In this study, we analyzed the bulk of genomic and transcribed CsRn1 sequences encompassing the putative frameshift region in C. sinensis and Opisthorchis viverrini, which is a nearest phylogenetic neighbor of the liver fluke, to address the issue regarding the expression strategy of CsRn1. Our results demonstrate that CsRn1 copies lacking frameshifting have arisen from the precedential counterparts with two overlapping ORFs by a single-nucleotide insertion at an upstream region of gag stop codon. The insertional event appeared to have occurred sporadically in multiple CsRn1 copies in the C. sinensis and O. viverrini genomes, although their evolutionary fate differed in the respective genomes. The newly evolving variant exhibited transcriptional
…show more content…
However, the usage of some synonymous codons generated by these base substitutions significantly differed compared to the consensus ones of Variant B: TCT1260 (relative synonymous codon usage value [RSCU], 0.81) vs. TCC1260 (1.50) vs. TCG1260 (0.66) for Ser; CCG1311 (0.50) vs.CCA1311 (1.12) for Pro (fig. 2 and 3C; Tang et al. 2007). Of the three downstream bases that were clonally mutated in the lineage A-V sequences, the first two bases comprised Leu (T1346TA) and Thr (AC1353C) codons of gag, as well as Phe (TT1346T) and His (CAC1353) codons of rt, in Variant B (fig. 1). The Leu TTA codon had the lowest frequency among the six synonymous codons (RSCU, 0.55), whereas ACC was the most frequent one for Thr (1.36). The TG1346T (1.14) in the prominent active lineage of Variant A (lineage A-V) was the more frequent codon than its synonymous counterpart to encode Cys. Therefore, considering the positions of the CHCC Gag-motif codons and the hungry Leu codon (fig. 3C), the short nucleotides CCC*TTTA encompassing the characteristic C/T1344-insertion site (*) might act as the signal for ribosomal -1 frameshifting in the precedential CsRn1 copies (Jacks et al. 1988; Hatfield and Oroszlan 1990; Kalmykova et al.
However, the usage of some synonymous codons generated by these base substitutions significantly differed compared to the consensus ones of Variant B: TCT1260 (relative synonymous codon usage value [RSCU], 0.81) vs. TCC1260 (1.50) vs. TCG1260 (0.66) for Ser; CCG1311 (0.50) vs.CCA1311 (1.12) for Pro (fig. 2 and 3C; Tang et al. 2007). Of the three downstream bases that were clonally mutated in the lineage A-V sequences, the first two bases comprised Leu (T1346TA) and Thr (AC1353C) codons of gag, as well as Phe (TT1346T) and His (CAC1353) codons of rt, in Variant B (fig. 1). The Leu TTA codon had the lowest frequency among the six synonymous codons (RSCU, 0.55), whereas ACC was the most frequent one for Thr (1.36). The TG1346T (1.14) in the prominent active lineage of Variant A (lineage A-V) was the more frequent codon than its synonymous counterpart to encode Cys. Therefore, considering the positions of the CHCC Gag-motif codons and the hungry Leu codon (fig. 3C), the short nucleotides CCC*TTTA encompassing the characteristic C/T1344-insertion site (*) might act as the signal for ribosomal -1 frameshifting in the precedential CsRn1 copies (Jacks et al. 1988; Hatfield and Oroszlan 1990; Kalmykova et al.