Phylogenetic Analysis of Proteins Associated in the Four Major Energy Metabolism Systems: Photosynthesis, Aerobic Respiration, Denitrification, and Sulfur Respiration

Abstract

The four electron transfer energy metabolism systems, photosynthesis, aerobic respiration, denitrification, and sulfur respiration, are thought to be evolutionarily related because of the similarity of electron transfer patterns and the existence of some homologous proteins. How these systems have evolved is elusive. We therefore conducted a comprehensive homology search using PSI-BLAST, and phylogenetic analyses were conducted for the three homologous groups (groups 1-3) based on multiple alignments of domains defined in the Pfam database. There are five electron transfer types important for catalytic reaction in group 1, and many proteins bind molybdenum. Deletions of two domains led to loss of the function of binding molybdenum and ferredoxin, and these deletions seem to be critical for the electron transfer pattern changes in group 1. Two types of electron transfer were found in group 2, and all its member proteins bind siroheme and ferredoxin. Insertion of the pyridine nucleotide disulfide oxidoreductase domain seemed to be the critical point for the electron transfer pattern change in this group. The proteins belonging to group 3 are all flavin enzymes, and they bind flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN). Types of electron transfer in this group are divergent, but there are two common characteristics. NAD(P)H works as an electron donor or acceptor, and FAD or FMN transfers electrons from/to NAD(P)H. Electron transfer functions might be added to these common characteristics by the addition of functional domains through the evolution of group 3 proteins. Based on the phylogenetic analyses in this study and previous studies, we inferred the phylogeny of the energy metabolism systems as follows: photosynthesis (and possibly aerobic respiration) and the sulfur/nitrogen assimilation system first diverged, then the sulfur/nitrogen dissimilation system was produced from the latter system.

Comparative genomics and evolution of molybdenum utilization

“…Previously, several studies have been conducted to investigate the evolution of certain molybdoenzymes in a limited number of organisms, such as nitrate reductase and other DMSOR family members [79,80], which showed complexity in their evolutionary trajectories. Based on recent comparative analyses of Moco-utilizing enzymes and nitrogenase, we characterized the distribution of each molybdoenzyme family in sequenced genomes in the three domains of life (Fig.…”

Main cellular redox couples

“…Flavoproteins con taining FMN and FAD as the prosthetic groups cata lyze many single and two electron redox reactions; they are the key enzymes in the processes, such as photosynthesis, Krebs cycle, β oxidation of fatty acids, aerobic respiration, and many others [175]. Fla voproteins play an important role in the biosynthesis of various native halogen derivatives, photorepair, and apoptosis [176][177][178].…”

A Brief History of Life

“…These networks should have the products of the long-term evolution, and it is interesting how they evolved. Tomiki and Saitou (2004;[ 12 ]) tried to infer the phylogenetic relationship of the fi ve electron transfer energy metabolism systems: photosynthesis, aerobic respiration, denitrifi cation, sulfur respiration, and sulfur metabolism. Because all these four systems exist in three domains of life, they must have evolved in the common ancestor of eubacteria, archaea, and eukaryotes.…”

“…Aerobic respiration might be utilized after the increase in oxygen by photosynthesis, while an ancestral sulfur and/or nitrogen metabolism system coexisted with that. Therefore, branching position 1 may be most plausible among the fi ve possibilities for the emergence of the aerobic respiration system [ 12 ]. In fact, the atmospheric oxygen was present at signifi cant levels around 2.3 billion years ago [ 14 ].…”