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Helicases are a class of
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 ...
s thought to be vital to all
organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...
s. Their main function is to unpack an organism's
genetic material Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main clas ...
. Helicases are motor proteins that move directionally along a
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...
phosphodiester backbone, separating two hybridized nucleic acid strands (hence '' helic- + -ase''), using energy from ATP
hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile. Biological hydrolys ...
. There are many helicases, representing the great variety of processes in which strand separation must be catalyzed. Approximately 1% of eukaryotic genes code for helicases. The
human genome The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the ...
codes for 95 non-redundant helicases: 64 RNA helicases and 31 DNA helicases. Many cellular processes, such as
DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
,
transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...
,
translation Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
, recombination,
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 ...
, and
ribosome biogenesis Ribosome biogenesis is the process of making ribosomes. In prokaryotes, this process takes place in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, it takes place both in the cytoplasm and in the nucleolus. I ...
involve the separation of nucleic acid strands that necessitates the use of helicases. Some specialized helicases are also involved in sensing of viral nucleic acids during infection and fulfill a immunological function.


Function

Helicases are often used to separate strands of a DNA
double helix A double is a look-alike or doppelgänger; one person or being that resembles another. Double, The Double or Dubble may also refer to: Film and television * Double (filmmaking), someone who substitutes for the credited actor of a character * ...
or a self-annealed
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
molecule using the energy from ATP hydrolysis, a process characterized by the breaking of
hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...
s between annealed nucleotide bases. They also function to remove nucleic acid-associated proteins and catalyze homologous DNA recombination. Metabolic processes of RNA such as translation, transcription,
ribosome biogenesis Ribosome biogenesis is the process of making ribosomes. In prokaryotes, this process takes place in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, it takes place both in the cytoplasm and in the nucleolus. I ...
, RNA splicing, RNA transport,
RNA editing RNA editing (also RNA modification) is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase. It occurs in all living organism ...
, and RNA degradation are all facilitated by helicases. Helicases move incrementally along one
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...
strand of the duplex with a directionality and
processivity In molecular biology and biochemistry, processivity is an enzyme's ability to catalyze "consecutive reactions without releasing its substrate". For example, processivity is the average number of nucleotides added by a polymerase enzyme, such as ...
specific to each particular enzyme. Helicases adopt different structures and
oligomerization In chemistry and biochemistry, an oligomer () is a molecule that consists of a few repeating units which could be derived, actually or conceptually, from smaller molecules, monomers.Quote: ''Oligomer molecule: A molecule of intermediate relativ ...
states. Whereas DnaB-like helicases unwind DNA as ring-shaped
hexamer In chemistry and biochemistry, an oligomer () is a molecule that consists of a few repeating units which could be derived, actually or conceptually, from smaller molecules, monomers.Quote: ''Oligomer molecule: A molecule of intermediate relative ...
s, other enzymes have been shown to be active as
monomer In chemistry, a monomer ( ; '' mono-'', "one" + ''-mer'', "part") is a molecule that can react together with other monomer molecules to form a larger polymer chain or three-dimensional network in a process called polymerization. Classification ...
s or
dimer Dimer may refer to: * Dimer (chemistry), a chemical structure formed from two similar sub-units ** Protein dimer, a protein quaternary structure ** d-dimer * Dimer model, an item in statistical mechanics, based on ''domino tiling'' * Julius Dimer ...
s. Studies have shown that helicases may act passively, waiting for uncatalyzed unwinding to take place and then translocating between displaced strands, or can play an active role in catalyzing strand separation using the energy generated in ATP hydrolysis. In the latter case, the helicase acts comparably to an active motor, unwinding and translocating along its substrate as a direct result of its ATPase activity. Helicases may process much faster ''
in vivo Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, and ...
'' than ''
in vitro ''In vitro'' (meaning in glass, or ''in the glass'') studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in biology an ...
'' due to the presence of accessory proteins that aid in the destabilization of the fork junction.


