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The mutational origin of overlapping genes typically involves point mutations to stop codons.
Mutations to stop codons are considered lethal and receive a fitness ℱ = 0.
Synonymous mutations are always accepted, whereas mutations to stop codons are always rejected.
Since the mutation load is calculated including mutations to stop codons, one would expect genetic codes containing more stop codons to have a larger mutation load than genetic codes containing fewer stop codons.
Genes were identified as pseudogenes when they showed similarity to a sequence classified as a gene in another species (E < 1e-20) but in which frameshift and substitution mutations to stop codons have started to accumulate [ 30].
When correcting for codon bias, both short overlaps – modal length 4 – and single strand usage can partly be accounted for in terms of the stochastic process of mutations to stop and start codons.
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This result suggested that these long contigs with short ORFs actually correspond to proteins fragmented by numerous mutations leading to stop codons.
The trend sometimes is less obvious, because about 4% loss of sites are due to mutations leading to stop codons, resulting in slightly underestimated Ka and Ks [ 4, 28].
This is not surprising, because the codon ends with dinucleotide TA, which is known to be suppressed in the coding sequences of several plant species possibly to discourage insertion events that target the TA dinucleotide, to reduce the likelihood of mutations leading to stop codons and to prevent attacks by TA-specific RNases.
A non-synonymous mutation (arginine to stop) at position 305 was observed in Rv0930 (phosphate transport integral membrane ABC Transporter, PstA1 (ABC transporter trans-membrane protein) of isolate LN8, which displays maximum number of non-synonymous mutations that result in stop codons (22) among all five isolates.
In the late 1960s, Leland Hartwell was studying the genetics of baker's yeast, Saccharomyces cerevisiae, when he discovered mutations that appeared to stop the process of cell division at a certain point in the cell cycle.
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