Figure 1

Atlantic cod g-type lysozyme proteins and electrostatic potential.

(A) Alignment of cod g-type lysozyme protein sequences. Amino acid sequence alignment was generated with Clustal Omega, with the symbols below the alignment complete conservation (*), sites with strongly conserved properties (:) and sites with weakly conserved properties (.). The sequences are numbered from the N-terminus of the mature LygF1b proteins, with the signal peptide in italic and numbered backwards. The catalytic residues equivalent to E73 (E71 in the cod LygF1a/LygF1b sequences) and D86 and D97 (D88 and D99 in the cod LygF1c/LygF1d sequences) in the g-type sequence are indicated, with residues compatible with enzymatic function in green and those that should prevent enzymatic activity shown in red. (B) Phylogenetic relationships of g-type lysozyme from cod and other fishes. A bootstrapped (1000 replications) neighbour-joining tree based on maximum composite likelihood distances was generated using MEGA6.2⁵⁴. Numbers at the nodes represent the number of bootstrap replicates (out of 1000) that supported each node. Branch lengths are proportional to amount of inferred change, with scale bar (changes per base) shown at the bottom. Trees were rooted based on previous phylogenetic analyses of g-type lysozyme sequences¹⁴. (C) 3-D models of LygF1a, LygF1c and LygF1d were constructed based on the previously identified structure of LygF1b²⁶ and the electrostatic surface potential is indicated in red (negative) and blue (positive). NAG molecules are presented as sticks docking into the LygF1 models in correspondence with the observations in native LygF1b.