Functions, structure, and read-through alternative splicing of feline APOBEC3 genes

Additional data file 1:

Information about the calculation of Ka/Ks.

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Additional data file 2:

Supplementary Table 1 lists percent identity of cat A3C introns. Supplementary Tables 2 and 3 list Ka/Ks ratios of cat A3s. Supplementary Table 4 lists A3C SNPs of cat breeds. Supplementary Tables 5 and 6 list percent identities of all described A3C and A3H cDNAs and proteins. Supplementary Table 7 lists results of different evolutionary models.

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Additional data file 3:

Figure S1: comparison of amino acid sequences of the feline A3C genes. Predicted amino acid sequence of the feline APOBEC3Ca, APOBEC3Cb and APOBEC3Cc proteins in comparison with the two additional variant cDNAs detected (A3Cx and A3Cy) in cat PBMCs. The zinc coordination domain is indicated. Residues different to A3Ca are shown in bold. Figure S2: amino acid alignment of feline, canine and human APOBEC3 proteins. (a) Amino acid alignment of feline APOBEC3Ca, APOBEC3Cb, APOBEC3Cc, human APOBEC3C, APOBEC3F and murine APOBEC3 NT. (b) Amino acid alignment of feline, canine, human APOBEC3H and murine APOBEC3 NT. (c) Amino acid alignment of human, canine APOBEC3A and human APOBEC3G CT. The zinc-coordinating domains are indicated. CT, carboxyl-terminal domain; NT, amino-terminal domain. Figure S3: prediction of transcription factor binding sites. Potential transcription factor binding sites in A3 cluster of the domestic cat in the region 1.1 kb upstream, including 100 bp of the predicted exon 1 for each gene (A3Ca, A3Cb, A3Cc and A3H) using ClustalW. The individual 5' flanking sequences were analyzed using the program Match, which uses a library of nucleotide weight matrices from the TRANSFAC6.0 database for transcription factor binding sites. Figure S4: analysis of Ka/Ks. Sliding window (300 bp window, 50 bp slide) analysis of Ka and Ks was performed on pairs of (a) cat A3C sequences and (b) cat A3H sequences and compared with corresponding selected felid and human sequences. Ka/Ks is plotted against the length of the coding region of the mRNAs with a schematic presentation of protein domains along the x-axis. Figure S5: analysis of cytidine deamination in the genomes of FIV by feline APOBEC3s. (a) A fragment of the reporter gene (egfp) was amplified from reverse transcripts of Δvif FIV (left panel) or wild-type FIV (right panel) generated in the presence of the indicated feline APOBEC3s 10 h post-infection. A total of eight independent nucleotide sequences were determined. The mutations in the clones of each group are shown. Each mutation is indicated and coded with respect to nucleotide mutation. (b) The number of G→A changes per 100 Gs is shown. (c) Comparison of the dinucleotide sequence context of G→A mutations in the positive-strand DNA of Δvif FIV derived from feA3-expressing 293T cells. (d) Sequence characteristics of Δvif FIV DNA genomes of virions derived from 293T-expressing feline APOBEC3 proteins or empty expression plasmid (vector).

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