Activation barrier in helicase activity

Enzymatic helicase action, such as unwinding nucleic acids is achieved through the lowering of the activation barrier (B) of each specific action. The activation barrier is a result of various factors, and can be defined using the following equation, where N = number of unwound base pairs (bps), \Delta G_ = free energy of base pair formation, G_ = reduction of free energy due to helicase, and G_ = reduction of free energy due to unzipping forces. :B=N(\Delta G_-G_-G_) Factors that contribute to the height of the activation barrier include: specific nucleic acid sequence of the molecule involved, the number of base pairs involved, tension present on the replication fork, and destabilization forces.


Active and passive helicases

The size of the activation barrier to overcome by the helicase contributes to its classification as an active or passive helicase. In passive helicases, a significant activation barrier exists (defined as B> k_T, where k_ is
Boltzmann's constant The Boltzmann constant ( or ) is the proportionality factor that relates the average relative kinetic energy of particles in a gas with the thermodynamic temperature of the gas. It occurs in the definitions of the kelvin and the gas constant ...
and T is temperature of the system). Because of this significant activation barrier, its unwinding progression is affected largely by the sequence of nucleic acids within the molecule to unwind, and the presence of destabilization forces acting on the replication fork. Certain nucleic acid combinations will decrease unwinding rates (i.e.
guanine Guanine () ( symbol G or Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is c ...
and
cytosine Cytosine () ( symbol C or Cyt) is one of the four nucleobases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an ...
), while various destabilizing forces can increase the unwinding rate. In passive systems, the rate of unwinding (V_) is less than the rate of translocation (V_) (translocation along the single-strand nucleic acid, ssNA). Another way to view the passive helicase is its reliance on the transient unraveling of the base pairs at the replication fork to determine its rate of unwinding. In active helicases, B< k_T, where the system lacks a significant barrier, as the helicase is able to destabilize the nucleic acids, unwinding the double-helix at a constant rate, regardless of the nucleic acid sequence. In active helicases, V_ is approximately equal to V_. Another way to view the active helicase is its ability to directly destabilize the replication fork to promote unwinding. Active helicases show similar behavior when acting on both double-strand nucleic acids, dsNA, or ssNA, in regards to the rates of unwinding and rates of translocation, where in both systems V_ and V_ are approximately equal. These two categories of helicases may also be modelled as mechanisms. In such models the passive helicases are conceptualized as Brownian ratchets, driven by thermal fluctuations and subsequent anisotropic gradients across the DNA lattice. The active helicases, in contrast, are conceptualized as stepping motors – also known as powerstroke motors – utilizing either a conformational "inch worm" or a hand-over-hand "walking" mechanism to progress. Depending upon the organism, such helix-traversing progress can occur at rotational speeds in the range of 5,000 to 10,000 R.P.M.


History of DNA helicases

DNA helicases were discovered in ''E. coli'' in 1976. This helicase was described as a "DNA unwinding enzyme" that is "found to denature DNA duplexes in an ATP-dependent reaction, without detectably degrading". The first eukaryotic DNA helicase discovered was in 1978 in the lily plant. Since then, DNA helicases were discovered and isolated in other bacteria, viruses, yeast, flies, and higher eukaryotes. To date, at least 14 different helicases have been isolated from single celled organisms, 6 helicases from bacteriophages, 12 from viruses, 15 from yeast, 8 from plants, 11 from calf thymus, and approximately 25 helicases from human cells. Below is a history of helicase discovery: *1976 – Discovery and isolation of ''E. coli''-based DNA helicase *1978 – Discovery of the first eukaryotic DNA helicases, isolated from the lily plant *1982 – "T4 gene 41 protein" is the first reported bacteriophage DNA helicase *1985 – First mammalian DNA helicases isolated from calf thymus *1986 – SV40 large tumor antigen reported as a viral helicase (1st reported viral protein that was determined to serve as a DNA helicase) *1986 – ATPaseIII, a yeast protein, determined to be a DNA helicase *1988 – Discovery of seven conserved amino acid domains determined to be helicase motifs *1989 – Designation of DNA helicase Superfamily I and Superfamily II *1989 – Identification of the DEAD box helicase family *1990 – Isolation of a human DNA helicase *1992 – Isolation of the first reported mitochondrial DNA helicase (from bovine brain) *1996 – Report of the discovery of the first purified chloroplast DNA helicase from the pea *2002 – Isolation and characterization of the first biochemically active malarial parasite DNA helicase – ''Plasmodium cynomolgi''.


