Ataxia telangiectasia and Rad3 related
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Serine/threonine-protein kinase ATR also known as ataxia telangiectasia and Rad3-related protein (ATR) or FRAP-related protein 1 (FRP1) is an
enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...
that, in humans, is encoded by the ''ATR''
gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
. It is a large kinase of about 301.66 kDa. ATR belongs to the
phosphatidylinositol 3-kinase-related kinase Phosphatidylinositol 3-kinase-related kinases (PIKKs) are a family of Ser/Thr-protein kinases with sequence similarity to phosphatidylinositol-3 kinases ( PI3Ks). Members The human PIKK family includes six members: Structure PIKKs protei ...
protein family. ATR is activated in response to
single strand break 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 dama ...
s, and works with ATM to ensure genome integrity.


Function

ATR is a serine/ threonine-specific
protein kinase A protein kinase is a kinase which selectively modifies other proteins by covalently adding phosphates to them (phosphorylation) as opposed to kinases which modify lipids, carbohydrates, or other molecules. Phosphorylation usually results in a fu ...
that is involved in sensing DNA damage and activating the DNA damage checkpoint, leading to
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 ...
arrest in eukaryotes. ATR is activated in response to persistent single-stranded DNA, which is a common intermediate formed during DNA damage detection and
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 installa ...
. Single-stranded DNA occurs at stalled
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 and as an intermediate in
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 ...
pathways such as nucleotide excision repair and
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may ...
repair. ATR is activated during more persistent issues with DNA damage; within cells, most DNA damage is repaired quickly and faithfully through other mechanisms. ATR works with a partner protein called ATRIP to recognize single-stranded DNA coated with RPA. RPA binds specifically to ATRIP, which then recruits ATR through an ATR activating domain (AAD) on its surface. This association of ATR with RPA is how ATR specifically binds to and works on single-stranded DNA—this was proven through experiments with cells that had mutated nucleotide excision pathways. In these cells, ATR was unable to activate after UV damage, showing the need for single stranded DNA for ATR activity. The acidic alpha-helix of ATRIP binds to a basic cleft in the large RPA subunit to create a site for effective ATR binding. Many other proteins exist that are recruited to the cite of ssDNA that are needed for ATR activation. While RPA recruits ATRIP, the RAD9-RAD1-HUS1 (9-1-1) complex is loaded onto the DNA adjacent to the ssDNA; though ATRIP and the 9-1-1 complex are recruited independently to the site of DNA damage, they interact extensively through massive phosphorylation once colocalized. The 9-1-1 complex, a ring-shaped molecule related to PCNA, allows the accumulation of ATR in a damage specific way. For effective association of the 9-1-1 complex with DNA, RAD17-RFC is also needed.   This complex also brings in topoisomerase binding protein 1 (
TOPBP1 DNA topoisomerase 2-binding protein 1 (TOPBP1) is a scaffold protein that in humans is encoded by the ''TOPBP1'' gene. TOPBP1 was first identified as a protein binding partner of DNA topoisomerase-IIβ by a yeast 2-hybrid screen, giving it its ...
) which binds ATR through a highly conserved AAD. TOPBP1 binding is dependent on the phosphorylation of the Ser387 residue of the RAD9 subunit of the 9-1-1 complex. This is likely one of the main functions of the 9-1-1 complex within this DNA damage response. Another important protein that binds TR was identified by Haahr et al. in 2016: Ewings tumor-associated antigen 1 (ETAA1). This protein works in parallel with TOPBP1 to activate ATR through a conserved AAD. It is hypothesized that this pathway, which works independently of TOPBP1 pathway, is used to divide labor and possibly respond to differential needs within the cell. It is hypothesized that one pathway may be most active when ATR is carrying out normal support for replicating cells, and the other may be active when the cell is under more extreme replicative stress. It is not just ssDNA that activates ATR, though the existence of RPA associated ssDNA is important. Instead, ATR activation is heavily dependent on the existence of all the proteins previously described, that colocalize around the site of DNA damage. An experiment where RAD9, ATRIP, and TOPBP1 were overexpressed proved that these proteins alone were enough to activate ATR in the absence of ssDNA, showing their importance in triggering this pathway. Once ATR is activated, it phosphorylates
Chk1 Checkpoint kinase 1, commonly referred to as Chk1, is a serine/threonine-specific protein kinase that, in humans, is encoded by the ''CHEK1'' gene. Chk1 coordinates the DNA damage response (DDR) and cell cycle checkpoint response. Activation of Chk ...
, initiating a signal transduction cascade that culminates in
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 ...
arrest. It acts to activate Chk1 through a claspin intermediate which binds the two proteins together. This claspin intermediate needs to be phosphorylated at two sites in order to do this job, something that can be carried out by ATR but is most likely under the control of some other kinase. This response, mediated by Chk1, is essential to regulating replication within a cell; through the Chk1-CDC25 pathway, which effects levels of CDC2, this response is thought to reduce the rate of DNA synthesis in the cell and inhibit origin firing during replication. In addition to its role in activating the DNA damage checkpoint, ATR is thought to function in unperturbed DNA replication. The response is dependent on how much ssDNA accumulates at stalled replication forks. ATR is activated during every S phase, even in normally cycling cells, as it works to monitor replication forks to repair and stop cell cycling when needed.  This means that ATR is activated at normal, background levels within all healthy cells. There are many points in the genome that are susceptible to stalling during replication due to complex sequences of DNA or endogenous damage that occurs during the replication. In these cases, ATR works to stabilize the forks so that DNA replication can occur as it should. ATR is related to a second checkpoint-activating kinase, ATM, which is activated by double strand breaks in DNA or chromatin disruption. ATR has also been shown to work on double strand breaks (DSB), acting a slower response to address the common end resections that occur in DSBs, and thus leave long strands of ssDNA (which then go on to signal ATR). In this circumstance, ATM recruits ATR and they work in partnership to respond to this DNA damage. They are responsible for the “slow” DNA damage response that can eventually trigger p53 in healthy cells and thus lead to cell cycle arrest or apoptosis.


