The Genetic Code: Consequences of altering the nucleotide sequence

Changing a single nucleotide base (a point mutation) in the coding region of an mRNA can lead to any one of three results (Fig. 1).

Figure 1:  Possible effects of changing a single nucleotide base in the coding region of a messenger RNA. A = adenine; C = cytosine; U = uracil.
1. Silent mutation: The codon containing the changed base may code for the same amino acid. For example, if the serine (Ser) codon UCA is changed at the third base and becomes UCU, it still codes for Ser. This is termed a silent mutation.
2. Missense mutation: The codon containing the changed base may code for a different amino acid. For example, if the Ser codon UCA is changed at the first base and becomes CCA, it will code for a different amino acid (in this case, proline [Pro]). This is termed a missense mutation.
3. Nonsense mutation: The codon containing the changed base may become a termination codon. For example, if the Ser codon UCA is changed at the second base and becomes UAA, the new codon causes premature termination of translation at that point and the production of a shortened (truncated) protein. This is termed a nonsense mutation. [Note: The nonsense-mediated degradation pathway can degrade mRNA containing premature stops.]
4. Other mutations: These can alter the amount or structure of the protein produced by translation.
a. Trinucleotide repeat expansion: Occasionally, a sequence of three bases that is repeated in tandem will become amplified in number so that too many copies of the triplet occur. If this happens within the coding region of a gene, the protein will contain many extra copies of one amino acid. For example, expansion of the CAG codon in exon 1 of the gene for huntingtin protein leads to the insertion of many extra
glutamine residues in the protein, causing the neurodegenerative disorder Huntington disease (Fig. 2). The additional glutamines result in an abnormally long protein that is cleaved, producing toxic fragments that aggregate in neurons. If the trinucleotide repeat expansion occurs in an untranslated region (UTR) of a gene, the result can be a decrease in the amount of protein produced, as seen in fragile X syndrome and myotonic dystrophy. Over 20 triplet expansion diseases are known. [Note: In fragile X syndrome, the most common cause of intellectual disability in males, the expansion results in gene silencing through DNA hypermethylation .]

Figure 2:  Tandem triplet repeats in messenger RNA (mRNA) causing Huntington disease and other triplet expansion diseases. [Note: In unaffected individuals, the number of repeats in the huntingtin protein is <27; in fragile X mental retardation protein, it is 5–44; and in myotonic dystrophy protein kinase, it is 5–34.] UTR = untranslated region; A = adenine; C = cytosine; G = guanine; U = uracil; Q = single-letter abbreviation for glutamine.
b. Splice site mutations: Mutations at splice sites  can alter the way in which introns are removed from pre-mRNA molecules, producing aberrant proteins. [Note: In myotonic dystrophy, a muscle disorder, gene silencing is the result of splicing alterations due to
triplet expansion.]
c. Frameshift mutations: If one or two nucleotides are either deleted from or added to the coding region of an mRNA, a frameshift mutation occurs, altering the reading frame. This can result in a product with a radically different amino acid sequence or a truncated product due to the eventual creation of a termination codon (Fig. 3). If three
nucleotides are added, a new amino acid is added to the peptide. If three are deleted, an amino acid is lost. Loss of three nucleotides maintains the reading frame but can result in serious pathology. For example, cystic fibrosis (CF), a chronic, progressive, inherited disease that primarily affects the pulmonary and digestive systems, is most commonly caused by deletion of three nucleotides from the coding region of a gene, resulting in the loss of phenylalanine (Phe, or F) at the 508th position (ΔF508) in the CF transmembrane conductance regulator (CFTR) protein encoded by that gene. This ΔF508 mutation prevents normal folding of CFTR, leading to its destruction by the proteasome. CFTR normally functions as a chloride channel in epithelial cells, and its loss results in the production of thick, sticky secretions in the lungs and pancreas, leading to lung damage and digestive deficiencies . The incidence of CF is highest (1 in 3,300) in those of Northern European origin. In >70% of individuals with CF, the ΔF508 mutation is the cause of the disease.

Figure 3:  Frameshift mutations as a result of addition or deletion of a base can cause an alteration in the reading frame of mRNA. A = adenine; C = cytosine; G = guanine; U = uracil.

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