Structural features

The common function of helicases accounts for the fact that they display a certain degree of
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
sequence homology Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spe ...
; they all possess sequence motifs located in the interior of their primary structure, involved in ATP binding, ATP
hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile. Biological hydrolys ...
and translocation along the
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...
substrate. The variable portion of the
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
sequence is related to the specific features of each helicase. The presence of these helicase motifs allows putative helicase activity to be attributed to a given protein, but does not necessarily confirm it as an active helicase. Conserved motifs do, however, support an evolutionary homology among enzymes. Based on these helicase motifs, a number of helicase superfamilies have been distinguished.


Superfamilies

Helicases are classified in 6 groups (superfamilies) based on their shared sequence motifs. Helicases not forming a ring structure are in superfamilies 1 and 2, and ring-forming helicases form part of superfamilies 3 to 6. Helicases are also classified as α or β depending on if they work with single or double-strand DNA; α helicases work with single-strand DNA and β helicases work with double-strand DNA. They are also classified by translocation polarity. If translocation occurs 3’-5’ the helicase is type A; if translocation occurs 5’-3’ it is type B. *Superfamily 1 (SF1): This superfamily can be further subdivided into SF1A and SF1B helicases. In this group helicases can have either 3’-5’ (SF1A subfamily) or 5’-3’(SF1B subfamily) translocation polarity. The most known SF1A helicases are Rep and UvrD in
gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
bacteria and PcrA helicase from
gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bact ...
bacteria. The most known Helicases in the SF1B group are RecD and Dda helicases. They have a RecA-like-fold core. *Superfamily 2 (SF2): This is the largest group of helicases that are involved in varied cellular processes. They are characterized by the presence of nine conserved motifs: Q, I, Ia, Ib, and II through VI. This group is mainly composed of DEAD-box RNA helicases. Some other helicases included in SF2 are the RecQ-like family and the Snf2-like enzymes. Most of the SF2 helicases are type A with a few exceptions such as the XPD family. They have a RecA-like-fold core. *Superfamily 3 (SF3): Superfamily 3 consists of AAA+ helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses. They have a 3’-5’ translocation directionality, meaning that they are all type A helicases. The most known SF3 helicase is the papilloma virus E1 helicase. *Superfamily 4 (SF4): All SF4 family helicases have a type B polarity (5’-3’). They have a RecA fold. The most studied SF4 helicase is gp4 from bacteriophage T7. *Superfamily 5 (SF5):
Rho Rho (uppercase Ρ, lowercase ρ or ; el, ρο or el, ρω, label=none) is the 17th letter of the Greek alphabet. In the system of Greek numerals it has a value of 100. It is derived from Phoenician letter res . Its uppercase form uses the sa ...
proteins conform the SF5 group. They have a RecA fold. *Superfamily 6 (SF6): They contain the core AAA+ that is not included in the SF3 classification. Some proteins in the SF6 group are: mini chromosome maintenance MCM, RuvB, RuvA, and RuvC. All helicases are members of a P-loop, or Walker motif-containing family.


Helicase disorders and diseases


ATRX helicase mutations

The ''
ATRX Transcriptional regulator ATRX also known as ATP-dependent helicase ATRX, X-linked helicase II, or X-linked nuclear protein (XNP) is a protein that in humans is encoded by the ''ATRX'' gene. Function Transcriptional regulator ATRX contains an ...
'' gene encodes the ATP-dependent helicase, ATRX (also known as XH2 and XNP) of the SNF2 subgroup family, that is thought to be responsible for functions such as chromatin remodeling, gene regulation, and DNA methylation.Nextprot Online Protein Database
" ATRX-Transcriptional regulator ATRX."
Retrieved on 12 November 2012.
These functions assist in prevention of apoptosis, resulting in cortical size regulation, as well as a contribution to the survival of hippocampal and cortical structures, affecting memory and learning. This helicase is located on the X chromosome (Xq13.1-q21.1), in the pericentromeric heterochromatin and binds to
heterochromatin protein 1 The family of heterochromatin protein 1 (HP1) ("Chromobox Homolog", CBX) consists of highly conserved proteins, which have important functions in the cell nucleus. These functions include gene repression by heterochromatin formation, transcrip ...
. Studies have shown that ATRX plays a role in rDNA methylation and is essential for embryonic development. Mutations have been found throughout the ''ATRX'' protein, with over 90% of them being located in the zinc finger and helicase domains. Mutations of ATRX can result in X-linked-alpha-thalassaemia-mental retardation ( ATR-X syndrome). Various types of mutations found in ATRX have been found to be associated with ATR-X, including most commonly single-base missense mutations, as well as nonsense, frameshift, and deletion mutations. Characteristics of ATR-X include: microcephaly, skeletal and facial abnormalities, mental retardation, genital abnormalities, seizures, limited language use and ability, and alpha-thalassemia. The phenotype seen in ATR-X suggests that the mutation of ATRX gene causes the downregulation of gene expression, such as the alpha-globin genes. It is still unknown what causes the expression of the various characteristics of ATR-X in different patients.


