Fig. 3
From: The transcriptome of the olm provides insights into its evolution and gene expression
a) Displayed is the C-terminal part of the NDUFS4 amino acid sequence alignment for the olm, other amphibian species, and humans. The numbering at the top refers to the sequence position in the olm. The site in the olm that deviates from the consensus sequence, with a positive selection probability of 98.39%, is highlighted (A139). Divergence times for humans and amphibians were taken from49. (b) Shown in blue is the predicted tertiary structure of the olm NDUFS4 amino acid sequence, with the site predicted to be under positive selection in the olm highlighted in red (alignment position 139, cf. with a). In green, the predicted 3D structure of a modified olm sequence is shown, where the single amino acid identified as positively selected in the olm is replaced by the amino acid present in the other species (S instead of A at alignment position 139). This replacement, according to the prediction, results in the formation of an antiparallel ß-sheet further downstream towards the C-terminus (dashed box). (c) In green, the predicted tertiary structure of the human NDUFS4 amino acid sequence is shown. Again, the formation of an antiparallel ß-sheet further downstream in the protein is predicted, similar to the modified olm sequence that matches the human and other species at alignment position 139 (dashed box). The amino acid site at alignment position 139 (cf. with a) in the olm is highlighted in red. If this site is modified to match the original olm sequence at alignment position 139 (A instead of S), as shown in blue, the antiparallel ß-sheet is lost according to the prediction. (d) A molecular model of the mouse (Mus musculus) I2 + III2 supercomplex derived from cryo-EM 8UCA, not available for human) is shown in grey. The predicted 3D structures of the mouse, human, and olm NDUFS4 subunit are shown in red, green, and blue, respectively. The inset displays details of the deep and narrow cleft hosting a loop between a.a. 99–113 in which the formation of an antiparallel ß-sheet is predicted for mouse and human but not in the olm NDUFS4 protein.
