Table 1.
Features of nucleotide and protein sequences for ATP synthase F0 subunit 6 and 8.
Fig 1.
Multiple sequence alignment for nucleotide sequences of ATP synthase subunit 8.
Multiple codon alignment of nucleotide sequences of ATP synthase subunit 8 was created using the Clustal omega alignment of nucleotides we screened five Antarctic and one sub-Antarctic fish species and eight vertebrate outgroups same as ATP6 MSA (See Fig 1 for colour key). The highlighted boxes show the overlap of the ATP8 and ATP6 sequences for different species where different colour of the boxes correspond to the different lengths of overlap.
Fig 2.
(a-d) Multiple sequence alignment for nucleotide sequences of ATP synthase subunit 6.
Multiple codon alignment of nucleotide sequences of ATP synthase subunit 6 was created using the Clustal omega alignment of nucleotides for five Antarctic and one sub-Antarctic fish species and eight vertebrate outgroups and visualised) using MATLAB. The colour of the codon boxes corresponds to the respective amino acid (See colour key).
Fig 3.
Multiple sequence alignment of ATP8 protein sequences.
The ATP8 protein sequences were aligned using Clustal omega and edited using zappo colour scheme in JalView. Notothenioidei are grouped together in blue; all species are displayed to the colour corresponding to their phylogenetic closeness. (Colours according to physio-chemical properties of amino acids; Aliphatic/hydrophobic-A, I, L, M, V- light pink; Aromatic-F, W, Y- mustard; Conformationally special- Glycine, P- magenta; C-yellow; Hydrophilic- N, Q, S, Q, T- light green; Negatively charged/D,E-Red; Positively charged/R,H,K-Blue) in jalview. The bar-graphs below represent a quantitative measure of conservation at each position. The figure was created using JalView.
Fig 4.
Multiple sequence alignment for protein sequences of ATP synthase F0 subunit 6.
The ATP6 protein sequences were aligned using Clustal omega and edited using zappo colour scheme.
Fig 5.
Sequence logos displaying conservation of residues created for all aligned blocks of the MSA for protein ATP synthase F0 subunit 6 for 5947 vertebrate species from NCBI using webserver WebLogo (http://weblogo.threeplusone.com/) the y axis represents probability of the residue occurring at that position from the MSA.
Fig 6.
Primary sequence features of ATP Synthase F0 subunit 6 in species C. gunnari (red), C. rastrospinosus, C. aceratus, N. coriiceps, T. bernacchii, E. maclovinus, N. furzeri and D. rerio.
Red Box: N-terminal property changes, Purple Box: Changes in properties observed at 35/39 variation, blue box: Conserved regions 90–170 (Active site 160–169), Pink Box: C-terminal low hydrophobicity. A difference in the peaks have been observed for different properties (highlighted) such as molecular weight and hydrophobicity of amino acid residues across the sequence and other properties such as tendency of amino acid residues towards beta-sheet, bulkiness and flexibility.
Fig 7.
Representative structures of ATP synthase F0 subunit 6 for the fourteen vertebrate species created using I-TASSER [41] suite and visualised and edited using PyMOL v. 2.3.2.
a) C. gunnari(-/-) residues 38 (valine) and 39 (isoleucine) shows strand structure b) C. aceratus(-/-) residues 42(valine) and 43 coil (isoleucine), aligning with 38/39 in MSA, show a coil structure c) C. rastrospinosus(-/+) residues 42-Valine and 43-Isoleucine has a coil structure d) T. bernacchii(+/+) residues 42-Valine and 43-Valine show a strand structure e) E. maclovinus (+/+) residues 42 -Valine and 43-Valine show a strand structure f) N. coriiceps(+/+) residues 42 (Valine) 43 (isoleucine) has a coil structure. g) A. carolinesis residues 38 (Leucine) and 39(Valine) show a strand structure h) D. rerio residues 38 (tryptophan) and 39(Isoleucine) show a strand structure i) N. furzeri residues 38 (Tryptophan) and 39 (Leucine) show a strand structure. j) C. porcellus residues 38 (Isoleucine) and 39 (Asparagine) show a coil structure k) B. mysticetus residues 38 (Isoleucine) and 39 (Asparagine) show a coil structure. l) H. glaber residues 38 (Isoleucine) and 39 (Asparagine) show a coil structure—m) L. borealis residues 38 (Isoleucine) and 39 (Asparagine) show a coil structure.