XPD helicase point mutations

XPD ''XPD'' is a spy novel by Len Deighton, published in 1981, and set in 1979, roughly contemporaneous with the time it was written. It concerns a plan by a group of former SS officers to seize power in West Germany, in which they intend to publi ...
(Xeroderma pigmentosum factor D, also known as protein ERCC2) is a 5'-3', Superfamily II, ATP-dependent helicase containing iron-sulphur cluster domains. Inherited point mutations in XPD helicase have been shown to be associated with accelerated aging disorders such as Cockayne syndrome (CS) and
trichothiodystrophy Trichothiodystrophy (TTD) is an autosomal recessive inherited disorder characterised by brittle hair and intellectual impairment. The word breaks down into ''tricho'' – "hair", '' thio'' – "sulphur", and ''dystrophy'' – "wasting away" or li ...
(TTD). Cockayne syndrome and trichothiodystrophy are both developmental disorders involving sensitivity to UV light and premature aging, and Cockayne syndrome exhibits severe mental retardation from the time of birth. The XPD helicase mutation has also been implicated in
xeroderma pigmentosum Xeroderma pigmentosum (XP) is a genetic disorder in which there is a decreased ability to repair DNA damage such as that caused by ultraviolet (UV) light. Symptoms may include a severe sunburn after only a few minutes in the sun, freckling in su ...
(XP), a disorder characterized by sensitivity to UV light and resulting in a several 1000-fold increase in the development of skin cancer. XPD is an essential component of the
TFIIH Transcription factor II Human (transcription factor II H; TFIIH) is an important protein complex, having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways. TFIIH first came to light in 1989 ...
complex, a transcription and repair factor in the cell. As part of this complex, it facilitates nucleotide excision repair by unwinding DNA. TFIIH assists in repairing damaged DNA such as sun damage. A mutation in the XPD helicase that helps form this complex and contributes to its function causes the sensitivity to sunlight seen in all three diseases, as well as the increased risk of cancer seen in XP and premature aging seen in trichothiodystrophy and Cockayne syndrome. XPD helicase mutations leading to trichothiodystrophy are found throughout the protein in various locations involved in protein-protein interactions. This mutation results in an unstable protein due to its inability to form stabilizing interactions with other proteins at the points of mutations. This, in turn, destabilizes the entire TFIIH complex, which leads to defects with transcription and repair mechanisms of the cell. It has been suggested that XPD helicase mutations leading to Cockayne syndrome could be the result of mutations within XPD, causing rigidity of the protein and subsequent inability to switch from repair functions to transcription functions due to a "locking" in repair mode. This could cause the helicase to cut DNA segments meant for transcription. Although current evidence points to a defect in the XPD helicase resulting in a loss of flexibility in the protein in cases of Cockayne syndrome, it is still unclear how this protein structure leads to the symptoms described in Cockayne syndrome. In xeroderma pigmentosa, the XPD helicase mutation exists at the site of ATP or DNA binding. This results in a structurally functional helicase able to facilitate transcription, however it inhibits its function in unwinding DNA and DNA repair. The lack of a cell's ability to repair mutations, such as those caused by sun damage, is the cause of the high cancer rate in xeroderma pigmentosa patients.


