Fig 1.
Mutation rates in tryptophan codons of the vif gene of HIV-1.
At each tryptophan site (TGG) of the gene vif the number of amino acid changes was estimated. Dark gray horizontal bars indicate the number of changes from TGG to stop codons (i.e., TAA, TAG, TGA) and light gray bars represents changes from TGG to any other codons such as AGG, TTG, TCA, etc. The next nucleotide after the TGG is shown in each codon. These nucleotides determine the context target by the human proteins A3 protein (see next figure). Codons 21 and 38 have distinct percentages of a certain nucleotide that is indicated in the figure.
Fig 2.
The context associated mutation rates of apobec3.
The Context refers to cDNA sequences edited by members of apobec3 (A3) protein family. The human A3G protein targets the CC sequences on minus-strand cDNA, thus causing GG to AG mutations in the positive strand of HIV. A3G mutates TGG codons mainly to TAG stop codon when the TGG codon is followed by a G (TGGG). A3F/H/D mutate TGG to stop codons when TGG is followed by an A (TGGA). Reverse transcriptase has no preferences and can change TGG into any codon, including stop codons. Arrows indicate a mutation from TGG to a certain stop codon and numbers are the estimated mutation rates of stop codons. Boxes close to the arrows indicate the enzyme likely associate with a mutation indicated by the arrow. RT = reverse transcriptase. TGG = Tryptophan, TGA, TAA, TGA = Stop codons.
Fig 3.
RNA levels and CD4+ cell counts.
Comparisons of RNA levels per ml (upper boxes) and counts of CD4+ cells per ml (lower boxes) between the sequences with stop codons at the tryptophan (grey boxes) and sequences without stop codons (white boxes). In the boxes the center lines show the medians; box limits indicate the 25th and 75th percentiles. Whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by open dots. RNA levels (upper boxes) are shown in log scale.
Table 1.
Hypermutation in vif gene and clinical parameters of HIV-1 infected patients.