Abstract
Convergent evolution is the process by which distantly related organisms independently evolve the similar traits. To understand the impact of convergence on protein structure, function, and mechanism, we studied the Cryptosporidium parvum lactate dehydrogenase (CpLDH). CpLDH evolved independently from all other lactate dehydrogenases (LDHs) in nature and has a unique protein structure. While all known LDHs follow the same enzymatic mechanism, we investigated if CpLDH follows a different mechanism due to its convergent evolution. Using steady state kinetic assays, we determined that CpLDH has a novel random bi-bi mechanism and is the only LDH known to do so. Furthermore, we studied the role of convergence in molecular phylogenetics and to elucidate the origins of SARS-CoV-2. Due to the redundancy of the genetic code or codon degeneracy, different codons can converge to the same amino acid. Previous work studying the amino acid sequences of SARS-CoV-2 suggested it was a recombinant virus from pangolins and bats. However, we surmised that amino acid convergence may have influenced this result. To investigate the origins of SARS-CoV-2, we generated maximum likelihood phylogenies on the codon level to eliminate the effects of codon degeneracy. Our codon sequence phylogenies indicated that SARS-CoV-2 originated from bats and is not a recombinant virus.