RecQ family mutations

RecQ helicase RecQ helicase is a family of helicase enzymes initially found in ''Escherichia coli'' that has been shown to be important in genome maintenance. They function through catalyzing the reaction ATP + H2O → ADP + P and thus driving the unwind ...
s (3'-5') belong to the Superfamily II group of helicases, which help to maintain stability of the genome and suppress inappropriate recombination. Deficiencies and/or mutations in RecQ family helicases display aberrant genetic recombination and/or DNA replication, which leads to chromosomal instability and an overall decreased ability to proliferate. Mutations in RecQ family helicases BLM,
RECQL4 ATP-dependent DNA helicase Q4 is an enzyme that in humans is encoded by the ''RECQL4'' gene. Mutations in ''RECQL4'' are associated with the autosomal recessive disease Rothmund–Thomson syndrome, a disorder that has features of premature aging. ...
, and WRN, which play a role in regulating homologous recombination, have been shown to result in the autosomal recessive diseases
Bloom syndrome Bloom syndrome (often abbreviated as BS in literature) is a rare autosomal recessive genetic disorder characterized by short stature, predisposition to the development of cancer, and genomic instability. BS is caused by mutations in the '' BLM'' ge ...
(BS),
Rothmund–Thomson syndrome Rothmund–Thomson syndrome (RTS) is a rare autosomal recessive skin condition. There have been several reported cases associated with osteosarcoma. A hereditary basis, mutations in the DNA helicase ''RECQL4'' gene, causing problems during initi ...
(RTS), and
Werner syndrome Werner syndrome (WS) or Werner's syndrome, also known as "adult progeria",James, William; Berger, Timothy; Elston, Dirk (2005). ''Andrews' Diseases of the Skin: Clinical Dermatology''. (10th ed.). Saunders. . is a rare, autosomal recessive disorder ...
(WS), respectively. Bloom syndrome is characterized by a predisposition to cancer with early onset, with a mean age-of-onset of 24 years. Cells of Bloom syndrome patients show a high frequency of reciprocal exchange between sister chromatids (SCEs) and excessive chromosomal damage. There is evidence to suggest that BLM plays a role in rescuing disrupted DNA replication at replication forks. Werner syndrome is a disorder of premature aging, with symptoms including early onset of atherosclerosis and osteoporosis and other age related diseases, a high occurrence of sarcoma, and death often occurring from myocardial infarction or cancer in the 4th to 6th decade of life. Cells of Werner syndrome patients exhibit a reduced reproductive lifespan with chromosomal breaks and translocations, as well as large deletions of chromosomal components, causing genomic instability. Rothmund-Thomson syndrome, also known as poikiloderma congenitale, is characterized by premature aging, skin and skeletal abnormalities, rash,
poikiloderma Poikiloderma is a skin condition that consists of areas of hypopigmentation, hyperpigmentation, telangiectasias and atrophy. Poikiloderma of Civatte is most frequently seen on the chest or the neck, characterized by red colored pigment on the skin ...
, juvenile cataracts, and a predisposition to cancers such as osteosarcomas. Chromosomal rearrangements causing genomic instability are found in the cells of Rothmund-Thomson syndrome patients.


Meiotic recombination

During
meiosis Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately resu ...
DNA double-strand breaks and other
DNA damage 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 d ...
s in a
chromatid A chromatid (Greek ''khrōmat-'' 'color' + ''-id'') is one half of a duplicated chromosome. Before replication, one chromosome is composed of one DNA molecule. In replication, the DNA molecule is copied, and the two molecules are known as chro ...
are repaired by
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 ...
using either the
sister chromatid A sister chromatid refers to the identical copies (chromatids) formed by the DNA replication of a chromosome, with both copies joined together by a common centromere. In other words, a sister chromatid may also be said to be 'one-half' of the dup ...
or a homologous non-sister chromatid as template. This repair can result in a
crossover Crossover may refer to: Entertainment Albums and songs * ''Cross Over'' (Dan Peek album) * ''Crossover'' (Dirty Rotten Imbeciles album), 1987 * ''Crossover'' (Intrigue album) * ''Crossover'' (Hitomi Shimatani album) * ''Crossover'' (Yoshino ...
(CO) or, more frequently, a non-crossover (NCO) recombinant. In the yeast ''
Schizosaccharomyces pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measur ...
'' the
FANCM Fanconi anemia, complementation group M, also known as FANCM is a human gene. It is an emerging target in cancer therapy, in particular cancers with specific genetic deficiencies. Function The protein encoded by this gene, FANCM displays DNA bi ...
-family DNA helicase FmI1 directs NCO recombination formation during meiosis. The RecQ-type helicase Rqh1 also directs NCO meiotic recombination. These helicases, through their ability to unwind
D-loop In molecular biology, a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. An R-loop is similar to a D-loop, but in this ca ...
intermediates, promote NCO recombination by the process of synthesis-dependent strand annealing. In the plant '' Arabidopsis thaliana'', FANCM helicase promotes NCO and antagonizes the formation of CO recombinants. Another helicase, RECQ4A/B, also independently reduces COs. It was suggested that COs are restricted because of the long term costs of CO recombination, that is, the breaking up of favorable genetic combinations of alleles built up by past
natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charle ...
.