ATR as an essential protein

Mutations in ATR are very uncommon. The total knockout of ATR is responsible for early death of mouse embryos, showing that it is a protein with essential life functions. It is hypothesized that this could be related to its likely activity in stabilizing Okazaki fragments on the lagging strands of DNA during replication, or due to its job stabilizing stalled replication forks, which naturally occur. In this setting, ATR is essential to preventing fork collapse, which would lead to extensive double strand breakage across the genome. The accumulation of these double strand breaks could lead to cell death.


Clinical significance

Mutations in ATR are responsible for
Seckel syndrome Seckel syndrome, or microcephalic primordial dwarfism (also known as bird-headed dwarfism, Harper's syndrome, Virchow–Seckel dwarfism and bird-headed dwarf of Seckel) is an extremely rare congenital nanosomic disorder. Inheritance is autosomal ...
, a rare human disorder that shares some characteristics with
ataxia telangiectasia Ataxia is a neurological sign consisting of lack of voluntary Motor coordination, coordination of muscle movements that can include gait abnormality, speech changes, and abnormalities in eye movements. Ataxia is a clinical manifestation indicati ...
, which results from ATM mutation. ATR is also linked to
familial cutaneous telangiectasia and cancer syndrome Familial may refer to: * ''Familial'' (album), a 2010 studio album by Phil Selway *Family, a group of people affiliated by consanguinity, affinity, or co-residence *Family (biology), one of the eight major taxonomic ranks, classified between orde ...
.


Inhibitors

ATR/ChK1 inhibitors can potentiate the effect of DNA cross-linking agents such as
cisplatin Cisplatin is a chemotherapy medication used to treat a number of cancers. These include testicular cancer, ovarian cancer, cervical cancer, breast cancer, bladder cancer, head and neck cancer, esophageal cancer, lung cancer, mesothelioma, ...
and
nucleoside Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (ribose or 2'-deoxyribose) whereas a nucleoti ...
analogues such as
gemcitabine Gemcitabine, with brand names including Gemzar, is a chemotherapy medication. It treats cancers including testicular cancer, breast cancer, ovarian cancer, non-small cell lung cancer, pancreatic cancer, and bladder cancer. It is administered by ...
. The first clinical trials using inhibitors of ATR have been initiated by AstraZeneca, preferably in ATM-mutated chronic lymphocytic leukaemia (CLL), prolymphocytic leukaemia (PLL) or B-cell lymphoma patients and by
Vertex Pharmaceuticals Vertex Pharmaceuticals is an American biopharmaceutical company based in Boston, Massachusetts. It was one of the first biotech firms to use an explicit strategy of rational drug design rather than combinatorial chemistry. It maintains headqu ...
in advanced solid tumours. ATR provided and exciting point for potential targeting in these solid tumors, as many tumors function through activating the DNA damage response. These tumor cells rely on pathways like ATR to reduce replicative stress within the cancerous cells that are uncontrollably dividing, and thus these same cells could be very susceptible to ATR knockout. In ATR-Seckel mice, after exposure to cancer-causing agents, the damage DNA damage response pathway actually conferred resistance to tumor development (6). After many screen to identify specific ATR inhibitors, currently four made it into phase I or phase II clinical trials since 2013; these include AZD6738, M6620 (VX-970), BAY1895344, and M4344 (VX-803) (10). These ATR inhibitors work to help the cell proceed through p53 independent apoptosis, as well as force mitotic entry that leads to mitotic catastrophe. One study by Flynn et al. found that ATR inhibitors work especially well in cancer cells which rely on the alternative lengthening of telomeres (ALT) pathway. This is due to RPA presence when ALT is being established, which recruits ATR to regulate homologous recombination. This ALT pathway was extremely fragile with ATR inhibition and thus using these inhibitors to target this pathway that keeps cancer cell immortal could provide high specificity to stubborn cancer cells. Examples include *
Berzosertib Berzosertib (VE-822, VX-970, M6620) is a drug originally invented by Vertex Pharmaceuticals and licensed to Merck KGaA, Darmstadt, Germany for development. It acts as a potent inhibitor of the enzyme ataxia telangiectasia and Rad3 related (ATR) ...


