Computational classification of SOD2 protein in coral and symbiotic algae from public genomic and transcriptomic data

Benjie Chen 

SOD2, or Manganese/Iron Superoxide Dismutase, plays a crucial role in maintaining cellular health across the tree of life. Existing literature is vague in identifying types of SOD2 proteins expressed in both corals and their symbiotic algae; most agree on the presence of a) mitochondrial targeting MnSOD in corals, and b) likely Mn dependent SOD2 in algae. This paper presents evidence for four classes of SOD2 proteins between coral hosts and their symbiotic algae. Public genomic and transcriptomic data reveal mitochondrial targeting and secreted versions of SOD2 among a wide range of cnidaria species, and chloroplast targeting (with a bipartite leader architecture) and secreted versions of SOD2 among several Symbiodinium species. The mature/catalytic region of SOD2 is well conserved within each class, but highly differentiated between classes. This paper presents the mature region HMM profiles for each class, with threshold scores high enough such that they are predictive of leader type.