Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis

Abstract

There are numerous examples of convergent evolution in nature. Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? Manganese Superoxide Dismutase (MnSOD) is a manganesedependant metallo-enzyme which plays a crucial role in protecting cells from anti-oxidative stress by eliminating reactive (superoxide) oxygen species. It is a ubiquitous housekeeping enzyme found in nearly all organisms. In this study we compare phylogenies based on MnSOD protein sequences to those based on scores from Hydrophobic Cluster Analysis (HCA). We calculated HCA similarity values for each pair of taxa to obtain a pair-wise distance matrix. A UPGMA tree based on the HCA distance matrix and a common tree based on the primary protein sequence for MnSOD was constructed. Differences between these two trees within animals, enterobacteriaceae, planctomycetes and cyanobacteria are presented and cited as possible examples of convergence. We note that several residue changes result in changes in hydrophobicity at positions which apparently are under the effect of positive selection.

On the Origin of Superoxide Dismutase: An Evolutionary Perspective of Superoxide-Mediated Redox Signaling

“…Exhaustive sequencing, alignment, and phylogenetic analyses have been performed examining primitive antioxidant systems [ 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ]. It is clear from these studies that three primary ROS removal enzymes existed prior to the GOE: SOD, catalase (CAT), and peroxiredoxins (PRDX; previously known as thioredoxin peroxidases).…”

Genomic characterization and molecular investigation of VP7 epitopes of uncommon G10P[8] group A rotavirus strains detected in Italy in 2009

“…HCA similarity scores (Table 1) were obtained by the following formula: HCA similarity score (%)5(2CR|100)/(RC1+RC2), where RC1 and RC2 are the numbers of hydrophobic residues in protein 1 and 2, respectively, and CR is the number of hydrophobic residues conserved between the compared sequences (Xiang et al, 2014).…”