Aging

Deficiency of ATR expression in adult mice leads to the appearance of age-related alterations such as hair graying, hair loss, kyphosis (rounded upper back), osteoporosis and thymic involution. Furthermore, there are dramatic reductions with age in tissue-specific stem and progenitor cells, and exhaustion of tissue renewal and homeostatic capacity. There was also an early and permanent loss of spermatogenesis. However, there was no significant increase in tumor risk.


Seckel syndrome

In humans, hypomorphic mutations (partial loss of gene function) in the ATR gene are linked to Seckel syndrome, an autosomal recessive condition characterized by proportionate dwarfism, developmental delay, marked
microcephaly Microcephaly (from New Latin ''microcephalia'', from Ancient Greek μικρός ''mikrós'' "small" and κεφαλή ''kephalé'' "head") is a medical condition involving a smaller-than-normal head. Microcephaly may be present at birth or it ...
, dental
malocclusion In orthodontics, a malocclusion is a misalignment or incorrect relation between the teeth of the upper and lower dental arches when they approach each other as the jaws close. The English-language term dates from 1864; Edward Angle (1855-19 ...
and thoracic
kyphosis Kyphosis is an abnormally excessive convex curvature of the spine as it occurs in the thoracic and sacral regions. Abnormal inward concave ''lordotic'' curving of the cervical and lumbar regions of the spine is called lordosis. It can result ...
. A senile or progeroid appearance has also been frequently noted in Seckel patients. For many years, the mutation found in the two families first diagnosed with Seckel Syndrome were the only mutations known to cause the disease. In 2012, Ogi and colleagues discovered multiple new mutations that also caused the disease. One form of the disease, which involved mutation in genes encoding the ATRIP partner protein, is considered more severe that the form that was first discovered. This mutation led to severe microcephaly and growth delay, microtia, micrognathia, dental crowding, and skeletal issues (evidenced in unique patellar growth). Sequencing revealed that this ATRIP mutation occurred most likely due to missplicing which led to fragments of the gene without exon 2. The cells also had a nonsense mutation in exon 12 of the ATR gene which led to a truncated ATR protein. Both of these mutations resulted in lower levels of ATR and ATRIP than in wild-type cells, leading to insufficient DNA damage response and the severe form of Seckel Syndrome noted above. Researchers also found that heterozygous mutations in ATR were responsible for causing Seckel Syndrome. Two novel mutations in one copy of the ATR gene caused under-expression of both ATR and ATRIP.


Homologous recombinational repair

Somatic cells of mice deficient in ATR have a decreased frequency of homologous recombination and an increased level of chromosomal damage. This finding implies that ATR is required for
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may ...
al repair of endogenous DNA damage.


''Drosophila'' mitosis and meiosis

Mei-41 is the ''Drosophila'' ortholog of ATR. During mitosis in ''Drosophila'' DNA damages caused by exogenous agents are repaired by a
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may ...
process that depends on mei-41(ATR). Mutants defective in mei-41(ATR) have increased sensitivity to killing by exposure to the DNA damaging agents UV , and
methyl methanesulfonate Methyl methanesulfonate (MMS), also known as methyl mesylate, is an alkylating agent and a carcinogen. It is also a suspected reproductive toxicant, and may also be a skin/sense organ toxicant. It is used in cancer treatment. Deficiency of mei-41(ATR) also causes reduced spontaneous allelic recombination (crossing over) 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 resu ...
suggesting that wild-type mei-41(ATR) is employed in recombinational repair of spontaneous DNA damages 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 resu ...
.


Interactions

Ataxia telangiectasia and Rad3-related protein has been shown to
interact Advocates for Informed Choice, dba interACT or interACT Advocates for Intersex Youth, is a 501(c)(3) nonprofit organization using innovative strategies to advocate for the legal and human rights of children with intersex traits. The organizati ...
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 ...
, *
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 ...
, *
HDAC2 Histone deacetylase 2 (HDAC2) is an enzyme that in humans is encoded by the ''HDAC2'' gene. It belongs to the histone deacetylase class of enzymes responsible for the removal of acetyl groups from lysine residues at the N-terminal region of the co ...
, *
MSH2 DNA mismatch repair protein Msh2 also known as MutS homolog 2 or MSH2 is a protein that in humans is encoded by the ''MSH2'' gene, which is located on chromosome 2. MSH2 is a tumor suppressor gene and more specifically a caretaker gene that codes ...
, *
P53 p53, also known as Tumor protein P53, cellular tumor antigen p53 (UniProt name), or transformation-related protein 53 (TRP53) is a regulatory protein that is often mutated in human cancers. The p53 proteins (originally thought to be, and often s ...
*
RAD17 Cell cycle checkpoint protein RAD17 is a protein that in humans is encoded by the ''RAD17'' gene. Function The protein encoded by this gene is highly similar to the gene product of Schizosaccharomyces pombe rad17, a cell cycle checkpoint gene ...
, and * RHEB.


References


Further reading

* * * * *


External links


''Drosophila'' ''meiotic-41'' - The Interactive Fly
* {{Intracellular signaling peptides and proteins Proteins EC 2.7.11