Missense mutation
In genetics, a missense mutation is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. It is a type of nonsynonymous substitution. Missense mutations change amino acids, which in turn alter proteins and may alter a protein's function or structure. These mutations may arise spontaneously from mutagens like UV radiation, tobacco smoke, an error in DNA replication, and other factors. Screening for missense mutations can be done by sequencing the genome of an organism and comparing the sequence to a reference genome to analyze for differences. Missense mutations can be repaired by the cell when there are errors in DNA replication by using mechanisms such as DNA proofreading and mismatch repair. They can also be repaired by using genetic engineering technologies or pharmaceuticals. Some notable examples of human diseases caused by missense mutations are Rett syndrome, cystic fibrosis, and sickle-cell disease.
Impact on protein function
Missense mutation refers to a change in one amino acid in a protein arising from a point mutation in a single nucleotide. Amino acids are the building blocks of proteins. Missense mutations are a type of nonsynonymous substitution in a DNA sequence. Two other types of nonsynonymous substitutions are nonsense mutations, in which a codon is changed to a premature stop codon that results in the resulting protein being cut short, and nonstop mutations, in which a stop codon deletion results in a longer but nonfunctional protein. The latter two types are not considered to be missense mutations.Missense mutations can render the resulting protein nonfunctional, due to misfolding of the protein. These mutations are responsible for human diseases, such as Epidermolysis bullosa, sickle-cell disease, SOD1 mediated ALS, and a substantial number of cancers.
Not all missense mutations lead to appreciable protein changes. An amino acid may be replaced by a different amino acid of very similar chemical properties in which case the protein may still function normally; this is termed a conservative mutation. Alternatively, the amino acid substitution could occur in a region of the protein which does not significantly affect the protein secondary structure or function. Lastly, when more than one codon codes for the same amino acid, the resulting mutation does not produce any change in translation and hence no change in protein is observed; degenerate coding would be classified as a synonymous substitution, or a silent mutation, and not a missense mutation.
Origin
Missense mutations may be inherited or arise spontaneously, termed de novo mutations. Well studied diseases arising from inherited missense mutations include sickle cell anemia, cystic fibrosis, and early-onset Alzheimer's and Parkinson's disease. De novo mutations that increase or decrease the activity of synapses have been implicated in the development of neurological and developmental disorders, such a Autism Spectrum Disorder and intellectual delay.Agents of spontaneous missense mutation
Environmental mutagens, such as tobacco smoke or UV radiation, may be a cause of spontaneous missense mutations. Tobacco smoke has been implicated in transversion mutations in the K-ras gene, with a meta-analysis of lung carcinomas showing 25 tumours containing a G to T mutation causing an amino acid change from glycine to cysteine, and 11 tumours with a G to T mutation causing an amino acid change from glycine to valine. Similarly, numerous studies have shown ultraviolet light induces missense mutations in the p53 gene, which when unregulated, reduces the cell's ability to recognize DNA damage and engage in apoptosis, leading to cell proliferation and potential skin carcinogenesis.DNA polymerase replication errors during cell division may lead to spontaneous missense mutations if DNA polymerase's proofreading ability does not detect and repair an error it makes. Spontaneous DNA polymerase errors are estimated to occur at a frequency of 1/109 base pairs.
Although rarer, tautomerization of bases also creates spontaneous missense mutations. Tautomerization occurs when hydrogen atoms on DNA bases spontaneously change locations, impacting the structure of the base, and allowing it to pair with an incorrect base. If this strand of DNA is replicated, the incorrect base will be the template for a new strand, leading to a mutation, possibly changing the amino acid and therefore, the protein. For example, Wang et al., used X-ray cystallography to demonstrate that a de novo mutation was created when DNA repair mechanisms did not recognize a C-A base mismatch due to tautomerization allowing the base structures to be compatible.