RNA helicases

RNA helicases are essential for most processes of RNA metabolism such as
ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...
biogenesis, pre-mRNA splicing, and
translation Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
initiation. They also play an important role in sensing viral RNAs. RNA helicases are involved in the mediation of antiviral immune response because they can identify foreign RNAs in vertebrates. About 80% of all viruses are RNA viruses and they contain their own RNA helicases. Defective RNA helicases have been linked to cancers, infectious diseases and neuro-degenerative disorders. Some neurological disorders associated with defective RNA helicases are: amyotrophic lateral sclerosis, spinal muscular atrophy, spinocerebellar ataxia type-2,
Alzheimer disease Alzheimer's disease (AD) is a neurodegenerative disease that usually starts slowly and progressively worsens. It is the cause of 60–70% of cases of dementia. The most common early symptom is difficulty in remembering recent events. As t ...
, and lethal congenital contracture syndrome. RNA helicases and DNA helicases can be found together in all the helicase superfamilies except for SF6. All the eukaryotic RNA helicases that have been identified up to date are non-ring forming and are part of SF1 and SF2. On the other hand, ring-forming RNA helicases have been found in bacteria and viruses. However, not all RNA helicases exhibit helicase activity as defined by enzymatic function, i.e., proteins of the Swi/Snf family. Although these proteins carry the typical helicase motifs, hydrolize ATP in a nucleic acid-dependent manner, and are built around a helicase core, in general, no unwinding activity is observed. RNA helicases that do exhibit unwinding activity have been characterized by at least two different mechanisms: canonical duplex unwinding and local strand separation. Canonical duplex unwinding is the stepwise directional separation of a duplex strand, as described above, for DNA unwinding. However, local strand separation occurs by a process wherein the helicase enzyme is loaded at any place along the duplex. This is usually aided by a single-strand region of the RNA, and the loading of the enzyme is accompanied with ATP binding. Once the helicase and ATP are bound, local strand separation occurs, which requires binding of ATP but not the actual process of ATP hydrolysis. Presented with fewer base pairs the duplex then dissociates without further assistance from the enzyme. This mode of unwinding is used by the DEAD/DEAH box helicases. An RNA helicase database is currently available online that contains a comprehensive list of RNA helicases with information such as sequence, structure, and biochemical and cellular functions.


