The term proofreading is used in genetics to refer to the error-correcting processes, first proposed by

John Hopfield John Joseph Hopfield (born July 15, 1933) is an American scientist most widely known for his invention of an associative neural network in 1982. It is now more commonly known as the Hopfield network. Biography Hopfield was born in 1933 to Po ...

and Jacques Ninio, involved in

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 ...

immune system The immune system is a network of biological processes that protects an organism from diseases. It detects and responds to a wide variety of pathogens, from viruses to parasitic worms, as well as cancer cells and objects such as wood splinte ...

specificity, enzyme-substrate recognition among many other processes that require enhanced specificity. The proofreading mechanisms of Hopfield and Ninio are non-equilibrium active processes that consume ATP to enhance specificity of various biochemical reactions. In

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

, all three

DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create ...

s (I, II and III) have the ability to proofread, using 3’ → 5’

exonuclease Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is the ...

activity. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA and excises the mismatched base. Following base excision, the polymerase can re-insert the correct base and replication can continue. In

eukaryotes Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...

, only the polymerases that deal with the elongation (delta and epsilon) have proofreading ability (3’ → 5’ exonuclease activity). Proofreading also occurs in

mRNA translation In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process ...

for ''protein'' synthesis.Pharmamotion --> Protein synthesis inhibitors: aminoglycosides mechanism of action animation. Classification of agents
Posted by Flavio Guzmán on 12/08/08 In this case, one mechanism is the release of any incorrect

aminoacyl-tRNA Aminoacyl-tRNA (also aa-tRNA or charged tRNA) is tRNA to which its cognate amino acid is chemically bonded (charged). The aa-tRNA, along with particular elongation factors, deliver the amino acid to the ribosome for incorporation into the polypept ...

before

peptide bond In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein cha ...

formation. The extent of proofreading in DNA replication determines the

mutation rate In genetics, the mutation rate is the frequency of new mutations in a single gene or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mutations. Mutation rates ...

, and is different in different species. For example, loss of proofreading due to mutations in the

DNA polymerase epsilon DNA polymerase epsilon is a member of the DNA polymerase family of enzymes found in eukaryotes. It is composed of the following four subunits: POLE (central catalytic unit), POLE2 (subunit 2), POLE3 (subunit 3), and POLE4 (subunit 4). Recent evi ...

gene results in a hyper-mutated genotype with >100 mutations per Mbase of DNA in human colorectal cancers. The extent of proofreading in other molecular processes can depend on the

effective population size The effective population size (''N'e'') is a number that, in some simplified scenarios, corresponds to the number of breeding individuals in the population. More generally, ''N'e'' is the number of individuals that an idealised population wo ...

of the species and the number of genes affected by the same proofreading mechanism.

Bacteriophage T4 DNA polymerase

Bacteriophage (phage) T4 gene 43 encodes the phage’s

replicative enzyme. Temperature-sensitive (''ts'') gene 43 mutants have been identified that have an antimutator

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...

, that is a lower rate of spontaneous

mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mi ...

than wild type. Studies of one of these mutants, ''tsB120'', showed that the DNA polymerase specified by this mutant copies DNA templates at a slower rate than the wild-type polymerase.Gillin FD, Nossal NG. Control of mutation frequency by bacteriophage T4 DNA polymerase. I. The CB120 antimutator DNA polymerase is defective in strand displacement. J Biol Chem. 1976 Sep 10;251(17):5219-24. PMID: 956182. However, the 3’ to 5’

activity was no higher than wild-type. During

the ratio of

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

s turned over to those stably incorporated into newly formed DNA is 10 to 100 times higher in the case of the ''tsB120'' mutant than in wild-type. It was proposed that the antimutator effect may be explained by both greater accuracy in nucleotide selection and an increased efficiency of removal of noncomplementary nucleotides (proofreading) by the ''tsB120'' polymerase. When phage T4 virions with a

wild-type The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, "m ...

gene 43 DNA polymerase are exposed to either

ultraviolet Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nanometer, nm (with a corresponding frequency around 30 Hertz, PHz) to 400 nm (750 Hertz, THz), shorter than that of visible light, but longer than ...

light, which introduces cyclobutane

pyrimidine dimer Pyrimidine dimers are molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions, commonly associated with direct DNA damage. Ultraviolet light (UV; particularly UVB) induces the formation of covalent linkages betwe ...

damages in DNA, or

psoralen Psoralen (also called psoralene) is the parent compound in a family of naturally occurring organic compounds known as the linear furanocoumarins. It is structurally related to coumarin by the addition of a fused furan ring, and may be considered a ...

-plus-light, which introduces pyrimidine adducts, the rate of mutation increases. However, these mutagenic effects are inhibited when the phage's DNA synthesis is catalyzed by the ''tsCB120'' antimutator polymerase, or another antimutator polymerase, ''tsCB87''. These findings indicate that the level of induction of mutations by DNA damage can be strongly influenced by the gene 43 DNA polymerase proofreading function.

SARS-CoV-2 proofreading enzyme

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. The SARS-CoV-2 RNA virus genome encodes a replication-and transcription complex, a multisubunit protein machine that carries out viral genome replication and transcription, processes essential to the virus life cycle. One of the proteins specified by the coronavirus genome is a non-structural protein, nsp14, that is a 3’-to-5’ exoribonuclease (ExoN). This protein resides in the protein complex nsp10-nsp14 that enhances replication fidelity by proofreading RNA synthesis, an activity critical for the virus life cycle. Furthermore the coronavirus proofreading exoribonuclease nsp14-ExoN is required for maintaining genetic recombination generated during infection.Gribble J, Stevens LJ, Agostini ML, Anderson-Daniels J, Chappell JD, Lu X, Pruijssers AJ, Routh AL, Denison MR. The coronavirus proofreading exoribonuclease mediates extensive viral recombination. PLoS Pathog. 2021 Jan 19;17(1):e1009226. doi: 10.1371/journal.ppat.1009226. PMID: 33465137; PMCID: PMC7846108

References

External links

Idaho U. DNA proofreading and repair

"DNA polymerase ε and δ proofreading suppress discrete mutator and cancer phenotypes in mice"
* Biological processes DNA replication Genetics Hydrolases {{Genetics-stub DNA repair