Tracking the molecular evolution of photosynthesis through characterization of atomic contents of the photosynthetic units.
ABSTRACT Oxygen molecules have a great impact on protein evolution. We have performed a comparative study of key photosynthetic proteins in order to seek the answer to the question; did the evolutionary substitution of oxygen- and nitrogen-containing residues in the photosynthetic proteins correspond to nutrient constraints and metabolic optimization? The D1 peptide in RC II complexes has higher oxygen-containing amino acid residues and PufL/PufM have lower oxygen content in their peptides. In this article, we also discuss the possible influences of micro-environment and the available nutrients on the protein structure and their atomic distribution.
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ABSTRACT: To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional groups analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution.Gene 11/2013; · 2.20 Impact Factor