Diagnostic tools for helicase measurement


Measuring and monitoring helicase activity

Various methods are used to measure helicase activity ''in vitro''. These methods range from assays that are qualitative (assays that usually entail results that do not involve values or measurements) to quantitative (assays with numerical results that can be utilized in statistical and numerical analysis). In 1982–1983, the first direct biochemical assay was developed for measuring helicase activity. This method was called a "strand displacement assay". :*Strand displacement assay involves the
radiolabeling A radioactive tracer, radiotracer, or radioactive label is a chemical compound in which one or more atoms have been replaced by a radionuclide so by virtue of its radioactive decay it can be used to explore the mechanism of chemical reactions by ...
of DNA duplexes. Following helicase treatment, the single-strand DNA is visually detected as separate from the double-strand DNA by non-denaturing PAGE electrophoresis. Following detection of the single-strand DNA, the amount of radioactive tag that is on the single-strand DNA is quantified to give a numerical value for the amount of double-strand DNA unwinding. ::The strand displacement assay is acceptable for qualitative analysis, its inability to display results for more than a single time point, its time consumption, and its dependence on radioactive compounds for labeling warranted the need for development of diagnostics that can monitor helicase activity in real time. Other methods were later developed that incorporated some, if not all of the following: high-throughput mechanics, the use of non-radioactive nucleotide labeling, faster reaction time/less time consumption, real-time monitoring of helicase activity (using kinetic measurement instead of endpoint/single point analysis). These methodologies include: "a rapid quench flow method, fluorescence-based assays, filtration assays, a scintillation proximity assay, a time resolved
fluorescence resonance energy transfer Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
assay, an assay based on flashplate technology, homogenous time-resolved fluorescence quenching assays, and electrochemiluminescence-based helicase assays". With the use of specialized mathematical equations, some of these assays can be utilized to determine how many base paired nucleotides a helicase can break per hydrolysis of 1 ATP molecule. Commercially available diagnostic kits are also available. One such kit is the "Trupoint" diagnostic assay from
PerkinElmer PerkinElmer, Inc., previously styled Perkin-Elmer, is an American global corporation focused in the business areas of diagnostics, life science research, food, environmental and industrial testing. Its capabilities include detection, imaging, in ...
, Inc. This assay is a time-resolved fluorescence quenching assay that utilizes the PerkinElmer "SignalClimb" technology that is based on two labels that bind in close proximity to one another but on opposite DNA strands. One label is a fluorescent lanthanide chelate, which serves as the label that is monitored through an adequate 96/384 well plate reader. The other label is an organic quencher molecule. The basis of this assay is the "quenching" or repressing of the lanthanide chelate signal by the organic quencher molecule when the two are in close proximity – as they would be when the DNA duplex is in its native state. Upon helicase activity on the duplex, the quencher and lanthanide labels get separated as the DNA is unwound. This loss in proximity negates the quenchers ability to repress the lanthanide signal, causing a detectable increase in fluorescence that is representative of the amount of unwound DNA and can be used as a quantifiable measurement of helicase activity. The execution and use of single-molecule fluorescence imaging techniques, focusing on methods that include optical trapping in conjunction with epifluorescent imaging, and also surface immobilization in conjunction with total internal reflection fluorescence visualization. Combined with microchannel flow cells and microfluidic control, allow individual fluorescently labeled protein and DNA molecules to be imaged and tracked, affording measurement of DNA unwinding and translocation at single-molecule resolution.


Determining helicase polarity

Helicase polarity, which is also deemed "directionality", is defined as the direction (characterized as 5'→3' or 3'→5') of helicase movement on the DNA/RNA single-strand along which it is moving. This determination of polarity is vital in f.ex. determining whether the tested helicase attaches to the DNA leading strand, or the DNA lagging strand. To characterize this helicase feature, a partially duplex DNA is used as the substrate that has a central single-strand DNA region with different lengths of duplex regions of DNA (one short region that runs 5'→3' and one longer region that runs 3'→5') on both sides of this region. Once the helicase is added to that central single-strand region, the polarity is determined by characterization on the newly formed single-strand DNA.