Screening
Next Generation Sequencing (NGS)
Next Generation Sequencing has changed the world of sequencing by decreasing the cost of sequencing and increasing the throughput. It does this by utilizing massively parallel sequencing to sequence the genome. This involves clonally amplified DNA fragments that can be spatially separated into second generation sequencing or third generation sequencing platforms. There is variation between these protocols, but the overall methods are similar. Using massively parallel sequencing allows the NGS platform to produce very large sequences in a single run. The DNA fragments are typically separated by length using gel electrophoresis.NGS consists of four main steps, DNA isolation, target enrichment, sequencing, and data analysis. The DNA isolation step involves breaking the genomic DNA into many small fragments. There are many different mechanisms that can be used to accomplish this such as mechanical methods, enzymatic digestion, and more. This step also consists of adding adaptors to either end of the DNA fragments that are complementary to the flow cell oligos and include primer binding sites for the target DNA. The target enrichment step amplifies the region of interest. This includes creating a complementary strand to the DNA fragments through hybridization to a flow cell oligo. It then gets denatured and bridge amplification occurs before the reverse strand is finally washed and sequencing can occur. The sequencing step involves massive parallel sequencing of all DNA fragments simultaneously using a NGS sequencer. This information is saved and analyzed in the last step, data analysis, using bioinformatics software. This compares the sequences to a reference genome to align the fragments and show mutations in the targeted area of the sequence.
Newborn Screening (NBS)
for missense mutations is increasingly incorporating genomic technologies in addition to traditional biochemical methods to improve the detection of genetic disorders early in life. Traditional NBS primarily relies on biochemical assays, such as tandem mass spectrometry, to detect metabolic abnormalities indicative of conditions like phenylketonuria or congenital hypothyroidism. However, these methods may miss genetic causes or produce ambiguous results. To address these deficiencies, next-generation sequencing is being added to NBS programs. For instance, targeted gene panels and whole-exome sequencing are used to identify disease causing missense mutations in genes associated with treatable conditions, such as severe combined immunodeficiency and cystic fibrosis. Studies like the BabyDetect project have demonstrated the utility of genomic screening in identifying disorders missed by conventional methods, with actionable results for conditions affecting more than 400 genes. In addition, genomic approaches allow for the detection of rare or recessive conditions that may not manifest biochemically at birth, significantly expanding the scope of diseases screened. These advancements align with the established principles of NBS, which emphasize early detection and intervention to prevent morbidity and mortality.Prevention and repair mechanisms
Cellular mechanisms
, used in DNA replication, have a high specificity of 104 to 106-fold in base pairing. They have proofreading abilities to correct incorrect matches, allowing 90-99.9% of mismatches to be excised and repaired. The base mismatches that go unnoticed are repaired by the DNA mismatch repair pathway, also inherent in cells. The DNA mismatch repair pathway uses exonucleases that move along the DNA strand and remove the incorrectly incorporated base in order for DNA polymerase to fill in the correct base.Exonuclease1 is involved in many DNA repair systems and moves 5' to 3' on the DNA strand.Genetic engineering and drug-based interventions
More recently, research has explored the use of genetic engineering and pharmaceuticals as potential treatments. tRNA therapies have emerged in research studies as a potential missense mutation treatment, following evidence supporting their use in nonsense mutation correction. Missense-correcting tRNAs are engineered to identify the mutated codon, but carry the correct charged amino acid which is inserted into the nascent protein.Pharmaceuticals that target specific proteins affected by missense mutations have also shown therapeutic potential. Pharmaceutical studies have particularly focused on targeting the p53 mutant protein and Ca2+ channel abnormalities, both caused by gain of function missense mutations due to their high prevalence in a number of cancers and genetic diseases respectively. In cystic fibrosis, most commonly caused by missense mutations, drugs known as modulators target the defective Cystic Fibrosis Transmembrane Conductance Regulator protein. For example, to reduce the defects caused by class III CFTR mutations, Ivacaftor, part of the modulator Kalydeco, forces the chloride channel to remain in an open position.