin Evans Sir Martin John Evans (born 1 January 1941) is a British biologist who, with Matthew Kaufman Matthew H. Kaufman (29 September 1942 – 11 August 2013) was a British biologist. He was Professor Emeritus at University of Edinburgh having be ...
and
Oliver Smithies Oliver Smithies (23 June 1925 – 10 January 2017) was a British-American geneticist and physical biochemistry, physical biochemist. He is known for introducing starch as a medium for gel electrophoresis in 1955, and for the discovery, simultaneou ...
were awarded the 2007 Nobel Prize in Physiology or Medicine, Nobel Prize for Physiology or Medicine. 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. 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 Chimera (protein), chimeric proteins by swapping fragments between two parental proteins. These techniques exploit the fact that recombination can introduce a high degree of Primary structure, sequence diversity while preserving a protein's ability to fold into its tertiary structure, or three-dimensional shape. This stands in contrast to other protein engineering techniques, like random point mutagenesis, in which the probability of maintaining protein function declines exponentially with increasing amino acid 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 Protein contact map, contact between different amino acids in the protein's structure. Computational methods like SCHEMA (bioinformatics), 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 hormones, carotenoids, visual pigments and monoterpene, certain pheromones. The chimeric proteins acquired an ability to catalyze an essential reaction in Isoprenoid#Biosynthesis, 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 family, which in humans is involved in Detoxification, 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, a PARP1 inhibitor, shrunk or stopped the growth of tumors from breast cancer, breast, ovarian cancer, ovarian and prostate cancers caused by mutations in the BRCA1 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 (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 directe ...
(NHEJ) for double strand breaks. By inhibiting BER in an HR-deficient cell, olaparib applies the concept of synthetic lethality 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 metastasis, metastatic 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