See also

*
Chromodomain A chromodomain (''chromatin organization modifier'') is a protein structural domain of about 40–50 amino acid residues commonly found in proteins associated with the remodeling and manipulation of chromatin. The domain is highly conserved amon ...
helicase DNA binding protein:
CHD1 The Chromodomain-Helicase DNA-binding 1 is a protein that, in humans, is encoded by the CHD1 gene. CHD1 is a chromatin remodeling protein that is widely conserved across many eukaryotic organisms, from yeast to humans. CHD1 is named for three of ...
,
CHD1L 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. ...
,
CHD2 Chromodomain-helicase-DNA-binding protein 2 is an enzyme that in humans is encoded by the ''CHD2'' gene. Function The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-relate ...
, CHD3,
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 ...
, CHD5, CHD6,
CHD7 Chromodomain-helicase-DNA-binding protein 7 also known as ATP-dependent helicase CHD7 is an enzyme that in humans is encoded by the ''CHD7'' gene. CHD7 is an ATP-dependent chromatin remodeler homologous to the Drosophila trithorax-group protei ...
,
CHD8 Chromodomain-helicase-DNA-binding protein 8 is an enzyme that in humans is encoded by the ''CHD8'' gene. Function The gene CHD8 encodes the protein chromodomain helicase DNA binding protein 8, which is a chromatin regulator enzyme that is esse ...
,
CHD9 Chromodomain-helicase-DNA-binding protein 9 is an enzyme that in humans is encoded by the ''CHD9'' gene. Model organisms Model organisms have been used in the study of CHD9 function. A conditional knockout mouse line called ''Chd9tm1a(EUCOMM)Wts ...
*
DEAD box Death is the irreversible cessation of all biological functions that sustain an organism. For organisms with a brain, death can also be defined as the irreversible cessation of functioning of the whole brain, including brainstem, and brain ...
/ DEAD/DEAH box helicase:
DDX3X ATP-dependent RNA helicase DDX3X is an enzyme that in humans is encoded by the ''DDX3X'' gene. Function DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a numbe ...
,
DDX5 Probable ATP-dependent RNA helicase DDX5 also known as DEAD box protein 5 or RNA helicase p68 is an enzyme that in humans is encoded by the ''DDX5'' gene. Function DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD) ...
, DDX6, DDX10, DDX11, DDX12, DDX58, DHX8,
DHX9 ATP-dependent RNA helicase A (RHA; also known as DHX9, LKP, and NDHI) is an enzyme that in humans is encoded by the ''DHX9'' gene. Function DEAD/DEAH box helicases are proteins, and are putative RNA helicases. They are implicated in a number o ...
, DHX37, DHX40,
DHX58 Probable ATP-dependent RNA helicase DHX58 also known as RIG-I-like receptor 3 (RLR-3) or RIG-I-like receptor LGP2 (RLR) is a RIG-I-like receptor dsRNA helicase enzyme that in humans is encoded by the ''DHX58'' gene. The protein encoded by the gen ...
* ASCC3,
BLM BLM most commonly refers to: * Black Lives Matter, an international anti-racism movement and organization * Bureau of Land Management, a U.S. federal government agency BLM may also refer to: Organizations * BLM (law firm), United Kingdom and ...
,
BRIP1 Fanconi anemia group J protein is a protein that in humans is encoded by the ''BRCA1-interacting protein 1'' (''BRIP1'') gene. Function The protein encoded by this gene is a member of the RecQ DEAH helicase family and interacts with the BRCT r ...
, DNA2, FBXO18, FBXO30, HELB, HELLS, HELQ, HELZ, HFM1,
HLTF Helicase-like transcription factor is an enzyme that in humans is encoded by the HLTF gene. Function This gene encodes a member of the SWI/SNF family. Members of this family have helicase and ATPase activities and are thought to regulate trans ...
,
IFIH1 MDA5 (melanoma differentiation-associated protein 5) is a RIG-I-like receptor dsRNA helicase enzyme that is encoded by the ''IFIH1'' gene in humans. MDA5 is part of the RIG-I-like receptor (RLR) family, which also includes RIG-I and LGP2, and f ...
,
NAV2 Neuron navigator 2 is a protein that in humans is encoded by the ''NAV2'' gene. The vitamin A metabolite, all-trans retinoic acid (atRA), plays an important role in neuronal development, including neurite outgrowth. RAINB1 is an atRA-responsive ge ...
,
PIF1 Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separati ...
,
RECQL ATP-dependent DNA helicase Q1 is an enzyme that in humans is encoded by the ''RECQL'' gene. The protein encoded by this gene is a member of the RecQ DNA helicase family. DNA helicases are enzymes involved in various types of DNA repair, including ...
, RTEL1,
SHPRH E3 ubiquitin-protein ligase SHPRH is an enzyme that in humans is encoded by the ''SHPRH'' gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''genera ...
,
SMARCA4 Transcription activator BRG1 also known as ATP-dependent chromatin remodeler SMARCA4 is a protein that in humans is encoded by the ''SMARCA4'' gene. Function The protein encoded by this gene is a member of the SWI/SNF family of proteins and i ...
, SMARCAL1, WRN, WRNIP1 * RNA helicase database


References


External links

* * {{Portal bar, Biology, border=no EC 3.6.4 DNA replication