Evolutionary implication of protein secondary structure among Archaea and Bacteria

Molecular structures and sequences are generally more revealing of evolutionary relationships than classical phenotypes, particularly among microorganisms. Archaea are unique group of organisms among other kingdoms, which are widely diverged in metabolic pathways and have well distinguished metabolic genes, particularly involved in methanogenesis, osmoregulation, sulfur toxicity, metal detoxification and stress response. Physiochemical characteristics and secondary structure of some superprotein families from archaeal domain were compared within Archaea and with Bacteria. The results of this work revealed that many of the proteins did not show close proximity to bacterial proteins, but few of them showed evolutionary relationship to proteins with similar biochemical functions in Bacteria. Proteins involved in methanogenesis were highly unique to methanogens in archaeal domain, but proteins responsible for carbon assimilation shared their ancestral behaviors among prokaryotes with reference to similarities in secondary structural elements. CO dehydrogenase, 4-vinyl reductase, allophanate reductase, quinine oxidase, dihydrolipoamide dehydrogenase and NADH oxidase were somehow similar to prokaryotes which indicated a wide diversification and mobilization of such families between Archaea and Bacteria during evolution process. Another one noteworthy of our study is that a stable divergence and slow evolutionary process were occurred in topoisomerase family of Archaea. Perhaps, this attempt can be helpful to understand evolutionary mechanisms of some key metabolic proteins at secondary structural level in Archaea.